sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley

+==============================================================================+
| plink 1.07+dfsg-4 (riscv64)                  Fri, 10 Jan 2025 19:14:48 +0000 |
+==============================================================================+

Package: plink
Version: 1.07+dfsg-4
Source Version: 1.07+dfsg-4
Distribution: unstable
Machine Architecture: amd64
Host Architecture: riscv64
Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-f6d5845e-1418-4172-b95c-254321772ba1' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/plink-yEeSAE/resolver-NMYsnc' with '<<RESOLVERDIR>>'

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

Get:1 http://localhost:3142/debian unstable InRelease [205 kB]
Get:2 http://localhost:3142/debian unstable/non-free-firmware Sources [6864 B]
Get:3 http://localhost:3142/debian unstable/non-free Sources [82.8 kB]
Get:4 http://localhost:3142/debian unstable/contrib Sources [63.2 kB]
Get:5 http://localhost:3142/debian unstable/main Sources [10.9 MB]
Get:6 http://localhost:3142/debian unstable/main riscv64 Packages [9639 kB]
Get:7 http://localhost:3142/debian unstable/main amd64 Packages [10.0 MB]
Fetched 30.9 MB in 3s (11.6 MB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages were automatically installed and are no longer required:
  gpgv libffi8 libgcrypt20 libgnutls30t64 libgpg-error0 libidn2-0 libp11-kit0
  libtasn1-6 libunistring5
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sqv
The following packages will be upgraded:
  apt base-files base-passwd bash binutils binutils-common
  binutils-x86-64-linux-gnu bsdutils coreutils cpp-14 cpp-14-x86-64-linux-gnu
  dash debconf debianutils diffutils dpkg dpkg-dev e2fsprogs g++-14
  g++-14-x86-64-linux-gnu gcc-14 gcc-14-base gcc-14-x86-64-linux-gnu gpgv gzip
  init-system-helpers libacl1 libapt-pkg6.0t64 libasan8 libatomic1
  libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6
  libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libctf-nobfd0 libctf0
  libdebconfclient0 libdpkg-perl libext2fs2t64 libgcc-14-dev libgcc-s1
  libgcrypt20 libgmp10 libgnutls30t64 libgomp1 libgpg-error0 libgprofng0
  libhogweed6t64 libhwasan0 libidn2-0 libitm1 libjansson4 liblsan0 liblz4-1
  liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libnettle8t64 libp11-kit0
  libpam-modules libpam-modules-bin libpam0g libpcre2-8-0 libperl5.40
  libquadmath0 libseccomp2 libselinux1 libsemanage2 libsframe1 libsmartcols1
  libss2 libssl3t64 libstdc++-14-dev libstdc++6 libsystemd0 libtasn1-6
  libtinfo6 libtsan2 libubsan1 libudev1 libunistring5 libuuid1 libxxhash0
  libzstd1 linux-libc-dev login login.defs logsave make mount ncurses-bin
  openssl-provider-legacy passwd perl perl-base perl-modules-5.40
  sysvinit-utils tar tzdata util-linux xz-utils zlib1g
112 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 114 MB of archives.
After this operation, 2916 kB of additional disk space will be used.
Get:1 http://localhost:3142/debian unstable/main amd64 libc6-dev amd64 2.40-5 [1957 kB]
Get:2 http://localhost:3142/debian unstable/main amd64 libc-dev-bin amd64 2.40-5 [52.4 kB]
Get:3 http://localhost:3142/debian unstable/main amd64 linux-libc-dev all 6.12.8-1 [2484 kB]
Get:4 http://localhost:3142/debian unstable/main amd64 libcc1-0 amd64 14.2.0-12 [42.8 kB]
Get:5 http://localhost:3142/debian unstable/main amd64 gcc-14-base amd64 14.2.0-12 [48.3 kB]
Get:6 http://localhost:3142/debian unstable/main amd64 libgcc-s1 amd64 14.2.0-12 [72.7 kB]
Get:7 http://localhost:3142/debian unstable/main amd64 libgomp1 amd64 14.2.0-12 [137 kB]
Get:8 http://localhost:3142/debian unstable/main amd64 libitm1 amd64 14.2.0-12 [25.9 kB]
Get:9 http://localhost:3142/debian unstable/main amd64 libatomic1 amd64 14.2.0-12 [9300 B]
Get:10 http://localhost:3142/debian unstable/main amd64 libasan8 amd64 14.2.0-12 [2727 kB]
Get:11 http://localhost:3142/debian unstable/main amd64 liblsan0 amd64 14.2.0-12 [1205 kB]
Get:12 http://localhost:3142/debian unstable/main amd64 libtsan2 amd64 14.2.0-12 [2460 kB]
Get:13 http://localhost:3142/debian unstable/main amd64 libubsan1 amd64 14.2.0-12 [1075 kB]
Get:14 http://localhost:3142/debian unstable/main amd64 libhwasan0 amd64 14.2.0-12 [1489 kB]
Get:15 http://localhost:3142/debian unstable/main amd64 libquadmath0 amd64 14.2.0-12 [145 kB]
Get:16 http://localhost:3142/debian unstable/main amd64 gcc-14 amd64 14.2.0-12 [534 kB]
Get:17 http://localhost:3142/debian unstable/main amd64 g++-14 amd64 14.2.0-12 [20.5 kB]
Get:18 http://localhost:3142/debian unstable/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-12 [12.1 MB]
Get:19 http://localhost:3142/debian unstable/main amd64 libstdc++-14-dev amd64 14.2.0-12 [2372 kB]
Get:20 http://localhost:3142/debian unstable/main amd64 libgcc-14-dev amd64 14.2.0-12 [2673 kB]
Get:21 http://localhost:3142/debian unstable/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-12 [21.4 MB]
Get:22 http://localhost:3142/debian unstable/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-12 [11.0 MB]
Get:23 http://localhost:3142/debian unstable/main amd64 cpp-14 amd64 14.2.0-12 [1280 B]
Get:24 http://localhost:3142/debian unstable/main amd64 libstdc++6 amd64 14.2.0-12 [714 kB]
Get:25 http://localhost:3142/debian unstable/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1+b1 [88.9 kB]
Get:26 http://localhost:3142/debian unstable/main amd64 libgprofng0 amd64 2.43.50.20250108-1 [807 kB]
Get:27 http://localhost:3142/debian unstable/main amd64 libctf0 amd64 2.43.50.20250108-1 [88.4 kB]
Get:28 http://localhost:3142/debian unstable/main amd64 libctf-nobfd0 amd64 2.43.50.20250108-1 [155 kB]
Get:29 http://localhost:3142/debian unstable/main amd64 libjansson4 amd64 2.14-2+b3 [39.8 kB]
Get:30 http://localhost:3142/debian unstable/main amd64 libsframe1 amd64 2.43.50.20250108-1 [77.7 kB]
Get:31 http://localhost:3142/debian unstable/main amd64 libzstd1 amd64 1.5.6+dfsg-2 [300 kB]
Get:32 http://localhost:3142/debian unstable/main amd64 libbinutils amd64 2.43.50.20250108-1 [532 kB]
Get:33 http://localhost:3142/debian unstable/main amd64 binutils-common amd64 2.43.50.20250108-1 [2628 kB]
Get:34 http://localhost:3142/debian unstable/main amd64 binutils amd64 2.43.50.20250108-1 [68.5 kB]
Get:35 http://localhost:3142/debian unstable/main amd64 binutils-x86-64-linux-gnu amd64 2.43.50.20250108-1 [2277 kB]
Get:36 http://localhost:3142/debian unstable/main amd64 libgmp10 amd64 2:6.3.0+dfsg-3 [560 kB]
Get:37 http://localhost:3142/debian unstable/main amd64 libmpfr6 amd64 4.2.1-1+b2 [724 kB]
Get:38 http://localhost:3142/debian unstable/main amd64 libmpc3 amd64 1.3.1-1+b3 [52.2 kB]
Get:39 http://localhost:3142/debian unstable/main amd64 libc6 amd64 2.40-5 [2810 kB]
Get:40 http://localhost:3142/debian unstable/main amd64 base-files amd64 13.6 [72.8 kB]
Get:41 http://localhost:3142/debian unstable/main amd64 debianutils amd64 5.21 [92.1 kB]
Get:42 http://localhost:3142/debian unstable/main amd64 bash amd64 5.2.37-1 [1501 kB]
Get:43 http://localhost:3142/debian unstable/main amd64 bsdutils amd64 1:2.40.3-1 [106 kB]
Get:44 http://localhost:3142/debian unstable/main amd64 coreutils amd64 9.5-1+b1 [2922 kB]
Get:45 http://localhost:3142/debian unstable/main amd64 dash amd64 0.5.12-11 [95.5 kB]
Get:46 http://localhost:3142/debian unstable/main amd64 diffutils amd64 1:3.10-2 [384 kB]
Get:47 http://localhost:3142/debian unstable/main amd64 libxxhash0 amd64 0.8.3-2 [27.1 kB]
Get:48 http://localhost:3142/debian unstable/main amd64 liblz4-1 amd64 1.9.4-4 [60.1 kB]
Get:49 http://localhost:3142/debian unstable/main amd64 liblzma5 amd64 5.6.3-1+b1 [272 kB]
Get:50 http://localhost:3142/debian unstable/main amd64 openssl-provider-legacy amd64 3.4.0-2 [301 kB]
Get:51 http://localhost:3142/debian unstable/main amd64 libssl3t64 amd64 3.4.0-2 [2302 kB]
Get:52 http://localhost:3142/debian unstable/main amd64 libcap2 amd64 1:2.66-5+b1 [27.8 kB]
Get:53 http://localhost:3142/debian unstable/main amd64 libsystemd0 amd64 257.2-1 [449 kB]
Get:54 http://localhost:3142/debian unstable/main amd64 libudev1 amd64 257.2-1 [148 kB]
Get:55 http://localhost:3142/debian unstable/main amd64 libapt-pkg6.0t64 amd64 2.9.21 [1115 kB]
Get:56 http://localhost:3142/debian unstable/main amd64 tar amd64 1.35+dfsg-3.1 [815 kB]
Get:57 http://localhost:3142/debian unstable/main amd64 dpkg amd64 1.22.13 [1534 kB]
Get:58 http://localhost:3142/debian unstable/main amd64 gzip amd64 1.12-1.2 [134 kB]
Get:59 http://localhost:3142/debian unstable/main amd64 ncurses-bin amd64 6.5-2+b1 [434 kB]
Get:60 http://localhost:3142/debian unstable/main amd64 libperl5.40 amd64 5.40.0-8 [4320 kB]
Get:61 http://localhost:3142/debian unstable/main amd64 perl amd64 5.40.0-8 [267 kB]
Get:62 http://localhost:3142/debian unstable/main amd64 perl-base amd64 5.40.0-8 [1675 kB]
Get:63 http://localhost:3142/debian unstable/main amd64 perl-modules-5.40 all 5.40.0-8 [3015 kB]
Get:64 http://localhost:3142/debian unstable/main amd64 libuuid1 amd64 2.40.3-1 [36.2 kB]
Get:65 http://localhost:3142/debian unstable/main amd64 libblkid1 amd64 2.40.3-1 [169 kB]
Get:66 http://localhost:3142/debian unstable/main amd64 libmount1 amd64 2.40.3-1 [200 kB]
Get:67 http://localhost:3142/debian unstable/main amd64 libsmartcols1 amd64 2.40.3-1 [140 kB]
Get:68 http://localhost:3142/debian unstable/main amd64 util-linux amd64 2.40.3-1 [1212 kB]
Get:69 http://localhost:3142/debian unstable/main amd64 mount amd64 2.40.3-1 [155 kB]
Get:70 http://localhost:3142/debian unstable/main amd64 libpcre2-8-0 amd64 10.44-5 [275 kB]
Get:71 http://localhost:3142/debian unstable/main amd64 libselinux1 amd64 3.7-3+b1 [77.0 kB]
Get:72 http://localhost:3142/debian unstable/main amd64 libnettle8t64 amd64 3.10-1+b1 [305 kB]
Get:73 http://localhost:3142/debian unstable/main amd64 libhogweed6t64 amd64 3.10-1+b1 [335 kB]
Get:74 http://localhost:3142/debian unstable/main amd64 sqv amd64 1.2.1-5 [615 kB]
Get:75 http://localhost:3142/debian unstable/main amd64 libdebconfclient0 amd64 0.277 [10.4 kB]
Get:76 http://localhost:3142/debian unstable/main amd64 base-passwd amd64 3.6.6 [53.1 kB]
Get:77 http://localhost:3142/debian unstable/main amd64 libseccomp2 amd64 2.5.5-2 [47.8 kB]
Get:78 http://localhost:3142/debian unstable/main amd64 apt amd64 2.9.21 [1390 kB]
Get:79 http://localhost:3142/debian unstable/main amd64 init-system-helpers all 1.68 [38.7 kB]
Get:80 http://localhost:3142/debian unstable/main amd64 libc-bin amd64 2.40-5 [627 kB]
Get:81 http://localhost:3142/debian unstable/main amd64 sysvinit-utils amd64 3.13-1 [33.2 kB]
Get:82 http://localhost:3142/debian unstable/main amd64 libaudit-common all 1:4.0.2-2 [12.7 kB]
Get:83 http://localhost:3142/debian unstable/main amd64 libcap-ng0 amd64 0.8.5-4 [17.3 kB]
Get:84 http://localhost:3142/debian unstable/main amd64 libaudit1 amd64 1:4.0.2-2 [54.9 kB]
Get:85 http://localhost:3142/debian unstable/main amd64 debconf all 1.5.89 [120 kB]
Get:86 http://localhost:3142/debian unstable/main amd64 libpam0g amd64 1.5.3-7+b1 [68.3 kB]
Get:87 http://localhost:3142/debian unstable/main amd64 libpam-modules-bin amd64 1.5.3-7+b1 [54.1 kB]
Get:88 http://localhost:3142/debian unstable/main amd64 libpam-modules amd64 1.5.3-7+b1 [267 kB]
Get:89 http://localhost:3142/debian unstable/main amd64 logsave amd64 1.47.2-1 [23.9 kB]
Get:90 http://localhost:3142/debian unstable/main amd64 libext2fs2t64 amd64 1.47.2-1 [212 kB]
Get:91 http://localhost:3142/debian unstable/main amd64 e2fsprogs amd64 1.47.2-1 [590 kB]
Get:92 http://localhost:3142/debian unstable/main amd64 login amd64 1:4.16.0-2+really2.40.3-1 [88.4 kB]
Get:93 http://localhost:3142/debian unstable/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB]
Get:94 http://localhost:3142/debian unstable/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB]
Get:95 http://localhost:3142/debian unstable/main amd64 gpgv amd64 2.2.46~pre1-1 [219 kB]
Get:96 http://localhost:3142/debian unstable/main amd64 libacl1 amd64 2.3.2-2+b1 [32.9 kB]
Get:97 http://localhost:3142/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get:98 http://localhost:3142/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB]
Get:99 http://localhost:3142/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get:100 http://localhost:3142/debian unstable/main amd64 libtasn1-6 amd64 4.19.0-3+b3 [49.5 kB]
Get:101 http://localhost:3142/debian unstable/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB]
Get:102 http://localhost:3142/debian unstable/main amd64 libmd0 amd64 1.1.0-2+b1 [36.3 kB]
Get:103 http://localhost:3142/debian unstable/main amd64 libtinfo6 amd64 6.5-2+b1 [344 kB]
Get:104 http://localhost:3142/debian unstable/main amd64 login.defs all 1:4.16.0-7 [185 kB]
Get:105 http://localhost:3142/debian unstable/main amd64 libsemanage2 amd64 3.7-2+b1 [91.2 kB]
Get:106 http://localhost:3142/debian unstable/main amd64 passwd amd64 1:4.16.0-7 [1233 kB]
Get:107 http://localhost:3142/debian unstable/main amd64 tzdata all 2024b-5 [256 kB]
Get:108 http://localhost:3142/debian unstable/main amd64 xz-utils amd64 5.6.3-1+b1 [542 kB]
Get:109 http://localhost:3142/debian unstable/main amd64 dpkg-dev all 1.22.13 [1334 kB]
Get:110 http://localhost:3142/debian unstable/main amd64 libdpkg-perl all 1.22.13 [642 kB]
Get:111 http://localhost:3142/debian unstable/main amd64 make amd64 4.4.1-1 [463 kB]
Get:112 http://localhost:3142/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get:113 http://localhost:3142/debian unstable/main amd64 libss2 amd64 1.47.2-1 [28.7 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Current default time zone: 'Etc/UTC'
Local time is now:      Fri Jan 10 19:15:05 UTC 2025.
Universal Time is now:  Fri Jan 10 19:15:05 UTC 2025.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

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Setting up xz-utils (5.6.3-1+b1) ...
Setting up libquadmath0:amd64 (14.2.0-12) ...
Setting up libmpc3:amd64 (1.3.1-1+b3) ...
Setting up libatomic1:amd64 (14.2.0-12) ...
Setting up libss2:amd64 (1.47.2-1) ...
Setting up cpp-14-x86-64-linux-gnu (14.2.0-12) ...
Setting up logsave (1.47.2-1) ...
Setting up cpp-14 (14.2.0-12) ...
Setting up libubsan1:amd64 (14.2.0-12) ...
Setting up mount (2.40.3-1) ...
Setting up perl-modules-5.40 (5.40.0-8) ...
Setting up libhwasan0:amd64 (14.2.0-12) ...
Setting up libasan8:amd64 (14.2.0-12) ...
Setting up libsemanage2:amd64 (3.7-2+b1) ...
Setting up libtsan2:amd64 (14.2.0-12) ...
Setting up libbinutils:amd64 (2.43.50.20250108-1) ...
Setting up libc-dev-bin (2.40-5) ...
Setting up libcc1-0:amd64 (14.2.0-12) ...
Setting up liblsan0:amd64 (14.2.0-12) ...
Setting up libitm1:amd64 (14.2.0-12) ...
Setting up login (1:4.16.0-2+really2.40.3-1) ...
Setting up libctf0:amd64 (2.43.50.20250108-1) ...
Setting up e2fsprogs (1.47.2-1) ...
Setting up libperl5.40:amd64 (5.40.0-8) ...
Setting up perl (5.40.0-8) ...
Setting up libgprofng0:amd64 (2.43.50.20250108-1) ...
Setting up libdpkg-perl (1.22.13) ...
Setting up passwd (1:4.16.0-7) ...
Setting up libc6-dev:amd64 (2.40-5) ...
Setting up libgcc-14-dev:amd64 (14.2.0-12) ...
Setting up libstdc++-14-dev:amd64 (14.2.0-12) ...
Setting up binutils-x86-64-linux-gnu (2.43.50.20250108-1) ...
Setting up binutils (2.43.50.20250108-1) ...
Setting up dpkg-dev (1.22.13) ...
Setting up gcc-14-x86-64-linux-gnu (14.2.0-12) ...
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Setting up g++-14-x86-64-linux-gnu (14.2.0-12) ...
Setting up g++-14 (14.2.0-12) ...
Processing triggers for debianutils (5.21) ...
Processing triggers for libc-bin (2.40-5) ...

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


Check APT
---------

Checking available source versions...

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

Reading package lists...
NOTICE: 'plink' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/plink.git
Please use:
git clone https://salsa.debian.org/med-team/plink.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 449 kB of source archives.
Get:1 http://localhost:3142/debian unstable/main plink 1.07+dfsg-4 (dsc) [2076 B]
Get:2 http://localhost:3142/debian unstable/main plink 1.07+dfsg-4 (tar) [429 kB]
Get:3 http://localhost:3142/debian unstable/main plink 1.07+dfsg-4 (diff) [17.4 kB]
Fetched 449 kB in 1s (503 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/plink-yEeSAE/plink-1.07+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/plink-yEeSAE' 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-riscv64:amd64, libc-dev:riscv64, libstdc++-dev:riscv64
Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-riscv64:amd64, libc-dev:riscv64, libstdc++-dev:riscv64
dpkg-deb: warning: root directory /<<RESOLVERDIR>>/sbuild-build-depends-main-dummy has unusual owner or group 1000:119
dpkg-deb: Hint: you might need to pass --root-owner-group, see <https://wiki.debian.org/Teams/Dpkg/RootlessBuilds> for further details
dpkg-deb: warning: ignoring 1 warning about the control file(s)
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 [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [732 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [777 B]
Fetched 2118 B in 0s (0 B/s)
Reading package lists...
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
Execute external solver...
The following packages were automatically installed and are no longer required:
  gpgv libffi8 libgcrypt20 libgnutls30t64 libgpg-error0 libidn2-0 libp11-kit0
  libtasn1-6
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev binutils-riscv64-linux-gnu
  bsdextrautils cpp-14-riscv64-linux-gnu cpp-riscv64-linux-gnu
  crossbuild-essential-riscv64 debhelper dh-autoreconf dh-strip-nondeterminism
  dwz fakeroot file g++-14-riscv64-linux-gnu g++-riscv64-linux-gnu
  gcc-14-base:riscv64 gcc-14-cross-base gcc-14-riscv64-linux-gnu
  gcc-14-riscv64-linux-gnu-base gcc-riscv64-linux-gnu gettext gettext-base
  groff-base intltool-debian libarchive-zip-perl libasan8:riscv64
  libasan8-riscv64-cross libatomic1:riscv64 libatomic1-riscv64-cross
  libc6:riscv64 libc6-dev:riscv64 libc6-dev-riscv64-cross libc6-riscv64-cross
  libcrypt-dev:riscv64 libcrypt1:riscv64 libdebhelper-perl libelf1t64
  libfakeroot libfile-stripnondeterminism-perl libgcc-14-dev:riscv64
  libgcc-14-dev-riscv64-cross libgcc-s1:riscv64 libgcc-s1-riscv64-cross
  libgomp1:riscv64 libgomp1-riscv64-cross libicu72 libitm1:riscv64
  libitm1-riscv64-cross liblsan0:riscv64 liblsan0-riscv64-cross libmagic-mgc
  libmagic1t64 libpipeline1 libstdc++-14-dev:riscv64
  libstdc++-14-dev-riscv64-cross libstdc++6:riscv64 libstdc++6-riscv64-cross
  libtool libtsan2:riscv64 libtsan2-riscv64-cross libubsan1:riscv64
  libubsan1-riscv64-cross libuchardet0 libxml2 linux-libc-dev-riscv64-cross m4
  man-db po-debconf sensible-utils zlib1g:riscv64 zlib1g-dev:riscv64
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-14-locales
  cpp-14-doc cpp-doc dh-make gcc-14-doc manpages-dev flex bison
  gdb-riscv64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev
  groff glibc-doc:riscv64 libc-l10n:riscv64 locales:riscv64 libnss-nis:riscv64
  libnss-nisplus:riscv64 manpages-dev:riscv64 libstdc++-14-doc:riscv64
  libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
  www-browser libmail-box-perl
Recommended packages:
  curl | wget | lynx libidn2-0:riscv64 libarchive-cpio-perl libltdl-dev
  libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev binutils-riscv64-linux-gnu
  bsdextrautils cpp-14-riscv64-linux-gnu cpp-riscv64-linux-gnu
  crossbuild-essential-riscv64 debhelper dh-autoreconf dh-strip-nondeterminism
  dwz fakeroot file g++-14-riscv64-linux-gnu g++-riscv64-linux-gnu
  gcc-14-base:riscv64 gcc-14-cross-base gcc-14-riscv64-linux-gnu
  gcc-14-riscv64-linux-gnu-base gcc-riscv64-linux-gnu gettext gettext-base
  groff-base intltool-debian libarchive-zip-perl libasan8:riscv64
  libasan8-riscv64-cross libatomic1:riscv64 libatomic1-riscv64-cross
  libc6:riscv64 libc6-dev:riscv64 libc6-dev-riscv64-cross libc6-riscv64-cross
  libcrypt-dev:riscv64 libcrypt1:riscv64 libdebhelper-perl libelf1t64
  libfakeroot libfile-stripnondeterminism-perl libgcc-14-dev:riscv64
  libgcc-14-dev-riscv64-cross libgcc-s1:riscv64 libgcc-s1-riscv64-cross
  libgomp1:riscv64 libgomp1-riscv64-cross libicu72 libitm1:riscv64
  libitm1-riscv64-cross liblsan0:riscv64 liblsan0-riscv64-cross libmagic-mgc
  libmagic1t64 libpipeline1 libstdc++-14-dev:riscv64
  libstdc++-14-dev-riscv64-cross libstdc++6:riscv64 libstdc++6-riscv64-cross
  libtool libtsan2:riscv64 libtsan2-riscv64-cross libubsan1:riscv64
  libubsan1-riscv64-cross libuchardet0 libxml2 linux-libc-dev-riscv64-cross m4
  man-db po-debconf sbuild-build-depends-main-dummy:riscv64 sensible-utils
  zlib1g:riscv64 zlib1g-dev:riscv64
0 upgraded, 74 newly installed, 0 to remove and 0 not upgraded.
Need to get 124 MB of archives.
After this operation, 653 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [924 B]
Get:2 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get:3 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get:4 http://localhost:3142/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get:5 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get:6 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.22.5-4 [200 kB]
Get:7 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get:8 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get:9 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.40.3-1 [92.1 kB]
Get:10 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get:11 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get:12 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get:13 http://localhost:3142/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get:14 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get:15 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get:16 http://localhost:3142/debian unstable/main amd64 autopoint all 0.22.5-4 [723 kB]
Get:17 http://localhost:3142/debian unstable/main amd64 binutils-riscv64-linux-gnu amd64 2.43.50.20250108-1 [1429 kB]
Get:18 http://localhost:3142/debian unstable/main amd64 gcc-14-riscv64-linux-gnu-base amd64 14.2.0-12cross1 [48.5 kB]
Get:19 http://localhost:3142/debian unstable/main amd64 cpp-14-riscv64-linux-gnu amd64 14.2.0-12cross1 [13.3 MB]
Get:20 http://localhost:3142/debian unstable/main amd64 cpp-riscv64-linux-gnu amd64 4:14.2.0-1 [4848 B]
Get:21 http://localhost:3142/debian unstable/main amd64 gcc-14-cross-base all 14.2.0-12cross1 [43.7 kB]
Get:22 http://localhost:3142/debian unstable/main amd64 libc6-riscv64-cross all 2.40-4cross1 [1142 kB]
Get:23 http://localhost:3142/debian unstable/main amd64 libgcc-s1-riscv64-cross all 14.2.0-12cross1 [56.7 kB]
Get:24 http://localhost:3142/debian unstable/main amd64 libgomp1-riscv64-cross all 14.2.0-12cross1 [129 kB]
Get:25 http://localhost:3142/debian unstable/main amd64 libitm1-riscv64-cross all 14.2.0-12cross1 [25.2 kB]
Get:26 http://localhost:3142/debian unstable/main amd64 libatomic1-riscv64-cross all 14.2.0-12cross1 [8336 B]
Get:27 http://localhost:3142/debian unstable/main amd64 libasan8-riscv64-cross all 14.2.0-12cross1 [2355 kB]
Get:28 http://localhost:3142/debian unstable/main amd64 liblsan0-riscv64-cross all 14.2.0-12cross1 [1077 kB]
Get:29 http://localhost:3142/debian unstable/main amd64 libtsan2-riscv64-cross all 14.2.0-12cross1 [2231 kB]
Get:30 http://localhost:3142/debian unstable/main amd64 libstdc++6-riscv64-cross all 14.2.0-12cross1 [660 kB]
Get:31 http://localhost:3142/debian unstable/main amd64 libubsan1-riscv64-cross all 14.2.0-12cross1 [979 kB]
Get:32 http://localhost:3142/debian unstable/main amd64 libgcc-14-dev-riscv64-cross all 14.2.0-12cross1 [5173 kB]
Get:33 http://localhost:3142/debian unstable/main amd64 gcc-14-riscv64-linux-gnu amd64 14.2.0-12cross1 [25.7 MB]
Get:34 http://localhost:3142/debian unstable/main amd64 gcc-riscv64-linux-gnu amd64 4:14.2.0-1 [1444 B]
Get:35 http://localhost:3142/debian unstable/main amd64 linux-libc-dev-riscv64-cross all 6.12.6-1cross1 [2291 kB]
Get:36 http://localhost:3142/debian unstable/main amd64 libc6-dev-riscv64-cross all 2.40-4cross1 [3088 kB]
Get:37 http://localhost:3142/debian unstable/main amd64 libstdc++-14-dev-riscv64-cross all 14.2.0-12cross1 [4949 kB]
Get:38 http://localhost:3142/debian unstable/main amd64 g++-14-riscv64-linux-gnu amd64 14.2.0-12cross1 [14.2 MB]
Get:39 http://localhost:3142/debian unstable/main amd64 g++-riscv64-linux-gnu amd64 4:14.2.0-1 [1200 B]
Get:40 http://localhost:3142/debian unstable/main amd64 crossbuild-essential-riscv64 all 12.12 [3544 B]
Get:41 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.23 [90.6 kB]
Get:42 http://localhost:3142/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB]
Get:43 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get:44 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:45 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get:46 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get:47 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get:48 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get:49 http://localhost:3142/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get:50 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
Get:51 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.22.5-4 [1600 kB]
Get:52 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:53 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:54 http://localhost:3142/debian unstable/main amd64 debhelper all 13.23 [919 kB]
Get:55 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.36.2-1 [29.6 kB]
Get:56 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.36.2-1 [75.4 kB]
Get:57 http://localhost:3142/debian unstable/main riscv64 gcc-14-base riscv64 14.2.0-12 [48.3 kB]
Get:58 http://localhost:3142/debian unstable/main riscv64 libgcc-s1 riscv64 14.2.0-12 [56.6 kB]
Get:59 http://localhost:3142/debian unstable/main riscv64 libc6 riscv64 2.40-5 [2440 kB]
Get:60 http://localhost:3142/debian unstable/main riscv64 libasan8 riscv64 14.2.0-12 [2366 kB]
Get:61 http://localhost:3142/debian unstable/main riscv64 libatomic1 riscv64 14.2.0-12 [8676 B]
Get:62 http://localhost:3142/debian unstable/main riscv64 libcrypt1 riscv64 1:4.4.36-5 [105 kB]
Get:63 http://localhost:3142/debian unstable/main riscv64 libcrypt-dev riscv64 1:4.4.36-5 [221 kB]
Get:64 http://localhost:3142/debian unstable/main riscv64 libc6-dev riscv64 2.40-5 [3092 kB]
Get:65 http://localhost:3142/debian unstable/main riscv64 libgomp1 riscv64 14.2.0-12 [131 kB]
Get:66 http://localhost:3142/debian unstable/main riscv64 libitm1 riscv64 14.2.0-12 [25.7 kB]
Get:67 http://localhost:3142/debian unstable/main riscv64 liblsan0 riscv64 14.2.0-12 [1078 kB]
Get:68 http://localhost:3142/debian unstable/main riscv64 libtsan2 riscv64 14.2.0-12 [2242 kB]
Get:69 http://localhost:3142/debian unstable/main riscv64 libstdc++6 riscv64 14.2.0-12 [708 kB]
Get:70 http://localhost:3142/debian unstable/main riscv64 libubsan1 riscv64 14.2.0-12 [979 kB]
Get:71 http://localhost:3142/debian unstable/main riscv64 libgcc-14-dev riscv64 14.2.0-12 [5197 kB]
Get:72 http://localhost:3142/debian unstable/main riscv64 libstdc++-14-dev riscv64 14.2.0-12 [5278 kB]
Get:73 http://localhost:3142/debian unstable/main riscv64 zlib1g riscv64 1:1.3.dfsg+really1.3.1-1+b1 [85.7 kB]
Get:74 http://localhost:3142/debian unstable/main riscv64 zlib1g-dev riscv64 1:1.3.dfsg+really1.3.1-1+b1 [978 kB]
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Processing triggers for libc-bin (2.40-5) ...

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

Arch check ok (riscv64 included in any)

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

Kernel: Linux 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) amd64 (x86_64)
Toolchain package versions: binutils_2.43.50.20250108-1 dpkg-dev_1.22.13 g++-14_14.2.0-12 gcc-14_14.2.0-12 libc6-dev_2.40-5 libstdc++-14-dev_14.2.0-12 libstdc++-14-dev-riscv64-cross_14.2.0-12cross1 libstdc++6_14.2.0-12 libstdc++6-riscv64-cross_14.2.0-12cross1 linux-libc-dev_6.12.8-1
Package versions: apt_2.9.21 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-4 autotools-dev_20220109.1 base-files_13.6 base-passwd_3.6.6 bash_5.2.37-1 binutils_2.43.50.20250108-1 binutils-common_2.43.50.20250108-1 binutils-riscv64-linux-gnu_2.43.50.20250108-1 binutils-x86-64-linux-gnu_2.43.50.20250108-1 bsdextrautils_2.40.3-1 bsdutils_1:2.40.3-1 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-14_14.2.0-12 cpp-14-riscv64-linux-gnu_14.2.0-12cross1 cpp-14-x86-64-linux-gnu_14.2.0-12 cpp-riscv64-linux-gnu_4:14.2.0-1 cpp-x86-64-linux-gnu_4:14.2.0-1 crossbuild-essential-riscv64_12.12 dash_0.5.12-11 debconf_1.5.89 debhelper_13.23 debian-archive-keyring_2023.4 debianutils_5.21 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-2 dpkg_1.22.13 dpkg-dev_1.22.13 dwz_0.15-1+b1 e2fsprogs_1.47.2-1 fakeroot_1.36.2-1 file_1:5.45-3+b1 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.2.0-12 g++-14-riscv64-linux-gnu_14.2.0-12cross1 g++-14-x86-64-linux-gnu_14.2.0-12 g++-riscv64-linux-gnu_4:14.2.0-1 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.2.0-12 gcc-14-base_14.2.0-12 gcc-14-cross-base_14.2.0-12cross1 gcc-14-riscv64-linux-gnu_14.2.0-12cross1 gcc-14-riscv64-linux-gnu-base_14.2.0-12cross1 gcc-14-x86-64-linux-gnu_14.2.0-12 gcc-riscv64-linux-gnu_4:14.2.0-1 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.22.5-4 gettext-base_0.22.5-4 gpgv_2.2.46~pre1-1 grep_3.11-4 groff-base_1.23.0-7 gzip_1.12-1.2 hostname_3.25 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg6.0t64_2.9.21 libarchive-zip-perl_1.68-1 libasan8_14.2.0-12 libasan8-riscv64-cross_14.2.0-12cross1 libatomic1_14.2.0-12 libatomic1-riscv64-cross_14.2.0-12cross1 libattr1_1:2.5.2-2 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2 libbinutils_2.43.50.20250108-1 libblkid1_2.40.3-1 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.40-5 libc-dev-bin_2.40-5 libc6_2.40-5 libc6-dev_2.40-5 libc6-dev-riscv64-cross_2.40-4cross1 libc6-riscv64-cross_2.40-4cross1 libcap-ng0_0.8.5-4 libcap2_1:2.66-5+b1 libcc1-0_14.2.0-12 libcom-err2_1.47.2-1 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.50.20250108-1 libctf0_2.43.50.20250108-1 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.277 libdebhelper-perl_13.23 libdpkg-perl_1.22.13 libelf1t64_0.192-4 libext2fs2t64_1.47.2-1 libfakeroot_1.36.2-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-14-dev_14.2.0-12 libgcc-14-dev-riscv64-cross_14.2.0-12cross1 libgcc-s1_14.2.0-12 libgcc-s1-riscv64-cross_14.2.0-12cross1 libgcrypt20_1.11.0-7 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp10_2:6.3.0+dfsg-3 libgnutls30t64_3.8.8-2 libgomp1_14.2.0-12 libgomp1-riscv64-cross_14.2.0-12cross1 libgpg-error0_1.51-3 libgprofng0_2.43.50.20250108-1 libhogweed6t64_3.10-1+b1 libhwasan0_14.2.0-12 libicu72_72.1-6 libidn2-0_2.3.7-2+b1 libisl23_0.27-1 libitm1_14.2.0-12 libitm1-riscv64-cross_14.2.0-12cross1 libjansson4_2.14-2+b3 liblsan0_14.2.0-12 liblsan0-riscv64-cross_14.2.0-12cross1 liblz4-1_1.9.4-4 liblzma5_5.6.3-1+b1 libmagic-mgc_1:5.45-3+b1 libmagic1t64_1:5.45-3+b1 libmd0_1.1.0-2+b1 libmount1_2.40.3-1 libmpc3_1.3.1-1+b3 libmpfr6_4.2.1-1+b2 libnettle8t64_3.10-1+b1 libp11-kit0_0.25.5-3 libpam-modules_1.5.3-7+b1 libpam-modules-bin_1.5.3-7+b1 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7+b1 libpcre2-8-0_10.44-5 libperl5.40_5.40.0-8 libpipeline1_1.5.8-1 libquadmath0_14.2.0-12 libseccomp2_2.5.5-2 libselinux1_3.7-3+b1 libsemanage-common_3.7-2 libsemanage2_3.7-2+b1 libsepol2_3.7-1 libsframe1_2.43.50.20250108-1 libsmartcols1_2.40.3-1 libss2_1.47.2-1 libssl3t64_3.4.0-2 libstdc++-14-dev_14.2.0-12 libstdc++-14-dev-riscv64-cross_14.2.0-12cross1 libstdc++6_14.2.0-12 libstdc++6-riscv64-cross_14.2.0-12cross1 libsystemd0_257.2-1 libtasn1-6_4.19.0-3+b3 libtinfo6_6.5-2+b1 libtool_2.5.4-2 libtsan2_14.2.0-12 libtsan2-riscv64-cross_14.2.0-12cross1 libubsan1_14.2.0-12 libubsan1-riscv64-cross_14.2.0-12cross1 libuchardet0_0.0.8-1+b2 libudev1_257.2-1 libunistring5_1.3-1 libuuid1_2.40.3-1 libxml2_2.12.7+dfsg+really2.9.14-0.2+b1 libxxhash0_0.8.3-2 libzstd1_1.5.6+dfsg-2 linux-libc-dev_6.12.8-1 linux-libc-dev-riscv64-cross_6.12.6-1cross1 login_1:4.16.0-2+really2.40.3-1 login.defs_1:4.16.0-7 logsave_1.47.2-1 m4_1.4.19-5 make_4.4.1-1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 mount_2.40.3-1 ncurses-base_6.5-2 ncurses-bin_6.5-2+b1 openssl-provider-legacy_3.4.0-2 passwd_1:4.16.0-7 patch_2.7.6-7 perl_5.40.0-8 perl-base_5.40.0-8 perl-modules-5.40_5.40.0-8 po-debconf_1.0.21+nmu1 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sqv_1.2.1-5 sysvinit-utils_3.13-1 tar_1.35+dfsg-3.1 tzdata_2024b-5 util-linux_2.40.3-1 xz-utils_5.6.3-1+b1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1

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


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

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

Format: 3.0 (quilt)
Source: plink
Binary: plink
Architecture: any
Version: 1.07+dfsg-4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>, Andreas Tille <tille@debian.org>, Charles Plessy <plessy@debian.org>, Dylan Aïssi <daissi@debian.org>
Homepage: http://zzz.bwh.harvard.edu/plink/
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/plink
Vcs-Git: https://salsa.debian.org/med-team/plink.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), zlib1g-dev
Package-List:
 plink deb science optional arch=any
Checksums-Sha1:
 c91f5de3a92ce44319870668dd81f34e076e9a38 429164 plink_1.07+dfsg.orig.tar.xz
 30da84e59157c428d54473d7e242e394a2dc6aaf 17356 plink_1.07+dfsg-4.debian.tar.xz
Checksums-Sha256:
 e11a1573101ca1a930f44db02050cd27790fec055fc6abcc0ebaad59fc99a5dd 429164 plink_1.07+dfsg.orig.tar.xz
 9cf0a2845eb96c95ed85347bdaf8afcc7bb0c933c960ce2adde2026ec78084c4 17356 plink_1.07+dfsg-4.debian.tar.xz
Files:
 fe49f1c648e5f318a9d4cdb23e343892 429164 plink_1.07+dfsg.orig.tar.xz
 d4701d1cd62de5c466ad92f54f17c8c8 17356 plink_1.07+dfsg-4.debian.tar.xz

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gpgv: Signature made Sun Oct 31 15:36:45 2021 UTC
gpgv:                using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv:                issuer "nilesh@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./plink_1.07+dfsg-4.dsc: no acceptable signature found
dpkg-source: info: extracting plink in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking plink_1.07+dfsg.orig.tar.xz
dpkg-source: info: unpacking plink_1.07+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 30_endiandetection.patch
dpkg-source: info: applying gcc-4.7.patch
dpkg-source: info: applying Fix_spelling_error.patch
dpkg-source: info: applying gcc11.patch

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

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
CONFIG_SITE=/etc/dpkg-cross/cross-config.riscv64
DEB_BUILD_OPTIONS=nocheck
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=crossqa
OLDPWD=/home/crossqa
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SBUILD_CONFIG=/tmp/tmp.qkcDBAd1Sg/sbuild.conf
SCHROOT_ALIAS_NAME=unstable-amd64-sbuild
SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=crossqa
SCHROOT_SESSION_ID=sid-amd64-sbuild-f6d5845e-1418-4172-b95c-254321772ba1
SCHROOT_UID=1000
SCHROOT_USER=crossqa
SHELL=/bin/sh
USER=crossqa

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

Command: dpkg-buildpackage --sanitize-env -ariscv64 -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 riscv64-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 riscv64
 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=riscv64-linux-gnu-pkg-config CXX=riscv64-linux-gnu-g\+\+ CC=riscv64-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>>'
riscv64-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++)
      |                   ~^~~~~~~~~~~
riscv64-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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
riscv64-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 [-Wmaybe-uninitialized]
   91 |           if ( feof(PED) )
      |                ~~~~^~~~~
input.cpp:60:10: note: ‘PED’ was declared here
   60 |   FILE * PED;
      |          ^~~
riscv64-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++)
      |                    ~~^~~~~~~~~~~~~~
riscv64-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() )
      |            ~~~^~~~~~~~~~~~~~~~~~~~
riscv64-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;
      |       ^~~~~~~
riscv64-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:378:58: warning: control reaches end of non-void function [-Wreturn-type]
  378 |       error("Not valid integer argument for : "+a+" [ "+s+" ]");
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
helper.cpp: In function ‘long unsigned int getLongUnsignedInt(std::string, std::string)’:
helper.cpp:391:58: warning: control reaches end of non-void function [-Wreturn-type]
  391 |       error("Not valid integer argument for : "+a+" [ "+s+" ]");
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
helper.cpp: In function ‘double getDouble(std::string, std::string)’:
helper.cpp:404:58: warning: control reaches end of non-void function [-Wreturn-type]
  404 |       error("Not valid numeric argument for : "+a+" [ "+s+" ]");
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
helper.cpp: In function ‘std::vector<bool> vif_prune(std::vector<std::vector<double> >, double, std::vector<int>&)’:
helper.cpp:1405:11: warning: ‘maxI’ may be used uninitialized [-Wmaybe-uninitialized]
 1405 |       int maxI;
      |           ^~~~
riscv64-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++)
      |                   ~~^~~~~~~~~~
riscv64-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;
      |       ^
riscv64-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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
riscv64-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;
      |        ^~~~~~~
riscv64-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
riscv64-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++)
      |                        ~^~~~~~~~~~~~~~
In file included from /usr/riscv64-linux-gnu/include/c++/14/string:51,
                 from /usr/riscv64-linux-gnu/include/c++/14/bits/locale_classes.h:40,
                 from /usr/riscv64-linux-gnu/include/c++/14/bits/ios_base.h:41,
                 from /usr/riscv64-linux-gnu/include/c++/14/ios:44,
                 from /usr/riscv64-linux-gnu/include/c++/14/ostream:40,
                 from /usr/riscv64-linux-gnu/include/c++/14/iostream:41,
                 from cluster.cpp:14:
In static member function ‘static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]’,
    inlined from ‘_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_algobase.h:521:30,
    inlined from ‘_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_algobase.h:548:42,
    inlined from ‘_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator<const int*, vector<int> >; _OI = int*]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_algobase.h:555:31,
    inlined from ‘_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<const int*, vector<int> >; _OI = int*]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_algobase.h:651:7,
    inlined from ‘static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const int*, std::vector<int> >; _ForwardIterator = int*]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_uninitialized.h:147:27,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const int*, vector<int> >; _ForwardIterator = int*]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const int*, vector<int> >; _ForwardIterator = int*; _Tp = int]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator<int>]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_vector.h:606:31,
    inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector<int>; _Args = {const std::vector<int, std::allocator<int> >&}; _Tp = std::vector<int>]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/new_allocator.h:191:4,
    inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector<int>; _Args = {const std::vector<int, std::allocator<int> >&}; _Tp = std::vector<int>]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/alloc_traits.h:569:17,
    inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector<int>; _Alloc = std::allocator<std::vector<int> >]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_vector.h:1288:30,
    inlined from ‘void Plink::buildCluster()’ at cluster.cpp:128:20:
/usr/riscv64-linux-gnu/include/c++/14/bits/stl_algobase.h:452:30: warning: ‘void* __builtin_memmove(void*, const void*, long unsigned int)’ forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=]
  452 |             __builtin_memmove(__result, __first, sizeof(_Tp) * _Num);
      |             ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]’,
    inlined from ‘_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_algobase.h:521:30,
    inlined from ‘_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_algobase.h:548:42,
    inlined from ‘_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator<const int*, vector<int> >; _OI = int*]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_algobase.h:555:31,
    inlined from ‘_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<const int*, vector<int> >; _OI = int*]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_algobase.h:651:7,
    inlined from ‘static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const int*, std::vector<int> >; _ForwardIterator = int*]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_uninitialized.h:147:27,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const int*, vector<int> >; _ForwardIterator = int*]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const int*, vector<int> >; _ForwardIterator = int*; _Tp = int]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator<int>]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_vector.h:606:31,
    inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector<int>; _Args = {const std::vector<int, std::allocator<int> >&}; _Tp = std::vector<int>]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/new_allocator.h:191:4,
    inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector<int>; _Args = {const std::vector<int, std::allocator<int> >&}; _Tp = std::vector<int>]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/alloc_traits.h:569:17,
    inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector<int>; _Alloc = std::allocator<std::vector<int> >]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_vector.h:1288:30,
    inlined from ‘void Plink::buildCluster()’ at cluster.cpp:139:16:
/usr/riscv64-linux-gnu/include/c++/14/bits/stl_algobase.h:452:30: warning: ‘void* __builtin_memmove(void*, const void*, long unsigned int)’ forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=]
  452 |             __builtin_memmove(__result, __first, sizeof(_Tp) * _Num);
      |             ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
riscv64-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);
      |        ^~~~
riscv64-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 [-Wmaybe-uninitialized]
  144 |           << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i1,l) << " "
      |                                                     ~~~~~~~~^~~~~~~~~~~~
output.cpp:116:7: note: ‘i1’ was declared here
  116 |   int i1, i2;
      |       ^~
output.cpp:145:61: warning: ‘i2’ may be used uninitialized [-Wmaybe-uninitialized]
  145 |           << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i2,l) << " "
      |                                                     ~~~~~~~~^~~~~~~~~~~~
output.cpp:116:11: note: ‘i2’ was declared here
  116 |   int i1, i2;
      |           ^~
output.cpp: In member function ‘void Plink::display_indivReport()’:
output.cpp:69:32: warning: ‘i1’ may be used uninitialized [-Wmaybe-uninitialized]
   69 |          << setw(6) << genotype(*this,i1,l) << "\n";
      |                        ~~~~~~~~^~~~~~~~~~~~
output.cpp:46:7: note: ‘i1’ was declared here
   46 |   int i1;
      |       ^~
riscv64-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++)
      |                        ~^~~~~~~~~~~~~~
riscv64-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:1108:11: warning: ‘pvalue’ may be used uninitialized [-Wmaybe-uninitialized]
 1108 |           if ( pvalue <= par::set_score_p && pvalue >= 0 )
      |           ^~
assoc.cpp:1019:14: note: ‘pvalue’ was declared here
 1019 |       double pvalue;
      |              ^~~~~~
In file included from /usr/riscv64-linux-gnu/include/c++/14/iostream:41,
                 from assoc.cpp:14:
In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]’,
    inlined from ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’ at assoc.cpp:1647:26:
/usr/riscv64-linux-gnu/include/c++/14/ostream:229:25: warning: ‘mult_chisq’ may be used uninitialized [-Wmaybe-uninitialized]
  229 |       { return _M_insert(__f); }
      |                ~~~~~~~~~^~~~~
assoc.cpp: In member function ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’:
assoc.cpp:1385:22: note: ‘mult_chisq’ was declared here
 1385 |       double mult_p, mult_chisq;
      |                      ^~~~~~~~~~
In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]’,
    inlined from ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’ at assoc.cpp:1672:26:
/usr/riscv64-linux-gnu/include/c++/14/ostream:229:25: warning: ‘dom_chisq’ may be used uninitialized [-Wmaybe-uninitialized]
  229 |       { return _M_insert(__f); }
      |                ~~~~~~~~~^~~~~
assoc.cpp: In member function ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’:
assoc.cpp:1430:14: note: ‘dom_chisq’ was declared here
 1430 |       double dom_chisq, rec_chisq, gen_chisq;
      |              ^~~~~~~~~
In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]’,
    inlined from ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’ at assoc.cpp:1697:26:
/usr/riscv64-linux-gnu/include/c++/14/ostream:229:25: warning: ‘rec_chisq’ may be used uninitialized [-Wmaybe-uninitialized]
  229 |       { return _M_insert(__f); }
      |                ~~~~~~~~~^~~~~
assoc.cpp: In member function ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’:
assoc.cpp:1430:25: note: ‘rec_chisq’ was declared here
 1430 |       double dom_chisq, rec_chisq, gen_chisq;
      |                         ^~~~~~~~~
In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]’,
    inlined from ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’ at assoc.cpp:1590:26:
/usr/riscv64-linux-gnu/include/c++/14/ostream:229:25: warning: ‘gen_chisq’ may be used uninitialized [-Wmaybe-uninitialized]
  229 |       { return _M_insert(__f); }
      |                ~~~~~~~~~^~~~~
assoc.cpp: In member function ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’:
assoc.cpp:1430:36: note: ‘gen_chisq’ was declared here
 1430 |       double dom_chisq, rec_chisq, gen_chisq;
      |                                    ^~~~~~~~~
riscv64-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;
      |           ^
riscv64-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++)
      |                 ~^~~~~~~~~~~~
riscv64-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++)
      |                       ~~^~~~~~~~~~~
riscv64-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++)
      |                          ~^~~~~~~~~~~~~~~~~~~~~~~~
riscv64-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:936:55: warning: ‘zt’ may be used uninitialized [-Wmaybe-uninitialized]
  936 |                   double OR_lower = exp( log(OR) - zt * sqrt(1/t1+1/t2)) ;
      |                                                    ~~~^~~~~~~~~~~~~~~~~
tdt.cpp:460:10: note: ‘zt’ was declared here
  460 |   double zt;
      |          ^~
riscv64-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++)
      |                 ~^~~~~~~~~~~~~~
riscv64-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;
      |        ^~~~~~~~~~~~~~~~~
genepi.cpp: In function ‘void CCA_logit(bool, std::vector<std::vector<int> >&, Set&, Plink&)’:
genepi.cpp:840:104: warning: ‘cancor1_pos’ may be used uninitialized [-Wmaybe-uninitialized]
  840 |                             gene2[i] += (1 - mean[j]) * coeff_gene2[order_eigenvalues_gene2[cancor1_pos]][cur_snp];
      |                                                                                                        ^
genepi.cpp:614:17: note: ‘cancor1_pos’ was declared here
  614 |             int cancor1_pos;
      |                 ^~~~~~~~~~~
riscv64-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++)
      |                 ~^~~~~~~~~~~~~~
riscv64-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++)
      |                                        ~^~~~~~~~~~~~~~~~~~~~~~~~
riscv64-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 | }
      | ^
riscv64-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++)
      |                 ~^~~~~~~~~~~~~~~~~~~~
riscv64-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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
riscv64-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 [-Wmaybe-uninitialized]
 1103 |   if (write)
      |   ^~
merge.cpp:943:8: note: ‘write’ was declared here
  943 |   bool write;
      |        ^~~~~
riscv64-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++)
      |                 ~^~~~~~~~~~~~~~
riscv64-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++)
      |                 ~^~~~~~~~~~~~
riscv64-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 ) )
      |                                        ~~^~~~~~~~~~~~~~
riscv64-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++)
      |                     ~^~~~~~~~~~~
riscv64-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;
      |          ^~
riscv64-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++)
      |                 ~^~~~~~~~~~~~~~
riscv64-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;
      |          ^~
riscv64-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;
      |        ^~~~
linear.cpp: In function ‘void gaussj(matrix_t&, matrix_t&)’:
linear.cpp:96:5: warning: ‘icol’ may be used uninitialized [-Wmaybe-uninitialized]
   96 |     if (irow != icol) {
      |     ^~
linear.cpp:75:9: note: ‘icol’ was declared here
   75 |   int i,icol,irow,j,k,l,ll;
      |         ^~~~
linear.cpp:96:5: warning: ‘irow’ may be used uninitialized [-Wmaybe-uninitialized]
   96 |     if (irow != icol) {
      |     ^~
linear.cpp:75:14: note: ‘irow’ was declared here
   75 |   int i,icol,irow,j,k,l,ll;
      |              ^~~~
riscv64-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++)
      |                         ~^~~~~~~~~~~~~~
In file included from /usr/riscv64-linux-gnu/include/c++/14/riscv64-linux-gnu/bits/c++allocator.h:33,
                 from /usr/riscv64-linux-gnu/include/c++/14/bits/allocator.h:46,
                 from /usr/riscv64-linux-gnu/include/c++/14/string:43,
                 from /usr/riscv64-linux-gnu/include/c++/14/bits/locale_classes.h:40,
                 from /usr/riscv64-linux-gnu/include/c++/14/bits/ios_base.h:41,
                 from /usr/riscv64-linux-gnu/include/c++/14/ios:44,
                 from /usr/riscv64-linux-gnu/include/c++/14/ostream:40,
                 from /usr/riscv64-linux-gnu/include/c++/14/iostream:41,
                 from bmerge.cpp:14:
In member function ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = int; _Args = {const int&}; _Tp = int]’,
    inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = int; _Args = {const int&}; _Tp = int]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/alloc_traits.h:569:17,
    inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const int&}; _Tp = int; _Alloc = std::allocator<int>]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/vector.tcc:634:26,
    inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = int; _Alloc = std::allocator<int>]’ at /usr/riscv64-linux-gnu/include/c++/14/bits/stl_vector.h:1294:21,
    inlined from ‘void Plink::mergeBinaryData()’ at bmerge.cpp:687:20:
/usr/riscv64-linux-gnu/include/c++/14/bits/new_allocator.h:191:11: warning: ‘indn’ may be used uninitialized [-Wmaybe-uninitialized]
  191 |         { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bmerge.cpp: In member function ‘void Plink::mergeBinaryData()’:
bmerge.cpp:682:16: note: ‘indn’ was declared here
  682 |            int indn;
      |                ^~~~
riscv64-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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
riscv64-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++)
      |                                ~~^~~~~~~~~~~~~~~~~~~~~~~
riscv64-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++)
      |                     ~^~~~~~~~~~~~~
legacy.cpp: In member function ‘void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)’:
legacy.cpp:203:32: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized]
  203 |                       << start - last - 1 << " ";
      |                          ~~~~~~^~~~~~
legacy.cpp:35:7: note: ‘last’ was declared here
   35 |   int last;
      |       ^~~~
riscv64-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;
riscv64-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 )
      |                     ~~~~~~~~~~~~~^~~
riscv64-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");
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
riscv64-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;
      |        ^~~~
riscv64-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 [-Wmaybe-uninitialized]
  610 |           double pvalue = chiprobP(chisq,df);
      |                           ~~~~~~~~^~~~~~~~~~
glm.cpp:556:15: note: ‘df’ was declared here
  556 |           int df;
      |               ^~
riscv64-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;
      |              ~~~~~~~~~~~~^~~~~~~~~~~~~~
riscv64-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 ‘void Plink::elfBaseline()’:
elf.cpp:1159:22: warning: ‘p_cnt’ may be used uninitialized [-Wmaybe-uninitialized]
 1159 |                   ++(*p_cnt);
      |                     ~^~~~~~~
elf.cpp:1111:13: note: ‘p_cnt’ was declared here
 1111 |       int * p_cnt;
      |             ^~~~~
elf.cpp:1142:18: warning: ‘p_gcnt’ may be used uninitialized [-Wmaybe-uninitialized]
 1142 |               ++(*p_gcnt);
      |                 ~^~~~~~~~
elf.cpp:1112:13: note: ‘p_gcnt’ was declared here
 1112 |       int * p_gcnt;
      |             ^~~~~~
riscv64-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;
      |           ^~~~~~~~~~~~~~~~
riscv64-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.");
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
riscv64-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++)
      |                 ~^~~~~~~~~~~~~~
riscv64-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;
      |       ^~~~~~~~~~~~~
riscv64-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++)
      |                          ~^~~~~~~~~~~~~~~~
riscv64-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];
      |          ^
proxy.cpp:422:7: warning: ‘ref’ may be used uninitialized [-Wmaybe-uninitialized]
  422 |   int ref;
      |       ^~~
riscv64-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;
      |           ^~~~~~~
riscv64-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++)
      |                            ~~^~~~~~~~~~~~~~~~
riscv64-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++)
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
riscv64-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++)
      |                                  ~~^~~~~~~~~~~~~~~
riscv64-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++)
      |                   ~^~~~~~~~~
riscv64-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;
      |              ^~~~~~~~~
riscv64-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)
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~
riscv64-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++)
      |                          ~~^~~~~~~~~~~~~~~~
riscv64-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++)
      |                                   ~^~~~~~~~~~~~~~~
riscv64-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++)
      |                     ~~^~~~~~~~~~
riscv64-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)
      |                  ~^~~~~~
riscv64-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++)
      |                 ~^~~~~~~~~
riscv64-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 )
      |                 ~~^~~~~~~~~~~~~~~
riscv64-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() )
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~
riscv64-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;
      |                              ^~~~
riscv64-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++)
      |                       ~^~~~~~~~~~~~~~
riscv64-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 ];
      |          ^~~~
riscv64-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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
riscv64-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;
      |       ^~~
riscv64-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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
riscv64-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;
      |            ^~~~~~
riscv64-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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
riscv64-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++)
      |                        ~~^~~~~~~~~~~~~
riscv64-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++)
      |                     ~~^~~~~~~~~~~~~~~~~~
riscv64-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++ )
      |                            ~~^~~~~~~~~~~~~~~~~~~~~~
riscv64-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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
riscv64-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++)
      |                     ~^~~~~~~~~~~
riscv64-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++)
      |                     ~~^~~~~~~~~~~~~~~
riscv64-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:510:10: warning: ‘pA1’ may be used uninitialized [-Wmaybe-uninitialized]
  510 |   double D = pA1 - (pA*p1);
      |          ^
blox.cpp:489:10: note: ‘pA1’ was declared here
  489 |   double pA1,pA2,pB1,pB2;
      |          ^~~
blox.cpp:503:10: warning: ‘pA2’ may be used uninitialized [-Wmaybe-uninitialized]
  503 |   double pA = pA1 + pA2;
      |          ^~
blox.cpp:489:14: note: ‘pA2’ was declared here
  489 |   double pA1,pA2,pB1,pB2;
      |              ^~~
blox.cpp:505:10: warning: ‘pB1’ may be used uninitialized [-Wmaybe-uninitialized]
  505 |   double p1 = pA1 + pB1;
      |          ^~
blox.cpp:489:18: note: ‘pB1’ was declared here
  489 |   double pA1,pA2,pB1,pB2;
      |                  ^~~
blox.cpp:565:51: warning: ‘pB2’ may be used uninitialized [-Wmaybe-uninitialized]
  565 |   double loglike1 = unknownDH * log( pA1*pB2 + pB1*pA2 );
      |                                                ~~~^~~~
blox.cpp:489:22: note: ‘pB2’ was declared here
  489 |   double pA1,pA2,pB1,pB2;
      |                      ^~~
riscv64-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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
riscv64-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;
      |       ^~~~~~~~~~
dosage.cpp:915:35: warning: ‘snp_code’ may be used uninitialized [-Wmaybe-uninitialized]
  915 |                       SNP[snp_code]->one[personPosition[f][i]] = s1;
      |                                   ^
dosage.cpp:725:15: note: ‘snp_code’ was declared here
  725 |           int snp_code;
      |               ^~~~~~~~
riscv64-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;
      |                ^~~~~~~
riscv64-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++)
      |                           ~^~~~~~~~~~~~~~~~~~~~~~~
riscv64-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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
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:176:17: warning: ‘rc’ may be used uninitialized [-Wmaybe-uninitialized]
  176 |       rc->assign("n", rN );
      |       ~~~~~~~~~~^~~~~~~~~~
r.cpp:68:16: note: ‘rc’ was declared here
   68 |   Rconnection *rc;
      |                ^~
r.cpp:376:14: warning: ‘rN’ may be used uninitialized [-Wmaybe-uninitialized]
  376 |       delete rN;
      |              ^~
r.cpp:162:14: note: ‘rN’ was declared here
  162 |   Rinteger * rN;
      |              ^~
r.cpp:377:14: warning: ‘rP’ may be used uninitialized [-Wmaybe-uninitialized]
  377 |       delete rP;
      |              ^~
r.cpp:163:13: note: ‘rP’ was declared here
  163 |   Rdouble * rP;
      |             ^~
r.cpp:378:14: warning: ‘rS’ may be used uninitialized [-Wmaybe-uninitialized]
  378 |       delete rS;
      |              ^~
r.cpp:164:14: note: ‘rS’ was declared here
  164 |   Rinteger * rS;
      |              ^~
r.cpp:380:16: warning: ‘rCov’ may be used uninitialized [-Wmaybe-uninitialized]
  380 |         delete rCov;
      |                ^~~~
r.cpp:165:13: note: ‘rCov’ was declared here
  165 |   Rdouble * rCov;
      |             ^~~~
riscv64-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
      |      ^~~~~~~
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;
      |                           ^~~~
riscv64-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
riscv64-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
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 from: /lib/ld-linux-riscv64-lp64d.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 to: /lib/ld-linux-riscv64-lp64d.so.1.usr-is-merged
   dh_installdeb -a
   dh_gencontrol -a
   dh_md5sums -a
   dh_builddeb -a
dpkg-deb: building package 'plink' in '../plink_1.07+dfsg-4_riscv64.deb'.
dpkg-deb: building package 'plink-dbgsym' in '../plink-dbgsym_1.07+dfsg-4_riscv64.deb'.
 dpkg-genbuildinfo --build=any -O../plink_1.07+dfsg-4_riscv64.buildinfo
 dpkg-genchanges --build=any -O../plink_1.07+dfsg-4_riscv64.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 2025-01-10T19:23:28Z

+------------------------------------------------------------------------------+
| Finished Timed Build Commands                                                |
+------------------------------------------------------------------------------+


rm -Rf /<<PKGBUILDDIR>>/
-------------------------------------------


I: Finished running 'rm -Rf /<<PKGBUILDDIR>>/'.

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

Finished
--------

I: Built successfully

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


plink_1.07+dfsg-4_riscv64.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: riscv64
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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Files:
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 3f027279370a44347969a4200e4c39a1 4974 science optional plink_1.07+dfsg-4_riscv64.buildinfo
 e037f82ce679e2cdd18096436746672d 1240140 science optional plink_1.07+dfsg-4_riscv64.deb

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

Format: 1.0
Source: plink
Binary: plink plink-dbgsym
Architecture: riscv64
Version: 1.07+dfsg-4
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 f1aedbe1454e917fd95b0f785e756cf28e235551f833c0216bd94d09d07e6023 1240140 plink_1.07+dfsg-4_riscv64.deb
Build-Origin: Debian
Build-Architecture: amd64
Build-Date: Fri, 10 Jan 2025 19:23:28 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
 autoconf (= 2.72-3),
 automake (= 1:1.16.5-1.3),
 autopoint (= 0.22.5-4),
 autotools-dev (= 20220109.1),
 base-files (= 13.6),
 base-passwd (= 3.6.6),
 bash (= 5.2.37-1),
 binutils (= 2.43.50.20250108-1),
 binutils-common (= 2.43.50.20250108-1),
 binutils-x86-64-linux-gnu (= 2.43.50.20250108-1),
 bsdextrautils (= 2.40.3-1),
 bsdutils (= 1:2.40.3-1),
 build-essential (= 12.12),
 bzip2 (= 1.0.8-6),
 coreutils (= 9.5-1+b1),
 cpp (= 4:14.2.0-1),
 cpp-14 (= 14.2.0-12),
 cpp-14-x86-64-linux-gnu (= 14.2.0-12),
 cpp-x86-64-linux-gnu (= 4:14.2.0-1),
 dash (= 0.5.12-11),
 debconf (= 1.5.89),
 debhelper (= 13.23),
 debianutils (= 5.21),
 dh-autoreconf (= 20),
 dh-strip-nondeterminism (= 1.14.0-1),
 diffutils (= 1:3.10-2),
 dpkg (= 1.22.13),
 dpkg-dev (= 1.22.13),
 dwz (= 0.15-1+b1),
 file (= 1:5.45-3+b1),
 findutils (= 4.10.0-3),
 g++ (= 4:14.2.0-1),
 g++-14 (= 14.2.0-12),
 g++-14-x86-64-linux-gnu (= 14.2.0-12),
 g++-x86-64-linux-gnu (= 4:14.2.0-1),
 gcc (= 4:14.2.0-1),
 gcc-14 (= 14.2.0-12),
 gcc-14-base (= 14.2.0-12),
 gcc-14-x86-64-linux-gnu (= 14.2.0-12),
 gcc-x86-64-linux-gnu (= 4:14.2.0-1),
 gettext (= 0.22.5-4),
 gettext-base (= 0.22.5-4),
 grep (= 3.11-4),
 groff-base (= 1.23.0-7),
 gzip (= 1.12-1.2),
 hostname (= 3.25),
 init-system-helpers (= 1.68),
 intltool-debian (= 0.35.0+20060710.6),
 libacl1 (= 2.3.2-2+b1),
 libarchive-zip-perl (= 1.68-1),
 libasan8 (= 14.2.0-12),
 libatomic1 (= 14.2.0-12),
 libattr1 (= 1:2.5.2-2),
 libaudit-common (= 1:4.0.2-2),
 libaudit1 (= 1:4.0.2-2),
 libbinutils (= 2.43.50.20250108-1),
 libblkid1 (= 2.40.3-1),
 libbz2-1.0 (= 1.0.8-6),
 libc-bin (= 2.40-5),
 libc-dev-bin (= 2.40-5),
 libc6 (= 2.40-5),
 libc6-dev (= 2.40-5),
 libcap-ng0 (= 0.8.5-4),
 libcap2 (= 1:2.66-5+b1),
 libcc1-0 (= 14.2.0-12),
 libcrypt-dev (= 1:4.4.36-5),
 libcrypt1 (= 1:4.4.36-5),
 libctf-nobfd0 (= 2.43.50.20250108-1),
 libctf0 (= 2.43.50.20250108-1),
 libdb5.3t64 (= 5.3.28+dfsg2-9),
 libdebconfclient0 (= 0.277),
 libdebhelper-perl (= 13.23),
 libdpkg-perl (= 1.22.13),
 libelf1t64 (= 0.192-4),
 libfile-stripnondeterminism-perl (= 1.14.0-1),
 libgcc-14-dev (= 14.2.0-12),
 libgcc-s1 (= 14.2.0-12),
 libgdbm-compat4t64 (= 1.24-2),
 libgdbm6t64 (= 1.24-2),
 libgmp10 (= 2:6.3.0+dfsg-3),
 libgomp1 (= 14.2.0-12),
 libgprofng0 (= 2.43.50.20250108-1),
 libhwasan0 (= 14.2.0-12),
 libicu72 (= 72.1-6),
 libisl23 (= 0.27-1),
 libitm1 (= 14.2.0-12),
 libjansson4 (= 2.14-2+b3),
 liblsan0 (= 14.2.0-12),
 liblzma5 (= 5.6.3-1+b1),
 libmagic-mgc (= 1:5.45-3+b1),
 libmagic1t64 (= 1:5.45-3+b1),
 libmd0 (= 1.1.0-2+b1),
 libmount1 (= 2.40.3-1),
 libmpc3 (= 1.3.1-1+b3),
 libmpfr6 (= 4.2.1-1+b2),
 libpam-modules (= 1.5.3-7+b1),
 libpam-modules-bin (= 1.5.3-7+b1),
 libpam-runtime (= 1.5.3-7),
 libpam0g (= 1.5.3-7+b1),
 libpcre2-8-0 (= 10.44-5),
 libperl5.40 (= 5.40.0-8),
 libpipeline1 (= 1.5.8-1),
 libquadmath0 (= 14.2.0-12),
 libseccomp2 (= 2.5.5-2),
 libselinux1 (= 3.7-3+b1),
 libsframe1 (= 2.43.50.20250108-1),
 libsmartcols1 (= 2.40.3-1),
 libssl3t64 (= 3.4.0-2),
 libstdc++-14-dev (= 14.2.0-12),
 libstdc++6 (= 14.2.0-12),
 libsystemd0 (= 257.2-1),
 libtinfo6 (= 6.5-2+b1),
 libtool (= 2.5.4-2),
 libtsan2 (= 14.2.0-12),
 libubsan1 (= 14.2.0-12),
 libuchardet0 (= 0.0.8-1+b2),
 libudev1 (= 257.2-1),
 libunistring5 (= 1.3-1),
 libuuid1 (= 2.40.3-1),
 libxml2 (= 2.12.7+dfsg+really2.9.14-0.2+b1),
 libzstd1 (= 1.5.6+dfsg-2),
 linux-libc-dev (= 6.12.8-1),
 m4 (= 1.4.19-5),
 make (= 4.4.1-1),
 man-db (= 2.13.0-1),
 mawk (= 1.3.4.20240905-1),
 ncurses-base (= 6.5-2),
 ncurses-bin (= 6.5-2+b1),
 openssl-provider-legacy (= 3.4.0-2),
 patch (= 2.7.6-7),
 perl (= 5.40.0-8),
 perl-base (= 5.40.0-8),
 perl-modules-5.40 (= 5.40.0-8),
 po-debconf (= 1.0.21+nmu1),
 rpcsvc-proto (= 1.4.3-1),
 sed (= 4.9-2),
 sensible-utils (= 0.0.24),
 sysvinit-utils (= 3.13-1),
 tar (= 1.35+dfsg-3.1),
 util-linux (= 2.40.3-1),
 xz-utils (= 5.6.3-1+b1),
 zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1),
 zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1)
Environment:
 DEB_BUILD_OPTIONS="nocheck parallel=1"
 DEB_BUILD_PROFILES="cross nocheck"
 LANG="C.UTF-8"
 LC_COLLATE="C.UTF-8"
 LC_CTYPE="C.UTF-8"
 SOURCE_DATE_EPOCH="1635694306"


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


plink-dbgsym_1.07+dfsg-4_riscv64.deb
------------------------------------

 new Debian package, version 2.0.
 size 18536988 bytes: control archive=540 bytes.
     374 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: riscv64
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 21029
 Depends: plink (= 1.07+dfsg-4)
 Section: debug
 Priority: optional
 Description: debug symbols for plink
 Build-Ids: 31b8ce05cd6a888965848bc01ce708ea5592ce65

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/31/
-rw-r--r-- root/root  21522504 2021-10-31 15:31 ./usr/lib/debug/.build-id/31/b8ce05cd6a888965848bc01ce708ea5592ce65.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_riscv64.deb
-----------------------------

 new Debian package, version 2.0.
 size 1240140 bytes: control archive=1304 bytes.
    1098 bytes,    26 lines      control
     915 bytes,    13 lines      md5sums
 Package: plink
 Version: 1.07+dfsg-4
 Architecture: riscv64
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 2759
 Depends: libc6 (>= 2.38), libcrypt1 (>= 1:4.1.0), libgcc-s1 (>= 3.4), libstdc++6 (>= 13.1), 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   2777240 2021-10-31 15:31 ./usr/lib/debian-med/bin/plink
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/debian-med/share/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/debian-med/share/man/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/debian-med/share/man/man1/
lrwxrwxrwx root/root         0 2021-10-31 15:31 ./usr/lib/debian-med/share/man/man1/plink.1.gz -> ../../../../../share/man/man1/p-link.1.gz
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/plink/
lrwxrwxrwx root/root         0 2021-10-31 15:31 ./usr/lib/plink/plink -> ../debian-med/bin/plink
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/doc/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/doc/plink/
-rw-r--r-- root/root       566 2021-10-31 15:11 ./usr/share/doc/plink/NEWS.Debian.gz
-rw-r--r-- root/root      1894 2021-10-31 15:11 ./usr/share/doc/plink/README.Debian
-rw-r--r-- root/root      1287 2007-07-27 14:51 ./usr/share/doc/plink/README.txt
-rw-r--r-- root/root       720 2021-10-31 15:31 ./usr/share/doc/plink/changelog.Debian.gz
-rw-r--r-- root/root      8639 2021-10-31 15:11 ./usr/share/doc/plink/changelog.gz
-rw-r--r-- root/root      2290 2021-10-31 15:11 ./usr/share/doc/plink/copyright
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/doc/plink/examples/
-rw-r--r-- root/root       358 2021-10-31 15:11 ./usr/share/doc/plink/examples/README
-rw-r--r-- root/root       267 2021-10-31 15:11 ./usr/share/doc/plink/examples/expected.plink.assoc
-rw-r--r-- root/root       126 2021-10-31 15:11 ./usr/share/doc/plink/examples/expected.plink.frq
-rw-r--r-- root/root        23 2007-07-27 14:51 ./usr/share/doc/plink/examples/test.map
-rw-r--r-- root/root       138 2007-07-27 14:51 ./usr/share/doc/plink/examples/test.ped
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/man/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/man/man1/
-rw-r--r-- root/root       688 2021-10-31 15:31 ./usr/share/man/man1/p-link.1.gz
lrwxrwxrwx root/root         0 2021-10-31 15:31 ./usr/share/man/man1/plink1.1.gz -> p-link.1.gz


lintian
-------


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

Merged Build-Depends: lintian:amd64
Filtered Build-Depends: lintian:amd64
dpkg-deb: warning: root directory /<<RESOLVERDIR>>/sbuild-build-depends-lintian-dummy has unusual owner or group 1000:119
dpkg-deb: Hint: you might need to pass --root-owner-group, see <https://wiki.debian.org/Teams/Dpkg/RootlessBuilds> for further details
dpkg-deb: warning: ignoring 1 warning about the control file(s)
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 [615 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [1314 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [1397 B]
Fetched 3326 B in 0s (0 B/s)
Reading package lists...
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
Execute external solver...
The following package was automatically installed and is no longer required:
  gpgv
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
  appstream ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl
  libappstream5 libapt-pkg-perl libassuan9 libb-hooks-endofscope-perl
  libb-hooks-op-check-perl libberkeleydb-perl libbrotli1 libcapture-tiny-perl
  libcgi-pm-perl libclass-data-inheritable-perl libclass-inspector-perl
  libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl
  libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl
  libcurl3t64-gnutls libdata-dpath-perl libdata-messagepack-perl
  libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl
  libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl
  libdevel-stacktrace-perl libdynaloader-functions-perl
  libemail-address-xs-perl libencode-locale-perl libexception-class-perl
  libfile-basedir-perl libfile-find-rule-perl libfile-listing-perl
  libfile-sharedir-perl libfont-ttf-perl libglib2.0-0t64 libgssapi-krb5-2
  libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl
  libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl
  libhttp-cookies-perl libhttp-date-perl libhttp-message-perl
  libhttp-negotiate-perl libimport-into-perl libio-html-perl
  libio-interactive-perl libio-socket-ssl-perl libio-string-perl
  libipc-run3-perl libipc-system-simple-perl libiterator-perl
  libiterator-util-perl libjson-maybexs-perl libk5crypto3 libkeyutils1
  libkrb5-3 libkrb5support0 libldap-2.5-0 liblist-compare-perl
  liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl
  liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl
  libmodule-implementation-perl libmodule-runtime-perl libmoo-perl
  libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libncursesw6
  libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl
  libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libnghttp2-14
  libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 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 libproc2-0 libpsl5t64 libreadline8t64
  libregexp-wildcards-perl librole-tiny-perl librtmp1 libsasl2-2
  libsasl2-modules-db libsereal-decoder-perl libsereal-encoder-perl
  libsort-versions-perl libsqlite3-0 libssh2-1t64 libstemmer0d
  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 libwww-mechanize-perl libwww-perl
  libwww-robotrules-perl libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxmlb2 libxs-parse-keyword-perl
  libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils
  perl-openssl-defaults plzip procps readline-common shared-mime-info t1utils
  ucf unzip
Suggested packages:
  apt-config-icons isoquery libxml-parser-perl low-memory-monitor krb5-doc
  krb5-user libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl
  libbareword-filehandles-perl libindirect-perl libmultidimensional-perl
  libbusiness-isbn-perl libmime-base32-perl libregexp-ipv6-perl
  libauthen-ntlm-perl binutils-multiarch libtext-template-perl readline-doc
  zip
Recommended packages:
  gnupg libcgi-fast-perl libglib2.0-data xdg-user-dirs libhtml-format-perl
  libio-compress-brotli-perl krb5-locales libldap-common
  liblist-someutils-xs-perl libfreezethaw-perl libgpm2 libmath-base85-perl
  libsocket6-perl libpackage-stash-xs-perl publicsuffix libsasl2-modules
  libxstring-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl
  libxml-sax-expat-perl psmisc linux-sysctl-defaults
The following NEW packages will be installed:
  appstream ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl
  libappstream5 libapt-pkg-perl libassuan9 libb-hooks-endofscope-perl
  libb-hooks-op-check-perl libberkeleydb-perl libbrotli1 libcapture-tiny-perl
  libcgi-pm-perl libclass-data-inheritable-perl libclass-inspector-perl
  libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl
  libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl
  libcurl3t64-gnutls libdata-dpath-perl libdata-messagepack-perl
  libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl
  libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl
  libdevel-stacktrace-perl libdynaloader-functions-perl
  libemail-address-xs-perl libencode-locale-perl libexception-class-perl
  libfile-basedir-perl libfile-find-rule-perl libfile-listing-perl
  libfile-sharedir-perl libfont-ttf-perl libglib2.0-0t64 libgssapi-krb5-2
  libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl
  libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl
  libhttp-cookies-perl libhttp-date-perl libhttp-message-perl
  libhttp-negotiate-perl libimport-into-perl libio-html-perl
  libio-interactive-perl libio-socket-ssl-perl libio-string-perl
  libipc-run3-perl libipc-system-simple-perl libiterator-perl
  libiterator-util-perl libjson-maybexs-perl libk5crypto3 libkeyutils1
  libkrb5-3 libkrb5support0 libldap-2.5-0 liblist-compare-perl
  liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl
  liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl
  libmodule-implementation-perl libmodule-runtime-perl libmoo-perl
  libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libncursesw6
  libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl
  libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libnghttp2-14
  libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 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 libproc2-0 libpsl5t64 libreadline8t64
  libregexp-wildcards-perl librole-tiny-perl librtmp1 libsasl2-2
  libsasl2-modules-db libsereal-decoder-perl libsereal-encoder-perl
  libsort-versions-perl libsqlite3-0 libssh2-1t64 libstemmer0d
  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 libwww-mechanize-perl libwww-perl
  libwww-robotrules-perl libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxmlb2 libxs-parse-keyword-perl
  libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils
  perl-openssl-defaults plzip procps readline-common
  sbuild-build-depends-lintian-dummy:riscv64 shared-mime-info t1utils ucf
  unzip
0 upgraded, 163 newly installed, 0 to remove and 0 not upgraded.
Need to get 20.0 MB of archives.
After this operation, 79.0 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 B]
Get:2 http://localhost:3142/debian unstable/main amd64 netbase all 6.4 [12.8 kB]
Get:3 http://localhost:3142/debian unstable/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB]
Get:4 http://localhost:3142/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB]
Get:5 http://localhost:3142/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB]
Get:6 http://localhost:3142/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB]
Get:7 http://localhost:3142/debian unstable/main amd64 openssl amd64 3.4.0-2 [1422 kB]
Get:8 http://localhost:3142/debian unstable/main amd64 ca-certificates all 20241223 [164 kB]
Get:9 http://localhost:3142/debian unstable/main amd64 ucf all 3.0046 [41.1 kB]
Get:10 http://localhost:3142/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.4-1 [1501 kB]
Get:11 http://localhost:3142/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b1 [759 kB]
Get:12 http://localhost:3142/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB]
Get:13 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB]
Get:14 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB]
Get:15 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get:16 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB]
Get:17 http://localhost:3142/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB]
Get:18 http://localhost:3142/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB]
Get:19 http://localhost:3142/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB]
Get:20 http://localhost:3142/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.19+dfsg-1 [187 kB]
Get:21 http://localhost:3142/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get:22 http://localhost:3142/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB]
Get:23 http://localhost:3142/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB]
Get:24 http://localhost:3142/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB]
Get:25 http://localhost:3142/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get:26 http://localhost:3142/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get:27 http://localhost:3142/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get:28 http://localhost:3142/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.1-1 [360 kB]
Get:29 http://localhost:3142/debian unstable/main amd64 libstemmer0d amd64 2.2.0-4+b2 [119 kB]
Get:30 http://localhost:3142/debian unstable/main amd64 libxmlb2 amd64 0.3.21-1 [63.0 kB]
Get:31 http://localhost:3142/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB]
Get:32 http://localhost:3142/debian unstable/main amd64 libappstream5 amd64 1.0.4-1 [225 kB]
Get:33 http://localhost:3142/debian unstable/main amd64 appstream amd64 1.0.4-1 [523 kB]
Get:34 http://localhost:3142/debian unstable/main amd64 diffstat amd64 1.67-1 [35.5 kB]
Get:35 http://localhost:3142/debian unstable/main amd64 libassuan9 amd64 3.0.1-2 [60.6 kB]
Get:36 http://localhost:3142/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get:37 http://localhost:3142/debian unstable/main amd64 gpgconf amd64 2.2.46~pre1-1 [121 kB]
Get:38 http://localhost:3142/debian unstable/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB]
Get:39 http://localhost:3142/debian unstable/main amd64 gpg amd64 2.2.46~pre1-1 [531 kB]
Get:40 http://localhost:3142/debian unstable/main amd64 iso-codes all 4.17.0-1 [3055 kB]
Get:41 http://localhost:3142/debian unstable/main amd64 libaliased-perl all 0.34-3 [13.5 kB]
Get:42 http://localhost:3142/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.40+b6 [67.8 kB]
Get:43 http://localhost:3142/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB]
Get:44 http://localhost:3142/debian unstable/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB]
Get:45 http://localhost:3142/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.2 kB]
Get:46 http://localhost:3142/debian unstable/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB]
Get:47 http://localhost:3142/debian unstable/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get:48 http://localhost:3142/debian unstable/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB]
Get:49 http://localhost:3142/debian unstable/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB]
Get:50 http://localhost:3142/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B]
Get:51 http://localhost:3142/debian unstable/main amd64 libvariable-magic-perl amd64 0.64-1+b1 [44.9 kB]
Get:52 http://localhost:3142/debian unstable/main amd64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB]
Get:53 http://localhost:3142/debian unstable/main amd64 libberkeleydb-perl amd64 0.66-1 [121 kB]
Get:54 http://localhost:3142/debian unstable/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB]
Get:55 http://localhost:3142/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB]
Get:56 http://localhost:3142/debian unstable/main amd64 liburi-perl all 5.30-1 [105 kB]
Get:57 http://localhost:3142/debian unstable/main amd64 libhtml-parser-perl amd64 3.83-1+b2 [99.7 kB]
Get:58 http://localhost:3142/debian unstable/main amd64 libcgi-pm-perl all 4.66-1 [217 kB]
Get:59 http://localhost:3142/debian unstable/main amd64 libclass-data-inheritable-perl all 0.10-1 [8632 B]
Get:60 http://localhost:3142/debian unstable/main amd64 libclass-inspector-perl all 1.36-3 [17.5 kB]
Get:61 http://localhost:3142/debian unstable/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB]
Get:62 http://localhost:3142/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b4 [36.1 kB]
Get:63 http://localhost:3142/debian unstable/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB]
Get:64 http://localhost:3142/debian unstable/main amd64 libconfig-tiny-perl all 2.30-1 [18.9 kB]
Get:65 http://localhost:3142/debian unstable/main amd64 libparams-util-perl amd64 1.102-3+b1 [24.4 kB]
Get:66 http://localhost:3142/debian unstable/main amd64 libsub-install-perl all 0.929-1 [10.5 kB]
Get:67 http://localhost:3142/debian unstable/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB]
Get:68 http://localhost:3142/debian unstable/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB]
Get:69 http://localhost:3142/debian unstable/main amd64 libconst-fast-perl all 0.014-2 [8792 B]
Get:70 http://localhost:3142/debian unstable/main amd64 libcpanel-json-xs-perl amd64 4.38-1+b1 [129 kB]
Get:71 http://localhost:3142/debian unstable/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB]
Get:72 http://localhost:3142/debian unstable/main amd64 libexception-class-perl all 1.45-1 [34.6 kB]
Get:73 http://localhost:3142/debian unstable/main amd64 libiterator-perl all 0.03+ds1-2 [18.8 kB]
Get:74 http://localhost:3142/debian unstable/main amd64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB]
Get:75 http://localhost:3142/debian unstable/main amd64 libdata-dpath-perl all 0.60-1 [41.8 kB]
Get:76 http://localhost:3142/debian unstable/main amd64 libdata-messagepack-perl amd64 1.02-1+b4 [32.8 kB]
Get:77 http://localhost:3142/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-4 [31.5 kB]
Get:78 http://localhost:3142/debian unstable/main amd64 libdata-validate-domain-perl all 0.15-1 [11.9 kB]
Get:79 http://localhost:3142/debian unstable/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB]
Get:80 http://localhost:3142/debian unstable/main amd64 libnet-netmask-perl all 2.0002-2 [28.6 kB]
Get:81 http://localhost:3142/debian unstable/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2+b4 [98.1 kB]
Get:82 http://localhost:3142/debian unstable/main amd64 libdata-validate-ip-perl all 0.31-1 [20.6 kB]
Get:83 http://localhost:3142/debian unstable/main amd64 libdata-validate-uri-perl all 0.07-3 [11.0 kB]
Get:84 http://localhost:3142/debian unstable/main amd64 libdevel-size-perl amd64 0.84-1+b1 [24.2 kB]
Get:85 http://localhost:3142/debian unstable/main amd64 libemail-address-xs-perl amd64 1.05-1+b4 [29.4 kB]
Get:86 http://localhost:3142/debian unstable/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB]
Get:87 http://localhost:3142/debian unstable/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB]
Get:88 http://localhost:3142/debian unstable/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB]
Get:89 http://localhost:3142/debian unstable/main amd64 libnumber-compare-perl all 0.03-3 [6332 B]
Get:90 http://localhost:3142/debian unstable/main amd64 libtext-glob-perl all 0.11-3 [7676 B]
Get:91 http://localhost:3142/debian unstable/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB]
Get:92 http://localhost:3142/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB]
Get:93 http://localhost:3142/debian unstable/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB]
Get:94 http://localhost:3142/debian unstable/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB]
Get:95 http://localhost:3142/debian unstable/main amd64 libfile-sharedir-perl all 1.118-3 [16.0 kB]
Get:96 http://localhost:3142/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB]
Get:97 http://localhost:3142/debian unstable/main amd64 libfont-ttf-perl all 1.06-2 [318 kB]
Get:98 http://localhost:3142/debian unstable/main amd64 libio-html-perl all 1.004-3 [16.2 kB]
Get:99 http://localhost:3142/debian unstable/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get:100 http://localhost:3142/debian unstable/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB]
Get:101 http://localhost:3142/debian unstable/main amd64 libhtml-form-perl all 6.12-1 [32.3 kB]
Get:102 http://localhost:3142/debian unstable/main amd64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB]
Get:103 http://localhost:3142/debian unstable/main amd64 libhtml-tree-perl all 5.07-3 [211 kB]
Get:104 http://localhost:3142/debian unstable/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB]
Get:105 http://localhost:3142/debian unstable/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB]
Get:106 http://localhost:3142/debian unstable/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B]
Get:107 http://localhost:3142/debian unstable/main amd64 libnet-ssleay-perl amd64 1.94-2 [339 kB]
Get:108 http://localhost:3142/debian unstable/main amd64 libio-socket-ssl-perl all 2.089-1 [223 kB]
Get:109 http://localhost:3142/debian unstable/main amd64 libnet-http-perl all 6.23-1 [23.9 kB]
Get:110 http://localhost:3142/debian unstable/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB]
Get:111 http://localhost:3142/debian unstable/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB]
Get:112 http://localhost:3142/debian unstable/main amd64 libwww-perl all 6.77-1 [183 kB]
Get:113 http://localhost:3142/debian unstable/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB]
Get:114 http://localhost:3142/debian unstable/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB]
Get:115 http://localhost:3142/debian unstable/main amd64 libio-interactive-perl all 1.025-1 [11.4 kB]
Get:116 http://localhost:3142/debian unstable/main amd64 libipc-run3-perl all 0.049-1 [31.5 kB]
Get:117 http://localhost:3142/debian unstable/main amd64 libjson-maybexs-perl all 1.004008-1 [12.9 kB]
Get:118 http://localhost:3142/debian unstable/main amd64 liblist-compare-perl all 0.55-2 [65.7 kB]
Get:119 http://localhost:3142/debian unstable/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB]
Get:120 http://localhost:3142/debian unstable/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB]
Get:121 http://localhost:3142/debian unstable/main amd64 liblz1 amd64 1.15~rc1-1 [38.8 kB]
Get:122 http://localhost:3142/debian unstable/main amd64 liblzo2-2 amd64 2.10-3+b1 [55.1 kB]
Get:123 http://localhost:3142/debian unstable/main amd64 libmarkdown2 amd64 2.2.7-2.1 [36.0 kB]
Get:124 http://localhost:3142/debian unstable/main amd64 libmldbm-perl all 2.05-4 [16.8 kB]
Get:125 http://localhost:3142/debian unstable/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB]
Get:126 http://localhost:3142/debian unstable/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB]
Get:127 http://localhost:3142/debian unstable/main amd64 libmoo-perl all 2.005005-1 [58.0 kB]
Get:128 http://localhost:3142/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB]
Get:129 http://localhost:3142/debian unstable/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B]
Get:130 http://localhost:3142/debian unstable/main amd64 libmouse-perl amd64 2.5.11-1+b1 [144 kB]
Get:131 http://localhost:3142/debian unstable/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB]
Get:132 http://localhost:3142/debian unstable/main amd64 libsub-identify-perl amd64 0.14-3+b3 [11.3 kB]
Get:133 http://localhost:3142/debian unstable/main amd64 libsub-name-perl amd64 0.28-1 [12.2 kB]
Get:134 http://localhost:3142/debian unstable/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB]
Get:135 http://localhost:3142/debian unstable/main amd64 libpath-tiny-perl all 0.146-1 [56.2 kB]
Get:136 http://localhost:3142/debian unstable/main amd64 libperlio-gzip-perl amd64 0.20-1+b4 [17.5 kB]
Get:137 http://localhost:3142/debian unstable/main amd64 libperlio-utf8-strict-perl amd64 0.010-1+b3 [11.4 kB]
Get:138 http://localhost:3142/debian unstable/main amd64 libproc-processtable-perl amd64 0.636-1+b3 [42.3 kB]
Get:139 http://localhost:3142/debian unstable/main amd64 libregexp-wildcards-perl all 1.05-3 [14.1 kB]
Get:140 http://localhost:3142/debian unstable/main amd64 libsereal-decoder-perl amd64 5.004+ds-1+b3 [100 kB]
Get:141 http://localhost:3142/debian unstable/main amd64 libsereal-encoder-perl amd64 5.004+ds-1+b3 [104 kB]
Get:142 http://localhost:3142/debian unstable/main amd64 libsort-versions-perl all 1.62-3 [8928 B]
Get:143 http://localhost:3142/debian unstable/main amd64 libxs-parse-keyword-perl amd64 0.47-1 [64.7 kB]
Get:144 http://localhost:3142/debian unstable/main amd64 libsyntax-keyword-try-perl amd64 0.30-1+b1 [27.4 kB]
Get:145 http://localhost:3142/debian unstable/main amd64 libterm-readkey-perl amd64 2.38-2+b4 [24.6 kB]
Get:146 http://localhost:3142/debian unstable/main amd64 libtext-levenshteinxs-perl amd64 0.03-5+b4 [8720 B]
Get:147 http://localhost:3142/debian unstable/main amd64 libtext-markdown-discount-perl amd64 0.16-1+b3 [13.0 kB]
Get:148 http://localhost:3142/debian unstable/main amd64 libtext-xslate-perl amd64 3.5.9-2+b1 [174 kB]
Get:149 http://localhost:3142/debian unstable/main amd64 libtime-duration-perl all 1.21-2 [13.1 kB]
Get:150 http://localhost:3142/debian unstable/main amd64 libtime-moment-perl amd64 0.44-2+b4 [73.2 kB]
Get:151 http://localhost:3142/debian unstable/main amd64 libunicode-utf8-perl amd64 0.62-2+b3 [20.4 kB]
Get:152 http://localhost:3142/debian unstable/main amd64 libwww-mechanize-perl all 2.19-1 [114 kB]
Get:153 http://localhost:3142/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB]
Get:154 http://localhost:3142/debian unstable/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB]
Get:155 http://localhost:3142/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-4 [53.4 kB]
Get:156 http://localhost:3142/debian unstable/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-5+b1 [314 kB]
Get:157 http://localhost:3142/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.902.0+ds-2+b1 [35.5 kB]
Get:158 http://localhost:3142/debian unstable/main amd64 plzip amd64 1.12~rc1-1 [65.1 kB]
Get:159 http://localhost:3142/debian unstable/main amd64 lzop amd64 1.04-2 [84.2 kB]
Get:160 http://localhost:3142/debian unstable/main amd64 patchutils amd64 0.4.2-1 [77.5 kB]
Get:161 http://localhost:3142/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB]
Get:162 http://localhost:3142/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB]
Get:163 http://localhost:3142/debian unstable/main amd64 lintian all 2.121.1 [1058 kB]
Preconfiguring packages ...
Fetched 20.0 MB in 0s (81.2 MB/s)
Selecting previously unselected package netbase.
(Reading database ... 18909 files and directories currently installed.)
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Unpacking netbase (6.4) ...
Selecting previously unselected package libncursesw6:amd64.
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Selecting previously unselected package libproc2-0:amd64.
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Unpacking procps (2:4.0.4-6) ...
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Unpacking readline-common (8.2-6) ...
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Unpacking openssl (3.4.0-2) ...
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Unpacking ca-certificates (20241223) ...
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Moving old data out of the way
Unpacking ucf (3.0046) ...
Selecting previously unselected package libglib2.0-0t64:amd64.
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Unpacking libglib2.0-0t64:amd64 (2.82.4-1) ...
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Unpacking shared-mime-info (2.4-5+b1) ...
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Unpacking libbrotli1:amd64 (1.1.0-2+b6) ...
Selecting previously unselected package libkrb5support0:amd64.
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Unpacking libkrb5support0:amd64 (1.21.3-3) ...
Selecting previously unselected package libk5crypto3:amd64.
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Unpacking libk5crypto3:amd64 (1.21.3-3) ...
Selecting previously unselected package libkeyutils1:amd64.
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Unpacking libkeyutils1:amd64 (1.6.3-4) ...
Selecting previously unselected package libkrb5-3:amd64.
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Unpacking libkrb5-3:amd64 (1.21.3-3) ...
Selecting previously unselected package libgssapi-krb5-2:amd64.
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Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ...
Selecting previously unselected package libsasl2-modules-db:amd64.
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Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ...
Selecting previously unselected package libsasl2-2:amd64.
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Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-8) ...
Selecting previously unselected package libldap-2.5-0:amd64.
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Unpacking libldap-2.5-0:amd64 (2.5.19+dfsg-1) ...
Selecting previously unselected package libnghttp2-14:amd64.
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Unpacking libnghttp2-14:amd64 (1.64.0-1) ...
Selecting previously unselected package libnghttp3-9:amd64.
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Unpacking libnghttp3-9:amd64 (1.6.0-2) ...
Selecting previously unselected package libngtcp2-16:amd64.
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Unpacking libngtcp2-16:amd64 (1.9.1-1) ...
Selecting previously unselected package libngtcp2-crypto-gnutls8:amd64.
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Unpacking libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ...
Selecting previously unselected package libpsl5t64:amd64.
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Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ...
Selecting previously unselected package librtmp1:amd64.
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Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ...
Selecting previously unselected package libssh2-1t64:amd64.
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Unpacking libssh2-1t64:amd64 (1.11.1-1) ...
Selecting previously unselected package libcurl3t64-gnutls:amd64.
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Unpacking libcurl3t64-gnutls:amd64 (8.11.1-1) ...
Selecting previously unselected package libstemmer0d:amd64.
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Unpacking libstemmer0d:amd64 (2.2.0-4+b2) ...
Selecting previously unselected package libxmlb2:amd64.
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Unpacking libxmlb2:amd64 (0.3.21-1) ...
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Selecting previously unselected package libappstream5:amd64.
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Unpacking appstream (1.0.4-1) ...
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Unpacking diffstat (1.67-1) ...
Selecting previously unselected package libassuan9:amd64.
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Unpacking libassuan9:amd64 (3.0.1-2) ...
Selecting previously unselected package libreadline8t64:amd64.
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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
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Selecting previously unselected package gpgconf.
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Selecting previously unselected package libb-hooks-op-check-perl:amd64.
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Selecting previously unselected package libdevel-callchecker-perl:amd64.
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Selecting previously unselected package libparams-classify-perl:amd64.
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Selecting previously unselected package libclass-inspector-perl.
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Selecting previously unselected package libclass-xsaccessor-perl.
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Selecting previously unselected package libsub-install-perl.
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Selecting previously unselected package libcpanel-json-xs-perl:amd64.
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Unpacking libcpanel-json-xs-perl:amd64 (4.38-1+b1) ...
Selecting previously unselected package libdevel-stacktrace-perl.
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update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode
update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode
update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode
Setting up libkeyutils1:amd64 (1.6.3-4) ...
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Setting up libcpanel-json-xs-perl:amd64 (4.38-1+b1) ...
Setting up libhtml-tagset-perl (3.24-1) ...
Setting up libdevel-size-perl (0.84-1+b1) ...
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Setting up libsqlite3-0:amd64 (3.46.1-1) ...
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No schema files found: doing nothing.
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Setting up libncursesw6:amd64 (6.5-2+b1) ...
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Setting up netbase (6.4) ...
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Setting up libfont-ttf-perl (1.06-2) ...
Setting up openssl (3.4.0-2) ...
Setting up libtext-levenshteinxs-perl (0.03-5+b4) ...
Setting up libperlio-gzip-perl (0.20-1+b4) ...
Setting up readline-common (8.2-6) ...
Setting up libhtml-html5-entities-perl (0.004-3) ...
Setting up libsereal-decoder-perl (5.004+ds-1+b3) ...
Setting up libmarkdown2:amd64 (2.2.7-2.1) ...
Setting up liburi-perl (5.30-1) ...
Setting up iso-codes (4.17.0-1) ...
Setting up libnet-ipv6addr-perl (1.02-1) ...
Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ...
Setting up libdata-validate-ip-perl (0.31-1) ...
Setting up libemail-address-xs-perl (1.05-1+b4) ...
Setting up libnet-ssleay-perl:amd64 (1.94-2) ...
Setting up libhttp-date-perl (6.06-1) ...
Setting up libfile-basedir-perl (0.09-2) ...
Setting up libfile-listing-perl (6.16-1) ...
Setting up libxmlb2:amd64 (0.3.21-1) ...
Setting up libnet-http-perl (6.23-1) ...
Setting up libtext-markdown-discount-perl (0.16-1+b3) ...
Setting up libexception-class-perl (1.45-1) ...
Setting up libdevel-callchecker-perl:amd64 (0.009-1+b1) ...
Setting up libldap-2.5-0:amd64 (2.5.19+dfsg-1) ...
Setting up ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
152 added, 0 removed; done.
Setting up libdata-validate-uri-perl (0.07-3) ...
Setting up libxs-parse-keyword-perl (0.47-1) ...
Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ...
Setting up libdata-optlist-perl (0.114-1) ...
Setting up ucf (3.0046) ...
Setting up libreadline8t64:amd64 (8.2-6) ...
Setting up libwww-robotrules-perl (6.02-1) ...
Setting up libsyntax-keyword-try-perl (0.30-1+b1) ...
Setting up libhtml-parser-perl:amd64 (3.83-1+b2) ...
Setting up gpgconf (2.2.46~pre1-1) ...
Setting up libio-socket-ssl-perl (2.089-1) ...
Setting up gpg (2.2.46~pre1-1) ...
Setting up libsub-exporter-perl (0.990-1) ...
Setting up libhttp-message-perl (7.00-2) ...
Setting up libhtml-form-perl (6.12-1) ...
Setting up libiterator-perl (0.03+ds1-2) ...
Setting up libhttp-negotiate-perl (6.01-2) ...
Setting up libiterator-util-perl (0.02+ds1-2) ...
Setting up libhttp-cookies-perl (6.11-1) ...
Setting up libhtml-tree-perl (5.07-3) ...
Setting up libparams-classify-perl:amd64 (0.015-2+b4) ...
Setting up libcgi-pm-perl (4.66-1) ...
Setting up libcurl3t64-gnutls:amd64 (8.11.1-1) ...
Setting up libappstream5:amd64 (1.0.4-1) ...
Setting up libxml-sax-perl (1.02+dfsg-4) ...
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 appstream (1.0.4-1) ...
✔ Metadata cache was updated successfully.
Setting up libmodule-runtime-perl (0.016-2) ...
Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-5+b1) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up libconst-fast-perl (0.014-2) ...
Setting up libdata-dpath-perl (0.60-1) ...
Setting up libmodule-implementation-perl (0.09-2) ...
Setting up libpackage-stash-perl (0.40-1) ...
Setting up libimport-into-perl (1.002005-2) ...
Setting up libmoo-perl (2.005005-1) ...
Setting up liblist-someutils-perl (0.59-1) ...
Setting up libmoox-aliases-perl (0.001006-2) ...
Setting up libb-hooks-endofscope-perl (0.28-1) ...
Setting up libnamespace-clean-perl (0.27-2) ...
Setting up liblwp-protocol-https-perl (6.14-1) ...
Setting up libwww-perl (6.77-1) ...
Setting up libhtml-tokeparser-simple-perl (3.16-4) ...
Setting up libwww-mechanize-perl (2.19-1) ...
Setting up lintian (2.121.1) ...
Setting up sbuild-build-depends-lintian-dummy:riscv64 (0.invalid.0) ...
Processing triggers for libc-bin (2.40-5) ...
Processing triggers for man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Processing triggers for ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Running lintian...

I: Lintian run was successful.

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


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

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

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

Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any
Build-Space: n/a
Build-Time: 489
Distribution: unstable
Foreign Architectures: riscv64
Host Architecture: riscv64
Install-Time: 10
Job: plink_1.07+dfsg-4
Lintian: pass
Machine Architecture: amd64
Package: plink
Package-Time: 520
Source-Version: 1.07+dfsg-4
Space: n/a
Status: successful
Version: 1.07+dfsg-4
--------------------------------------------------------------------------------
Finished at 2025-01-10T19:23:28Z
Build needed 00:08:40, no disk space