sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley
+==============================================================================+
| plink 1.07+dfsg-4 (arm64) Thu, 13 Mar 2025 21:53:24 +0000 |
+==============================================================================+
Package: plink
Version: 1.07+dfsg-4
Source Version: 1.07+dfsg-4
Distribution: unstable
Machine Architecture: amd64
Host Architecture: arm64
Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-855ff5c1-1aff-49df-86b5-12415053292b' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/plink-7Mur1x/resolver-NYhbLY' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://localhost:3142/debian unstable InRelease [205 kB]
Get:2 http://localhost:3142/debian unstable/non-free Sources.diff/Index [63.3 kB]
Get:3 http://localhost:3142/debian unstable/contrib Sources.diff/Index [63.3 kB]
Get:4 http://localhost:3142/debian unstable/main Sources.diff/Index [63.6 kB]
Get:5 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [63.6 kB]
Get:6 http://localhost:3142/debian unstable/non-free Sources T-2025-03-13-2013.38-F-2025-03-13-1405.02.pdiff [1982 B]
Get:7 http://localhost:3142/debian unstable/contrib Sources T-2025-03-13-2013.38-F-2025-03-13-1405.02.pdiff [599 B]
Get:8 http://localhost:3142/debian unstable/main Sources T-2025-03-13-2013.38-F-2025-03-13-0204.09.pdiff [65.9 kB]
Get:6 http://localhost:3142/debian unstable/non-free Sources T-2025-03-13-2013.38-F-2025-03-13-1405.02.pdiff [1982 B]
Get:8 http://localhost:3142/debian unstable/main Sources T-2025-03-13-2013.38-F-2025-03-13-0204.09.pdiff [65.9 kB]
Get:7 http://localhost:3142/debian unstable/contrib Sources T-2025-03-13-2013.38-F-2025-03-13-1405.02.pdiff [599 B]
Get:9 http://localhost:3142/debian unstable/main amd64 Packages T-2025-03-13-2013.38-F-2025-03-13-0204.09.pdiff [85.7 kB]
Get:9 http://localhost:3142/debian unstable/main amd64 Packages T-2025-03-13-2013.38-F-2025-03-13-0204.09.pdiff [85.7 kB]
Get:10 http://localhost:3142/debian unstable/main arm64 Packages [10.0 MB]
Fetched 10.6 MB in 3s (4036 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
libcap2 libsystemd0 libudev1
3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 628 kB of archives.
After this operation, 1024 B of additional disk space will be used.
Get:1 http://localhost:3142/debian unstable/main amd64 libcap2 amd64 1:2.75-2 [27.7 kB]
Get:2 http://localhost:3142/debian unstable/main amd64 libsystemd0 amd64 257.4-3 [451 kB]
Get:3 http://localhost:3142/debian unstable/main amd64 libudev1 amd64 257.4-3 [149 kB]
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Preparing to unpack .../libcap2_1%3a2.75-2_amd64.deb ...
Unpacking libcap2:amd64 (1:2.75-2) over (1:2.75-1) ...
Setting up libcap2:amd64 (1:2.75-2) ...
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Preparing to unpack .../libsystemd0_257.4-3_amd64.deb ...
Unpacking libsystemd0:amd64 (257.4-3) over (257.4-1) ...
Setting up libsystemd0:amd64 (257.4-3) ...
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Preparing to unpack .../libudev1_257.4-3_amd64.deb ...
Unpacking libudev1:amd64 (257.4-3) over (257.4-1) ...
Setting up libudev1:amd64 (257.4-3) ...
Processing triggers for libc-bin (2.41-4) ...
+------------------------------------------------------------------------------+
| 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 (593 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/plink-7Mur1x/plink-1.07+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/plink-7Mur1x' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64
Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64
dpkg-deb: 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 [726 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [769 B]
Fetched 2104 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 additional packages will be installed:
autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu
bsdextrautils cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu
crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism
dwz fakeroot file g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu
gcc-14-aarch64-linux-gnu gcc-14-aarch64-linux-gnu-base gcc-14-base:arm64
gcc-14-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libasan8:arm64 libasan8-arm64-cross
libatomic1:arm64 libatomic1-arm64-cross libc6:arm64 libc6-arm64-cross
libc6-dev:arm64 libc6-dev-arm64-cross libcrypt-dev:arm64 libcrypt1:arm64
libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl
libgcc-14-dev:arm64 libgcc-14-dev-arm64-cross libgcc-s1:arm64
libgcc-s1-arm64-cross libgomp1:arm64 libgomp1-arm64-cross libhwasan0:arm64
libhwasan0-arm64-cross libicu72 libitm1:arm64 libitm1-arm64-cross
liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1t64 libpipeline1
libstdc++-14-dev:arm64 libstdc++-14-dev-arm64-cross libstdc++6:arm64
libstdc++6-arm64-cross libtool libtsan2:arm64 libtsan2-arm64-cross
libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libunistring5 libxml2
linux-libc-dev-arm64-cross m4 man-db po-debconf sensible-utils zlib1g:arm64
zlib1g-dev:arm64
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-aarch64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev
groff glibc-doc:arm64 libc-l10n:arm64 locales:arm64 libnss-nis:arm64
libnss-nisplus:arm64 manpages-dev:arm64 libstdc++-14-doc:arm64 libtool-doc
gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx libidn2-0:arm64 libarchive-cpio-perl libltdl-dev
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu
bsdextrautils cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu
crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism
dwz fakeroot file g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu
gcc-14-aarch64-linux-gnu gcc-14-aarch64-linux-gnu-base gcc-14-base:arm64
gcc-14-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libasan8:arm64 libasan8-arm64-cross
libatomic1:arm64 libatomic1-arm64-cross libc6:arm64 libc6-arm64-cross
libc6-dev:arm64 libc6-dev-arm64-cross libcrypt-dev:arm64 libcrypt1:arm64
libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl
libgcc-14-dev:arm64 libgcc-14-dev-arm64-cross libgcc-s1:arm64
libgcc-s1-arm64-cross libgomp1:arm64 libgomp1-arm64-cross libhwasan0:arm64
libhwasan0-arm64-cross libicu72 libitm1:arm64 libitm1-arm64-cross
liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1t64 libpipeline1
libstdc++-14-dev:arm64 libstdc++-14-dev-arm64-cross libstdc++6:arm64
libstdc++6-arm64-cross libtool libtsan2:arm64 libtsan2-arm64-cross
libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libunistring5 libxml2
linux-libc-dev-arm64-cross m4 man-db po-debconf
sbuild-build-depends-main-dummy:arm64 sensible-utils zlib1g:arm64
zlib1g-dev:arm64
0 upgraded, 77 newly installed, 0 to remove and 0 not upgraded.
Need to get 99.3 MB of archives.
After this operation, 436 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 0.23.1-1 [243 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 2.40.4-5 [92.4 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 1.4.19-7 [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 1:1.17-3 [862 kB]
Get:16 http://localhost:3142/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get:17 http://localhost:3142/debian unstable/main amd64 binutils-aarch64-linux-gnu amd64 2.44-3 [1687 kB]
Get:18 http://localhost:3142/debian unstable/main amd64 gcc-14-aarch64-linux-gnu-base amd64 14.2.0-12cross1 [48.5 kB]
Get:19 http://localhost:3142/debian unstable/main amd64 cpp-14-aarch64-linux-gnu amd64 14.2.0-12cross1 [11.2 MB]
Get:20 http://localhost:3142/debian unstable/main amd64 cpp-aarch64-linux-gnu amd64 4:14.2.0-1 [4844 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-arm64-cross all 2.41-4cross1 [1162 kB]
Get:23 http://localhost:3142/debian unstable/main amd64 libgcc-s1-arm64-cross all 14.2.0-12cross1 [54.1 kB]
Get:24 http://localhost:3142/debian unstable/main amd64 libgomp1-arm64-cross all 14.2.0-12cross1 [91.7 kB]
Get:25 http://localhost:3142/debian unstable/main amd64 libitm1-arm64-cross all 14.2.0-12cross1 [25.9 kB]
Get:26 http://localhost:3142/debian unstable/main amd64 libatomic1-arm64-cross all 14.2.0-12cross1 [10.3 kB]
Get:27 http://localhost:3142/debian unstable/main amd64 libasan8-arm64-cross all 14.2.0-12cross1 [435 kB]
Get:28 http://localhost:3142/debian unstable/main amd64 liblsan0-arm64-cross all 14.2.0-12cross1 [202 kB]
Get:29 http://localhost:3142/debian unstable/main amd64 libtsan2-arm64-cross all 14.2.0-12cross1 [415 kB]
Get:30 http://localhost:3142/debian unstable/main amd64 libstdc++6-arm64-cross all 14.2.0-12cross1 [546 kB]
Get:31 http://localhost:3142/debian unstable/main amd64 libubsan1-arm64-cross all 14.2.0-12cross1 [186 kB]
Get:32 http://localhost:3142/debian unstable/main amd64 libhwasan0-arm64-cross all 14.2.0-12cross1 [256 kB]
Get:33 http://localhost:3142/debian unstable/main amd64 libgcc-14-dev-arm64-cross all 14.2.0-12cross1 [2463 kB]
Get:34 http://localhost:3142/debian unstable/main amd64 gcc-14-aarch64-linux-gnu amd64 14.2.0-12cross1 [21.6 MB]
Get:35 http://localhost:3142/debian unstable/main amd64 gcc-aarch64-linux-gnu amd64 4:14.2.0-1 [1448 B]
Get:36 http://localhost:3142/debian unstable/main amd64 linux-libc-dev-arm64-cross all 6.12.17-1cross1 [2345 kB]
Get:37 http://localhost:3142/debian unstable/main amd64 libc6-dev-arm64-cross all 2.41-4cross1 [1615 kB]
Get:38 http://localhost:3142/debian unstable/main amd64 libstdc++-14-dev-arm64-cross all 14.2.0-12cross1 [2563 kB]
Get:39 http://localhost:3142/debian unstable/main amd64 g++-14-aarch64-linux-gnu amd64 14.2.0-12cross1 [12.2 MB]
Get:40 http://localhost:3142/debian unstable/main amd64 g++-aarch64-linux-gnu amd64 4:14.2.0-1 [1200 B]
Get:41 http://localhost:3142/debian unstable/main amd64 crossbuild-essential-arm64 all 12.12 [3548 B]
Get:42 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get:43 http://localhost:3142/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB]
Get:44 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get:45 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:46 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get:47 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get:48 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get:49 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get:50 http://localhost:3142/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get:51 http://localhost:3142/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get:52 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get:53 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get:54 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:55 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:56 http://localhost:3142/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get:57 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.37-1 [29.7 kB]
Get:58 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.37-1 [75.6 kB]
Get:59 http://localhost:3142/debian unstable/main arm64 gcc-14-base arm64 14.2.0-18 [49.4 kB]
Get:60 http://localhost:3142/debian unstable/main arm64 libgcc-s1 arm64 14.2.0-18 [54.1 kB]
Get:61 http://localhost:3142/debian unstable/main arm64 libc6 arm64 2.41-4 [2484 kB]
Get:62 http://localhost:3142/debian unstable/main arm64 libasan8 arm64 14.2.0-18 [2579 kB]
Get:63 http://localhost:3142/debian unstable/main arm64 libatomic1 arm64 14.2.0-18 [10.1 kB]
Get:64 http://localhost:3142/debian unstable/main arm64 libcrypt1 arm64 1:4.4.38-1 [91.8 kB]
Get:65 http://localhost:3142/debian unstable/main arm64 libcrypt-dev arm64 1:4.4.38-1 [123 kB]
Get:66 http://localhost:3142/debian unstable/main arm64 libc6-dev arm64 2.41-4 [1620 kB]
Get:67 http://localhost:3142/debian unstable/main arm64 libgomp1 arm64 14.2.0-18 [124 kB]
Get:68 http://localhost:3142/debian unstable/main arm64 libitm1 arm64 14.2.0-18 [24.1 kB]
Get:69 http://localhost:3142/debian unstable/main arm64 liblsan0 arm64 14.2.0-18 [1161 kB]
Get:70 http://localhost:3142/debian unstable/main arm64 libtsan2 arm64 14.2.0-18 [2386 kB]
Get:71 http://localhost:3142/debian unstable/main arm64 libstdc++6 arm64 14.2.0-18 [638 kB]
Get:72 http://localhost:3142/debian unstable/main arm64 libubsan1 arm64 14.2.0-18 [1039 kB]
Get:73 http://localhost:3142/debian unstable/main arm64 libhwasan0 arm64 14.2.0-18 [1442 kB]
Get:74 http://localhost:3142/debian unstable/main arm64 libgcc-14-dev arm64 14.2.0-18 [2356 kB]
Get:75 http://localhost:3142/debian unstable/main arm64 libstdc++-14-dev arm64 14.2.0-18 [2295 kB]
Get:76 http://localhost:3142/debian unstable/main arm64 zlib1g arm64 1:1.3.dfsg+really1.3.1-1+b1 [85.1 kB]
Get:77 http://localhost:3142/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Preconfiguring packages ...
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Selecting previously unselected package sensible-utils.
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+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (arm64 included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) amd64 (x86_64)
Toolchain package versions: binutils_2.44-3 dpkg-dev_1.22.18 g++-14_14.2.0-18 gcc-14_14.2.0-18 libc6-dev_2.41-4 libstdc++-14-dev_14.2.0-18 libstdc++-14-dev-arm64-cross_14.2.0-12cross1 libstdc++6_14.2.0-18 libstdc++6-arm64-cross_14.2.0-12cross1 linux-libc-dev_6.12.17-1
Package versions: apt_2.9.33 apt-utils_2.9.33 autoconf_2.72-3 automake_1:1.17-3 autopoint_0.23.1-1 autotools-dev_20220109.1 base-files_13.7 base-passwd_3.6.6 bash_5.2.37-1.1 binutils_2.44-3 binutils-aarch64-linux-gnu_2.44-3 binutils-common_2.44-3 binutils-x86-64-linux-gnu_2.44-3 bsdextrautils_2.40.4-5 bsdutils_1:2.40.4-5 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-14_14.2.0-18 cpp-14-aarch64-linux-gnu_14.2.0-12cross1 cpp-14-x86-64-linux-gnu_14.2.0-18 cpp-aarch64-linux-gnu_4:14.2.0-1 cpp-x86-64-linux-gnu_4:14.2.0-1 crossbuild-essential-arm64_12.12 dash_0.5.12-12 debconf_1.5.91 debhelper_13.24.1 debian-archive-keyring_2023.4 debianutils_5.21 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-2 dpkg_1.22.18 dpkg-dev_1.22.18 dwz_0.15-1+b1 fakeroot_1.37-1 file_1:5.45-3+b1 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.2.0-18 g++-14-aarch64-linux-gnu_14.2.0-12cross1 g++-14-x86-64-linux-gnu_14.2.0-18 g++-aarch64-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_14.2.0-18 gcc-14-aarch64-linux-gnu_14.2.0-12cross1 gcc-14-aarch64-linux-gnu-base_14.2.0-12cross1 gcc-14-base_14.2.0-18 gcc-14-cross-base_14.2.0-12cross1 gcc-14-x86-64-linux-gnu_14.2.0-18 gcc-aarch64-linux-gnu_4:14.2.0-1 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-1 gettext-base_0.23.1-1 grep_3.11-4 groff-base_1.23.0-7 gzip_1.13-1 hostname_3.25 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg7.0_2.9.33 libarchive-zip-perl_1.68-1 libasan8_14.2.0-18 libasan8-arm64-cross_14.2.0-12cross1 libatomic1_14.2.0-18 libatomic1-arm64-cross_14.2.0-12cross1 libattr1_1:2.5.2-3 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2+b2 libbinutils_2.44-3 libblkid1_2.40.4-5 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.41-4 libc-dev-bin_2.41-4 libc6_2.41-4 libc6-arm64-cross_2.41-4cross1 libc6-dev_2.41-4 libc6-dev-arm64-cross_2.41-4cross1 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-2 libcc1-0_14.2.0-18 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.44-3 libctf0_2.44-3 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.277 libdebhelper-perl_13.24.1 libdpkg-perl_1.22.18 libelf1t64_0.192-4 libfakeroot_1.37-1 libfile-stripnondeterminism-perl_1.14.1-2 libgcc-14-dev_14.2.0-18 libgcc-14-dev-arm64-cross_14.2.0-12cross1 libgcc-s1_14.2.0-18 libgcc-s1-arm64-cross_14.2.0-12cross1 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp10_2:6.3.0+dfsg-3 libgomp1_14.2.0-18 libgomp1-arm64-cross_14.2.0-12cross1 libgprofng0_2.44-3 libhogweed6t64_3.10.1-1 libhwasan0_14.2.0-18 libhwasan0-arm64-cross_14.2.0-12cross1 libicu72_72.1-6 libisl23_0.27-1 libitm1_14.2.0-18 libitm1-arm64-cross_14.2.0-12cross1 libjansson4_2.14-2+b3 liblsan0_14.2.0-18 liblsan0-arm64-cross_14.2.0-12cross1 liblz4-1_1.10.0-4 liblzma5_5.6.4-1 libmagic-mgc_1:5.45-3+b1 libmagic1t64_1:5.45-3+b1 libmd0_1.1.0-2+b1 libmount1_2.40.4-5 libmpc3_1.3.1-1+b3 libmpfr6_4.2.1-1+b2 libnettle8t64_3.10.1-1 libpam-modules_1.7.0-3 libpam-modules-bin_1.7.0-3 libpam-runtime_1.7.0-3 libpam0g_1.7.0-3 libpcre2-8-0_10.45-1 libperl5.40_5.40.1-2 libpipeline1_1.5.8-1 libquadmath0_14.2.0-18 libseccomp2_2.5.5-2+b1 libselinux1_3.8-4 libsemanage-common_3.8-1 libsemanage2_3.8-1+b1 libsepol2_3.8-1 libsframe1_2.44-3 libsmartcols1_2.40.4-5 libssl3t64_3.4.1-1 libstdc++-14-dev_14.2.0-18 libstdc++-14-dev-arm64-cross_14.2.0-12cross1 libstdc++6_14.2.0-18 libstdc++6-arm64-cross_14.2.0-12cross1 libsystemd0_257.4-3 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_14.2.0-18 libtsan2-arm64-cross_14.2.0-12cross1 libubsan1_14.2.0-18 libubsan1-arm64-cross_14.2.0-12cross1 libuchardet0_0.0.8-1+b2 libudev1_257.4-3 libunistring5_1.3-1 libuuid1_2.40.4-5 libxml2_2.12.7+dfsg+really2.9.14-0.2+b2 libxxhash0_0.8.3-2 libzstd1_1.5.6+dfsg-2 linux-libc-dev_6.12.17-1 linux-libc-dev-arm64-cross_6.12.17-1cross1 login_1:4.16.0-2+really2.40.4-5 login.defs_1:4.17.3-1 m4_1.4.19-7 make_4.4.1-1 man-db_2.13.0-1 mawk_1.3.4.20250131-1 mount_2.40.4-5 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 openssl-provider-legacy_3.4.1-1 passwd_1:4.17.3-1 patch_2.7.6-7 perl_5.40.1-2 perl-base_5.40.1-2 perl-modules-5.40_5.40.1-2 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_1.2.1-6+b1 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 tzdata_2025a-2 util-linux_2.40.4-5 xz-utils_5.6.4-1 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:
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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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dpkg-source: warning: cannot verify inline signature for ./plink_1.07+dfsg-4.dsc: unsupported subcommand
dpkg-source: info: extracting plink in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking plink_1.07+dfsg.orig.tar.xz
dpkg-source: info: unpacking plink_1.07+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 30_endiandetection.patch
dpkg-source: info: applying gcc-4.7.patch
dpkg-source: info: applying Fix_spelling_error.patch
dpkg-source: info: applying gcc11.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
CONFIG_SITE=/etc/dpkg-cross/cross-config.arm64
DEB_BUILD_OPTIONS=nocheck
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=crossqa
OLDPWD=/home/crossqa
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SBUILD_CONFIG=/tmp/tmp.V9W3cjX7CR/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-855ff5c1-1aff-49df-86b5-12415053292b
SCHROOT_UID=1000
SCHROOT_USER=crossqa
SHELL=/bin/sh
USER=crossqa
XDG_SESSION_CLASS=user
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -aarm64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1
dpkg-buildpackage: info: source package plink
dpkg-buildpackage: info: source version 1.07+dfsg-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh@debian.org>
dpkg-architecture: warning: specified GNU system type aarch64-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
make -j1 clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f *.o *~
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f plink
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- CXXFLAGS='-Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3' FORCE_DYNAMIC=1
make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=aarch64-linux-gnu-pkg-config CXX=aarch64-linux-gnu-g\+\+ CC=aarch64-linux-gnu-gcc "CXXFLAGS=-Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3" FORCE_DYNAMIC=1
make[2]: Entering directory '/<<PKGBUILDDIR>>'
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c plink.cpp
In file included from plink.cpp:28:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from plink.cpp:35:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
In file included from plink.cpp:40:
idhelp.h: In member function ‘void IDGroup::display()’:
idhelp.h:196:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
196 | for (int k=0; k<values.size(); k++)
| ~^~~~~~~~~~~~~~
plink.cpp: In function ‘int main(int, char**)’:
plink.cpp:763:26: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
763 | par::make_founders &&
| ~~~~~~~~~~~~~~~~~~~^~
764 | !par::built_families)
| ~~~~~~~~~~~~~~~~~~~~
plink.cpp:2106:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2106 | for (int i=0;i<chrs.size();i++)
| ~^~~~~~~~~~~~
plink.cpp: In member function ‘void Plink::cleanUp()’:
plink.cpp:2359:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2359 | for (int i=0; i<sample.size(); i++)
| ~^~~~~~~~~~~~~~
plink.cpp:2362:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2362 | for (int l=0; l<locus.size(); l++)
| ~^~~~~~~~~~~~~
plink.cpp:2366:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CSNP*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2366 | for (int l=0; l<SNP.size(); l++)
| ~^~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c options.cpp
In file included from options.cpp:16:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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;
| ^~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c binput.cpp
In file included from binput.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
binput.cpp: In member function ‘void Plink::readBinData()’:
binput.cpp:126:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
126 | for (int i=0; i<locus.size(); i++)
| ~^~~~~~~~~~~~~
binput.cpp:157:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
157 | for (int j=0; j<ordered.size(); j++)
| ~^~~~~~~~~~~~~~~
binput.cpp:176:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
176 | for (int j=0; j<ordered.size(); j++)
| ~^~~~~~~~~~~~~~~
binput.cpp:186:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
186 | for (int j=0; j<ordered.size(); j++)
| ~^~~~~~~~~~~~~~~
binput.cpp:261:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
261 | while (s<locus.size()) // for all SNPs
| ~^~~~~~~~~~~~~
binput.cpp:339:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
339 | while (s<locus.size()) // for all SNPs
| ~^~~~~~~~~~~~~
binput.cpp:351:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
351 | while (c<7 && s<locus.size())
| ~^~~~~~~~~~~~~
binput.cpp:398:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
398 | for(int l=0; l < locus.size(); l++)
| ~~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tinput.cpp
In file included from tinput.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
tinput.cpp: In member function ‘void Plink::readTransposedData()’:
tinput.cpp:161:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
161 | for (int i=0; i<include.size(); i++)
| ~^~~~~~~~~~~~~~~
tinput.cpp:218:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
218 | for (int j=0; j<ordered.size(); j++)
| ~^~~~~~~~~~~~~~~
tinput.cpp:246:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
246 | for (int j=0; j<ordered.size(); j++)
| ~^~~~~~~~~~~~~~~
tinput.cpp:256:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
256 | for (int j=0; j<ordered.size(); j++)
| ~^~~~~~~~~~~~~~~
tinput.cpp:261:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
261 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() )
| ~~~~~~~~~~^~~~~~~~~~~~~~
tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
271 | for(int l=0; l < locus.size(); l++)
| ~~^~~~~~~~~~~~~~
tinput.cpp:309:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
309 | for (int i=0; i<sample.size(); i++)
| ~^~~~~~~~~~~~~~
tinput.cpp:591:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
591 | if ( c > sample.size())
| ~~^~~~~~~~~~~~~~~
tinput.cpp:603:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
603 | if ( gn != 2 * sample.size() )
| ~~~^~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genome.cpp
In file included from genome.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
genome.cpp: In member function ‘void Plink::calcStratifiedAlleleFreqs()’:
genome.cpp:99:15: warning: unused variable ‘geno_nm’ [-Wunused-variable]
99 | int geno_nm = 0;
| ^~~~~~~
genome.cpp:81:14: warning: unused variable ‘tothet’ [-Wunused-variable]
81 | double tothet = 0;
| ^~~~~~
genome.cpp: In member function ‘void Plink::calcFst()’:
genome.cpp:391:14: warning: unused variable ‘ht’ [-Wunused-variable]
391 | double ht = 2 * locus[l]->freq * ( 1 - locus[l]->freq );
| ^~
genome.cpp: In member function ‘Z Plink::calcGenomeIBD(Individual*, Individual*, Z)’:
genome.cpp:843:10: warning: unused variable ‘e10’ [-Wunused-variable]
843 | double e10 = E10*S;
| ^~~
genome.cpp:844:10: warning: unused variable ‘e20’ [-Wunused-variable]
844 | double e20 = E20*S;
| ^~~
genome.cpp:848:10: warning: unused variable ‘e21’ [-Wunused-variable]
848 | double e21 = E21*S;
| ^~~
genome.cpp: In member function ‘void Plink::displayGenomeWideInfo()’:
genome.cpp:1067:30: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
1067 | if ( (!par::silent ) && c==c2 || c==np)
| ~~~~~~~~~~~~~~~~^~~~~~~~
genome.cpp: In member function ‘void Plink::pruneLD()’:
genome.cpp:1227:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1227 | for (int i=0;i<chrs.size();i++)
| ~^~~~~~~~~~~~
genome.cpp:1189:7: warning: unused variable ‘win_end’ [-Wunused-variable]
1189 | int win_end = win_start + par::prune_ld_win;
| ^~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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;
| ^~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c stats.cpp
In file included from helper.h:24,
from stats.cpp:30:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
stats.cpp: In function ‘void tqli(std::vector<double>&, std::vector<double>&, std::vector<std::vector<double> >&)’:
stats.cpp:458:18: warning: unused variable ‘k’ [-Wunused-variable]
458 | int m,l,iter,i,k;
| ^
stats.cpp: In function ‘bool svd(matrix_t&, vector_t&, matrix_t&)’:
stats.cpp:813:16: warning: unused variable ‘eps’ [-Wunused-variable]
813 | const double eps = 1e-12;
| ^~~
stats.cpp:818:7: warning: unused variable ‘r’ [-Wunused-variable]
818 | int r = u.size();
| ^
stats.cpp: In function ‘std::vector<std::vector<double> > msqrt(std::vector<std::vector<double> >&)’:
stats.cpp:906:16: warning: unused variable ‘eps’ [-Wunused-variable]
906 | const double eps = 1e-12;
| ^~~
stats.cpp: In function ‘int pca(matrix_t&, boolmatrix_t&, vector_t&, matrix_t&, matrix_t&, bool)’:
stats.cpp:1477:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1477 | for (int c = 0 ; c < keep.size(); c++)
| ~~^~~~~~~~~~~~~
stats.cpp:1483:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1483 | for (int c = 0 ; c < keep.size(); c++)
| ~~^~~~~~~~~~~~~
stats.cpp:1515:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1515 | for (int c = 0 ; c < keep.size(); c++)
| ~~^~~~~~~~~~~~~
stats.cpp:1521:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1521 | for (int c = 0 ; c < keep.size(); c++)
| ~~^~~~~~~~~~~~~
stats.cpp: In function ‘matrix_t vec2diag(vector_t&)’:
stats.cpp:1531:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1531 | for (int i = 0; i < v.size(); i++)
| ~~^~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c filters.cpp
In file included from filters.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
filters.cpp: In member function ‘void Plink::filterSNPs()’:
filters.cpp:95:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
95 | for (int i=0; i<sample.size(); i++)
| ~^~~~~~~~~~~~~~
filters.cpp:123:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
123 | for (int i=0;i<sample.size();i++)
| ~^~~~~~~~~~~~~~
filters.cpp:132:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
132 | for (int l=0; l<locus.size();l++)
| ~^~~~~~~~~~~~~
filters.cpp:155:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
155 | for (int i=0;i<sample.size();i++)
| ~^~~~~~~~~~~~~~
filters.cpp:163:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
163 | for (int l=0; l<locus.size();l++)
| ~^~~~~~~~~~~~~
filters.cpp:198:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
198 | for (int i=0;i<sample.size();i++)
| ~^~~~~~~~~~~~~~
filters.cpp:273:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
273 | for (int i=0; i<tokens.size(); i++)
| ~^~~~~~~~~~~~~~
filters.cpp:249:14: warning: unused variable ‘freq’ [-Wunused-variable]
249 | double freq;
| ^~~~
filters.cpp:250:11: warning: unused variable ‘nm’ [-Wunused-variable]
250 | int nm;
| ^~
filters.cpp:591:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
591 | for (int i=0; i<hetlist.size(); i++)
| ~^~~~~~~~~~~~~~~
filters.cpp:611:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
611 | for (int i=0; i<no_founders_found_list.size(); i++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
filters.cpp:739:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
739 | for ( int l = 0 ; l < locus.size() ; l++ )
| ~~^~~~~~~~~~~~~~
filters.cpp:762:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
762 | for ( int i = 0 ; i < sample.size() ; i++ )
| ~~^~~~~~~~~~~~~~~
filters.cpp:1078:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1078 | for (int l=0; l<locus.size();l++)
| ~^~~~~~~~~~~~~
filters.cpp:1091:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1091 | for (int l=0; l<locus.size();l++)
| ~^~~~~~~~~~~~~
filters.cpp:1143:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1143 | for (int l=0; l<locus.size(); l++)
| ~^~~~~~~~~~~~~
filters.cpp:1165:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1165 | for ( int i=0; i<sample.size(); i++)
| ~^~~~~~~~~~~~~~
filters.cpp:1257:7: warning: unused variable ‘tmp’ [-Wunused-variable]
1257 | int tmp = deleteSNPs(del);
| ^~~
filters.cpp: In member function ‘void Plink::thinSNPs()’:
filters.cpp:1277:7: warning: unused variable ‘x’ [-Wunused-variable]
1277 | int x = 0;
| ^
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c locus.cpp
In file included from locus.cpp:16:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multi.cpp
In file included from multi.cpp:16:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
multi.cpp: In member function ‘std::vector<double> Plink::calcMultiPoint(std::vector<Z>&, Z, std::ofstream&)’:
multi.cpp:295:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Z>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
295 | for (int i=0;i<left.size();i++)
| ~^~~~~~~~~~~~
multi.cpp:304:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Z>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
304 | for (int i=0;i<left.size();i++)
| ~^~~~~~~~~~~~
multi.cpp:357:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Z>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
357 | for (int i=0;i<right.size();i++)
| ~^~~~~~~~~~~~~
multi.cpp:372:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
372 | for (int i=0; i<pos.size()-1; i++)
| ~^~~~~~~~~~~~~
multi.cpp:154:8: warning: unused variable ‘is0zero’ [-Wunused-variable]
154 | bool is0zero = IBDg.z0 < EPS ? true : false;
| ^~~~~~~
multi.cpp:155:8: warning: unused variable ‘is1zero’ [-Wunused-variable]
155 | bool is1zero = IBDg.z1 < EPS ? true : false;
| ^~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c crandom.cpp
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/include/c++/14/string:51,
from /usr/aarch64-linux-gnu/include/c++/14/bits/locale_classes.h:40,
from /usr/aarch64-linux-gnu/include/c++/14/bits/ios_base.h:41,
from /usr/aarch64-linux-gnu/include/c++/14/ios:44,
from /usr/aarch64-linux-gnu/include/c++/14/ostream:40,
from /usr/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/bits/stl_vector.h:1288:30,
inlined from ‘void Plink::buildCluster()’ at cluster.cpp:128:20:
/usr/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/bits/stl_vector.h:1288:30,
inlined from ‘void Plink::buildCluster()’ at cluster.cpp:139:16:
/usr/aarch64-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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mds.cpp
In file included from mds.cpp:21:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
mds.cpp: In member function ‘void Plink::generateMDS()’:
mds.cpp:190:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
190 | for (int i1=0; i1<cl[c1].size(); i1++)
| ~~^~~~~~~~~~~~~~
mds.cpp:191:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
191 | for (int i2=0; i2<cl[c2].size(); i2++)
| ~~^~~~~~~~~~~~~~
mds.cpp:279:21: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
279 | if ( elist.size() != par::cluster_mds_dim )
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
mds.cpp:242:8: warning: unused variable ‘flag’ [-Wunused-variable]
242 | bool flag = svd(D,eigenvalue,eigenvector);
| ^~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c output.cpp
In file included from output.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
output.cpp: In member function ‘void Plink::displayGenomePV()’:
output.cpp:84:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
84 | for (int i=0; i<original.size();i++)
| ~^~~~~~~~~~~~~~~~
output.cpp:86:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
86 | for (int j=0; j<original[i].size(); j++)
| ~^~~~~~~~~~~~~~~~~~~
output.cpp:89:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
89 | for (int k=0; k<maxr2.size(); k++)
| ~^~~~~~~~~~~~~
output.cpp: In member function ‘void Plink::display_twolocus()’:
output.cpp:402:28: warning: variable ‘loc1’ set but not used [-Wunused-but-set-variable]
402 | vector<Locus*>::iterator loc1 = locus.begin()+m1;
| ^~~~
output.cpp:403:28: warning: variable ‘loc2’ set but not used [-Wunused-but-set-variable]
403 | vector<Locus*>::iterator loc2 = locus.begin()+m2;
| ^~~~
output.cpp: In member function ‘void Plink::extractExcludeSet(bool)’:
output.cpp:520:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
520 | for (int s=0; s<setname.size(); s++)
| ~^~~~~~~~~~~~~~~
output.cpp:526:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
526 | for (int l=0; l<snpset[s].size(); l++)
| ~^~~~~~~~~~~~~~~~~
output.cpp:553:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
553 | for (int l=0; l<lst.size(); l++)
| ~^~~~~~~~~~~
output.cpp: In member function ‘void Plink::keep2SetsForGenome()’:
output.cpp:788:7: warning: unused variable ‘n_removed’ [-Wunused-variable]
788 | int n_removed = deleteIndividuals(del);
| ^~~~~~~~~
output.cpp: In member function ‘void Plink::outputSetFile()’:
output.cpp:2200:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2200 | for (int i=0; i<snpset.size();i++)
| ~^~~~~~~~~~~~~~
output.cpp:2322:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2322 | for (int j=0; j<inSet.size(); j++)
| ~^~~~~~~~~~~~~
output.cpp: In member function ‘void Plink::setTable()’:
output.cpp:2367:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2367 | for (int i=0; i < setname.size();i++)
| ~~^~~~~~~~~~~~~~~~
output.cpp:2380:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2380 | for (int i=0;i<setname.size();i++)
| ~^~~~~~~~~~~~~~~
output.cpp: In member function ‘void Plink::writeSetFile()’:
output.cpp:2409:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2409 | for (int j=0; j<snpset.size(); j++)
| ~^~~~~~~~~~~~~~
output.cpp:2412:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2412 | for (int l=0; l<snpset[j].size(); l++)
| ~^~~~~~~~~~~~~~~~~
output.cpp: In member function ‘void Plink::display_pairList()’:
output.cpp:145:61: warning: ‘i2’ may be used uninitialized [-Wmaybe-uninitialized]
145 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i2,l) << " "
| ~~~~~~~~^~~~~~~~~~~~
output.cpp:116:11: note: ‘i2’ was declared here
116 | int i1, i2;
| ^~
output.cpp:144:61: warning: ‘i1’ may be used uninitialized [-Wmaybe-uninitialized]
144 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i1,l) << " "
| ~~~~~~~~^~~~~~~~~~~~
output.cpp:116:7: note: ‘i1’ was declared here
116 | int i1, i2;
| ^~
output.cpp: In member function ‘void Plink::display_indivReport()’:
output.cpp:69:32: warning: ‘i1’ may be used uninitialized [-Wmaybe-uninitialized]
69 | << setw(6) << genotype(*this,i1,l) << "\n";
| ~~~~~~~~^~~~~~~~~~~~
output.cpp:46:7: note: ‘i1’ was declared here
46 | int i1;
| ^~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c informative.cpp
In file included from informative.cpp:18:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
informative.cpp: In member function ‘int Plink::readInformative()’:
informative.cpp:80:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
80 | for ( int i = 4; i<tokens.size(); i++)
| ~^~~~~~~~~~~~~~
informative.cpp:102:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
102 | if ( col_length != tokens.size() )
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~
informative.cpp:105:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
105 | for (int i=0;i<tokens.size();i++)
| ~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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;
| ^~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c epi.cpp
In file included from epi.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
epi.cpp: In member function ‘void Plink::calcEpistasis()’:
epi.cpp:146:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
146 | for (int e=0;e<snpset[0].size();e++)
| ~^~~~~~~~~~~~~~~~~
epi.cpp:154:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
154 | for (int e=0;e<snpset[1].size();e++)
| ~^~~~~~~~~~~~~~~~~
epi.cpp:161:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
161 | for (int e=0;e<snpset[0].size();e++)
| ~^~~~~~~~~~~~~~~~~
epi.cpp:438:26: warning: unused variable ‘zero’ [-Wunused-variable]
438 | double zero = 0;
| ^~~~
epi.cpp:701:11: warning: unused variable ‘c’ [-Wunused-variable]
701 | int c=0;
| ^
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c prephap.cpp
In file included from prephap.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from prephap.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
prephap.cpp: In member function ‘void HaploPhase::readTagFile()’:
prephap.cpp:226:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
226 | if (len != tokens.size() - offset )
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
prephap.cpp:283:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
283 | for ( int i = allele ; i < tokens.size() ; i++ )
| ~~^~~~~~~~~~~~~~~
prephap.cpp:412:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
412 | while ( index < tokens.size() )
| ~~~~~~^~~~~~~~~~~~~~~
prephap.cpp:416:41: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
416 | if ( tokens[index].size() != len )
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
prephap.cpp:420:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
420 | if ( index == tokens.size() - 1 )
| ~~~~~~^~~~~~~~~~~~~~~~~~~~
prephap.cpp:470:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
470 | for (int s=0;s<S.size();s++)
| ~^~~~~~~~~
prephap.cpp: In member function ‘void HaploPhase::makeSlidingWindow(std::string)’:
prephap.cpp:533:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
533 | for (int i=0; i<tok.size(); i++)
| ~^~~~~~~~~~~
prephap.cpp:560:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
560 | for (int i=0; i<spec.size(); i++)
| ~^~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c phase.cpp
In file included from phase.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from phase.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
34 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
In file included from phase.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
phase.cpp: In member function ‘vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)’:
phase.cpp:373:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
373 | for (int i=0; i<t.size(); i++)
| ~^~~~~~~~~
phase.cpp: In member function ‘void HaploPhase::enumerateHaplotypes(std::vector<int>&)’:
phase.cpp:472:11: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
472 | while (h<nh)
| ~^~~
phase.cpp: In member function ‘void HaploPhase::performAlternEM()’:
phase.cpp:678:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
678 | for (int z=0; z<currentStub.size(); z++)
| ~^~~~~~~~~~~~~~~~~~~
phase.cpp:1187:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::vector<int>, int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1187 | if ( nh != hapmap.size() )
| ~~~^~~~~~~~~~~~~~~~
phase.cpp:1238:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1238 | for (int z=0; z<hap1[par::haplo_plem_follow_ind].size(); z++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phase.cpp:1280:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1280 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
phase.cpp:1299:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1299 | for (int z=0; z<hap1[par::haplo_plem_follow_ind].size(); z++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phase.cpp:1575:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1575 | for ( int z = 0 ; z < pp[i].size() ; z++ )
| ~~^~~~~~~~~~~~~~
phase.cpp: In member function ‘void HaploPhase::prunePhase(int)’:
phase.cpp:1829:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1829 | for (int z=0; z < hap1[i].size(); z++)
| ~~^~~~~~~~~~~~~~~~
phase.cpp:1843:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1843 | for (int z=0; z < new_pp.size(); z++)
| ~~^~~~~~~~~~~~~~~
phase.cpp: In member function ‘double HaploPhase::dosage(int, std::set<int>&)’:
phase.cpp:1888:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1888 | for (int z = 0; z < h1.size(); z++)
| ~~^~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c trio.cpp
In file included from trio.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
trio.cpp: In function ‘void addPerson(Family*, Individual*)’:
trio.cpp:91:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
91 | for (int c=0; c<f->kid.size(); c++)
| ~^~~~~~~~~~~~~~
trio.cpp: In member function ‘void Plink::parseTrios()’:
trio.cpp:258:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
258 | for (int k=0; k<mf->kid.size(); k++)
| ~^~~~~~~~~~~~~~~
trio.cpp:272:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
272 | for (int k=0; k<mf->kid.size(); k++)
| ~^~~~~~~~~~~~~~~
trio.cpp:335:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
335 | for (int k=0; k < (*f)->kid.size() ;k++)
| ~~^~~~~~~~~~~~~~~~~~
trio.cpp:342:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
342 | for ( int k=0; k<(*f)->kid.size(); k++)
| ~^~~~~~~~~~~~~~~~~
trio.cpp:350:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
350 | for ( int k=0; k<(*f)->kid.size(); k++)
| ~^~~~~~~~~~~~~~~~~
trio.cpp: In member function ‘void Plink::checkMendel()’:
trio.cpp:469:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
469 | for (int f=0; f<family.size(); f++)
| ~^~~~~~~~~~~~~~
trio.cpp:474:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
474 | for (int f=0; f<family.size(); f++)
| ~^~~~~~~~~~~~~~
trio.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
492 | for (int f=0; f<family.size(); f++)
| ~^~~~~~~~~~~~~~
trio.cpp:504:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
504 | for (int c=0; c<kid.size(); c++)
| ~^~~~~~~~~~~
trio.cpp:871:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
871 | for (int f=0; f<family.size(); f++)
| ~^~~~~~~~~~~~~~
trio.cpp:882:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
882 | for (int f=0; f<family.size(); f++)
| ~^~~~~~~~~~~~~~
trio.cpp:895:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
895 | for (int c=0; c<kid.size(); c++)
| ~^~~~~~~~~~~
trio.cpp:931:13: warning: unused variable ‘tmp’ [-Wunused-variable]
931 | int tmp = deleteSNPs(mendel_locus);
| ^~~
trio.cpp:936:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
936 | for (int f=0;f<family.size();f++)
| ~^~~~~~~~~~~~~~
trio.cpp:943:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
943 | for (int c=0; c<family[f]->kid.size(); c++)
| ~^~~~~~~~~~~~~~~~~~~~~~
trio.cpp:962:13: warning: unused variable ‘tmp’ [-Wunused-variable]
962 | int tmp = deleteIndividuals(indel);
| ^~~
trio.cpp: In member function ‘void Plink::pseudoCaseControl()’:
trio.cpp:1038:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1038 | for (int f=0; f<family.size(); f++)
| ~^~~~~~~~~~~~~~
trio.cpp:1048:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1048 | for (int c=0; c<kid.size(); c++)
| ~^~~~~~~~~~~
trio.cpp: In member function ‘void Plink::makeMissingParents()’:
trio.cpp:1236:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1236 | for ( int k=0; k<person->pm->kids.size(); k++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~
trio.cpp:1245:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1245 | for ( int k=0; k<person->pp->kids.size(); k++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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;
| ^~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sharing.cpp
In file included from perm.h:17,
from sharing.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
sharing.cpp: In member function ‘void Plink::perm_sharingIBSTest(Perm&)’:
sharing.cpp:102:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
102 | for (int l=0; l<snpset.size(); l++)
| ~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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;
| ^~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sets.cpp
In file included from sets.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from sets.cpp:24:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
sets.cpp: In member function ‘void Set::sizeSets()’:
sets.cpp:37:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
37 | for(int s=0;s<snpset.size();s++)
| ~^~~~~~~~~~~~~~
sets.cpp:52:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
52 | for(int i=0;i<snpset.size();i++)
| ~^~~~~~~~~~~~~~
sets.cpp:59:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
59 | else if (par::set_min > snpset[i].size() )
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
sets.cpp:62:48: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
62 | if (par::set_max==-1 || par::set_max > snpset[i].size() )
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::pruneSets(Plink&)’:
sets.cpp:99:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
99 | for(int i=0;i<snpset.size();i++)
| ~^~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::pruneMC(Plink&, bool, double)’:
sets.cpp:129:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
129 | for (int s=0; s<snpset.size(); s++)
| ~^~~~~~~~~~~~~~
sets.cpp:176:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
176 | for (int s=0; s<snpset.size(); s++)
| ~^~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::dropNotSet(Plink&)’:
sets.cpp:216:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
216 | for (int i=0;i<snpset.size();i++)
| ~^~~~~~~~~~~~~~
sets.cpp:218:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
218 | for (int j=0; j < snpset[i].size(); j++)
| ~~^~~~~~~~~~~~~~~~~~
sets.cpp:236:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
236 | for (int i=0;i<snpset.size();i++)
| ~^~~~~~~~~~~~~~
sets.cpp:237:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
237 | for (int j=0; j < snpset[i].size(); j++)
| ~~^~~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::makeLDSets()’:
sets.cpp:317:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
317 | for (int i=0;i<snpset.size();i++)
| ~^~~~~~~~~~~~~~
sets.cpp:323:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
323 | for (int j=0; j < snpset[i].size(); j++)
| ~~^~~~~~~~~~~~~~~~~~
sets.cpp:329:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
329 | for (int j=0; j < snpset[i].size(); j++)
| ~~^~~~~~~~~~~~~~~~~~
sets.cpp:332:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
332 | for (int k=j+1; k < snpset[i].size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
sets.cpp:367:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
367 | for (int i=0;i<snpset.size();i++)
| ~^~~~~~~~~~~~~~
sets.cpp:370:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
370 | for (int j=0; j < snpset[i].size(); j++)
| ~~^~~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::initialiseSetMapping()’:
sets.cpp:412:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
412 | for (int i=0;i<snpset.size();i++)
| ~^~~~~~~~~~~~~~
sets.cpp:413:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
413 | for (int j=0; j < snpset[i].size(); j++)
| ~~^~~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::empiricalSetPValues()’:
sets.cpp:618:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
618 | for (int i=0;i<stat_set.size();i++)
| ~^~~~~~~~~~~~~~~~
sets.cpp:619:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
619 | for (int j=0;j<stat_set[i].size();j++)
| ~^~~~~~~~~~~~~~~~~~~
sets.cpp:631:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
631 | for (int i=0;i<pv_set.size();i++)
| ~^~~~~~~~~~~~~~
sets.cpp:632:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
632 | for (int j=0;j<pv_set[i].size();j++)
| ~^~~~~~~~~~~~~~~~~
sets.cpp:642:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
642 | for (int i=0;i<pv_set.size();i++)
| ~^~~~~~~~~~~~~~
sets.cpp:643:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
643 | for (int j=0;j<pv_set[i].size();j++)
| ~^~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘vector_t Set::profileTestScore()’:
sets.cpp:703:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
703 | for (int i=0; i<snpset.size(); i++)
| ~^~~~~~~~~~~~~~
sets.cpp:713:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
713 | for (int j=0; j<profileSNPs[i].size(); j++)
| ~^~~~~~~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘vector_t Set::fitLDSetTest(vector_t&, bool)’:
sets.cpp:905:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
905 | for (int i=0; i<snpset.size(); i++)
| ~^~~~~~~~~~~~~~
sets.cpp:975:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
975 | for (int k=0; k<selected.size(); k++)
| ~^~~~~~~~~~~~~~~~
sets.cpp: In member function ‘vector_t Set::fitStepwiseModel()’:
sets.cpp:1042:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1042 | for (int i=0; i<snpset.size(); i++)
| ~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c perm.cpp
In file included from perm.h:17,
from perm.cpp:17:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
perm.cpp: In member function ‘void Perm::permuteInCluster()’:
perm.cpp:144:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
144 | for (int j=0; j<s.size(); j++)
| ~^~~~~~~~~
perm.cpp:145:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
145 | for (int k=0; k<s[j].size(); k++)
| ~^~~~~~~~~~~~
perm.cpp: In member function ‘void Perm::setOriginalRanking(vector_t&)’:
perm.cpp:187:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
187 | for (int i=0; i<original.size(); i++)
| ~^~~~~~~~~~~~~~~~
perm.cpp:199:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
199 | for(int i=0; i<original.size(); i++)
| ~^~~~~~~~~~~~~~~~
perm.cpp: In member function ‘bool Perm::update(std::vector<double>&, std::vector<double>&)’:
perm.cpp:273:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
273 | for (int j=0;j< P.pS->snpset[l].size();j++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mh.cpp
In file included from perm.h:17,
from mh.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
mh.cpp: In member function ‘std::vector<double> Plink::calcMantelHaenszel_IxJxK(std::vector<int>&, std::vector<int>&, std::vector<int>&)’:
mh.cpp:747:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
747 | for (int i=0; i<X.size(); i++)
| ~^~~~~~~~~
mh.cpp: In member function ‘std::vector<double> Plink::calcMantelHaenszel_ORD(std::vector<int>&, std::vector<int>&, std::vector<int>&)’:
mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1249 | for (int i=0; i<X.size(); i++)
| ~^~~~~~~~~
mh.cpp:1312:1: warning: no return statement in function returning non-void [-Wreturn-type]
1312 | }
| ^
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genedrop.cpp
In file included from perm.h:17,
from genedrop.cpp:17:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
genedrop.cpp: In member function ‘void Perm::preGeneDrop()’:
genedrop.cpp:64:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
64 | for (int i=0; i<P.sample.size(); i++)
| ~^~~~~~~~~~~~~~~~
genedrop.cpp: In member function ‘void Perm::dropAlleles(Plink&, Individual*, int, int, std::vector<bool>&, std::vector<bool>&, std::vector<bool>&, std::map<Individual*, int>&)’:
genedrop.cpp:340:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
340 | for (int k=0; k<person->kids.size(); k++)
| ~^~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gxe.cpp
In file included from helper.h:24,
from gxe.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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;
| ^~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hotel.cpp
In file included from hotel.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
hotel.cpp: In member function ‘void Plink::perm_testHotel(Perm&)’:
hotel.cpp:77:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
77 | if (!sample[i]->missing)
| ^
hotel.cpp:173:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
173 | for (int s=0; s<snpset.size(); s++)
| ~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multiple.cpp
In file included from helper.h:24,
from multiple.cpp:22:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
multiple.cpp: In member function ‘void Plink::multcomp(std::vector<double>&, std::string)’:
multiple.cpp:85:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
85 | for (int l=0; l<chi.size(); l++)
| ~^~~~~~~~~~~
multiple.cpp:131:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Pair>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
131 | for (int i=0; i<schi.size(); i++)
| ~^~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploCC.cpp
In file included from haploCC.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from haploCC.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
haploCC.cpp: In member function ‘void HaploPhase::haplotypicCC(std::map<int, int>&, int, bool)’:
haploCC.cpp:48:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
48 | for (int z = 0 ; z < hap1[i].size(); z++)
| ~~^~~~~~~~~~~~~~~~
haploCC.cpp:62:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
62 | if ( ! ( haploid || X && person->sex ) )
| ~~^~~~~~~~~~~~~~
haploCC.cpp:79:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
79 | for (int z = 0 ; z < hap1[i].size(); z++)
| ~~^~~~~~~~~~~~~~~~
haploCC.cpp:93:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
93 | if ( ! ( haploid || X && person->sex ) )
| ~~^~~~~~~~~~~~~~
haploCC.cpp:268:14: warning: unused variable ‘p’ [-Wunused-variable]
268 | double p = ( n1 * p1 + n2 * p2 ) / ( n1 + n2 );
| ^
haploCC.cpp: In member function ‘void HaploPhase::haplotypicWeightedCC()’:
haploCC.cpp:340:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
340 | for (int z = 0 ; z < hap1[i].size(); z++)
| ~~^~~~~~~~~~~~~~~~
haploCC.cpp:357:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
357 | if ( ! ( haploid || X && person->sex ) )
| ~~^~~~~~~~~~~~~~
haploCC.cpp:375:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
375 | for (int z = 0 ; z < hap1[i].size(); z++)
| ~~^~~~~~~~~~~~~~~~
haploCC.cpp:392:42: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
392 | if ( ! ( haploid || X && person->sex ) )
| ~~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploTDT.cpp
In file included from haploTDT.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from haploTDT.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c poo.cpp
In file included from poo.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
poo.cpp: In member function ‘void Plink::perm_testTDT_POO(Perm&)’:
poo.cpp:93:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
93 | for (int f=0; f<family.size(); f++)
| ~^~~~~~~~~~~~~~
poo.cpp:195:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
195 | for (int i=0;i<pS->pv_set.size();i++)
| ~^~~~~~~~~~~~~~~~~~
poo.cpp:198:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
198 | for (int j=0;j<pS->pv_set[i].size();j++)
| ~^~~~~~~~~~~~~~~~~~~~~
poo.cpp: In member function ‘std::vector<double> Plink::testTDT_POO(bool, bool, Perm&, std::vector<bool>&, std::vector<bool>&)’:
poo.cpp:293:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
293 | for (int f=0; f<family.size(); f++)
| ~^~~~~~~~~~~~~~
poo.cpp:328:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
328 | for (int c=0; c<kid.size(); c++)
| ~^~~~~~~~~~~
poo.cpp:239:10: warning: unused variable ‘zt’ [-Wunused-variable]
239 | double zt;
| ^~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c webcheck.cpp
In file included from helper.h:24,
from webcheck.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
webcheck.cpp: In member function ‘void Plink::webcheck(CArgs&)’:
webcheck.cpp:117:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
117 | for (int i=0; i<tokens.size(); i++)
| ~^~~~~~~~~~~~~~
webcheck.cpp:130:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
130 | if ( i < tokens.size()-1 )
| ~~^~~~~~~~~~~~~~~~~
webcheck.cpp:146:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
146 | if ( i < tokens.size()-1 )
| ~~^~~~~~~~~~~~~~~~~
webcheck.cpp:180:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
180 | if ( i < tokens.size() - 1)
| ~~^~~~~~~~~~~~~~~~~~~
webcheck.cpp:218:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
218 | for (int i=0; i<tokens.size(); i++)
| ~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qfam.cpp
In file included from helper.h:24,
from qfam.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
qfam.cpp: In function ‘void scoreBetween(Plink&, int)’:
qfam.cpp:82:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
82 | for (int k=0; k < (*f)->kid.size() ;k++)
| ~~^~~~~~~~~~~~~~~~~~
qfam.cpp:89:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
89 | for ( int k=0; k<(*f)->kid.size(); k++)
| ~^~~~~~~~~~~~~~~~~
qfam.cpp:97:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
97 | for ( int k=0; k<(*f)->kid.size(); k++)
| ~^~~~~~~~~~~~~~~~~
qfam.cpp: In member function ‘void Plink::perm_testQTDT(Perm&)’:
qfam.cpp:267:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
267 | for (int i=0; i < family.size(); i++)
| ~~^~~~~~~~~~~~~~~
qfam.cpp:315:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
315 | for (int f = 0 ; f < family.size() ; f++)
| ~~^~~~~~~~~~~~~~~
qfam.cpp: In member function ‘vector_t Plink::calcQTDT(std::vector<int>&, std::ofstream&, bool, Perm&, std::vector<int>&, std::vector<bool>&)’:
qfam.cpp:505:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
505 | for ( int k = 0 ; k < (*f)->kid.size() ; k++)
| ~~^~~~~~~~~~~~~~~~~~
qfam.cpp:648:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
648 | for (int i=0; i<family.size(); i++)
| ~^~~~~~~~~~~~~~
qfam.cpp:657:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
657 | for (int f=0; f<pbetween.size(); f++)
| ~^~~~~~~~~~~~~~~~
qfam.cpp:639:10: warning: unused variable ‘tc’ [-Wunused-variable]
639 | int tc = 0;
| ^~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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;
| ^~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/include/c++/14/aarch64-linux-gnu/bits/c++allocator.h:33,
from /usr/aarch64-linux-gnu/include/c++/14/bits/allocator.h:46,
from /usr/aarch64-linux-gnu/include/c++/14/string:43,
from /usr/aarch64-linux-gnu/include/c++/14/bits/locale_classes.h:40,
from /usr/aarch64-linux-gnu/include/c++/14/bits/ios_base.h:41,
from /usr/aarch64-linux-gnu/include/c++/14/ios:44,
from /usr/aarch64-linux-gnu/include/c++/14/ostream:40,
from /usr/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/bits/stl_vector.h:1294:21,
inlined from ‘void Plink::mergeBinaryData()’ at bmerge.cpp:687:20:
/usr/aarch64-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;
| ^~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++)
| ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mishap.cpp
In file included from mishap.cpp:17:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from mishap.cpp:20:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
mishap.cpp: In member function ‘void Plink::performMisHapTests()’:
mishap.cpp:209:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
209 | for (int z = 0 ; z < haplo->hap1[i].size(); z++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~
mishap.cpp:236:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
236 | for (int z = 0 ; z < haplo->hap1[i].size(); z++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~
mishap.cpp:349:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
349 | for (int z = 0 ; z < haplo->hap1[i].size(); z++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~
mishap.cpp:373:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
373 | for (int z = 0 ; z < haplo->hap1[i].size(); z++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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;
| ^~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c homozyg.cpp
In file included from helper.h:24,
from homozyg.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
homozyg.cpp: In function ‘void displayPoolVerbose(Plink&, Pool*, std::ofstream&)’:
homozyg.cpp:673:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
673 | for (int i=0; i < plist.size(); i++)
| ~~^~~~~~~~~~~~~~
homozyg.cpp:695:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
695 | for (int i=0; i < plist.size(); i++)
| ~~^~~~~~~~~~~~~~
homozyg.cpp:722:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
722 | for (int i=0; i < plist.size(); i++)
| ~~^~~~~~~~~~~~~~
homozyg.cpp:756:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
756 | for (int i=0; i < plist.size(); i++)
| ~~^~~~~~~~~~~~~~
homozyg.cpp:773:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
773 | for (int i=0; i < plist.size(); i++)
| ~~^~~~~~~~~~~~~~
homozyg.cpp:861:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
861 | for (int i=0; i < plist.size(); i++)
| ~~^~~~~~~~~~~~~~
homozyg.cpp: In member function ‘void Plink::summariseHomoRuns()’:
homozyg.cpp:1134:34: warning: comparison of integer expressions of different signedness: ‘std::set<Segment*, std::less<Segment*> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
1134 | if ( thispool->segs.size() >= par::pool_size_min )
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
homozyg.cpp:1178:38: warning: comparison of integer expressions of different signedness: ‘std::set<Segment*, std::less<Segment*> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
1178 | if ( thispool->segs.size() >= par::pool_size_min )
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
homozyg.cpp:1331:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::set<Segment*, std::less<Segment*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1331 | for (int i=0; i< (*pA)->segs.size(); i++)
| ~^~~~~~~~~~~~~~~~~~~~
homozyg.cpp:1437:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1437 | for (int i=0; i < (*pA)->group.size() ; i++)
| ~~^~~~~~~~~~~~~~~~~~~~~
homozyg.cpp:1441:47: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
1441 | if ( (*pA)->match[i].size() >= maxlist )
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
homozyg.cpp:1461:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1461 | for (int i=0; i < (*pA)->group.size() ; i++)
| ~~^~~~~~~~~~~~~~~~~~~~~
homozyg.cpp: In member function ‘void Plink::findHomoWindow(Individual*, std::ofstream&)’:
homozyg.cpp:2155:27: warning: value computed is not used [-Wunused-value]
2155 | homozygWindows[l] == 0;
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c segment.cpp
In file included from helper.h:24,
from segment.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
segment.cpp: In member function ‘void Plink::segmentPermutationTest(Perm&, bool, std::string, std::vector<int>&, std::vector<int>&, std::vector<int>&)’:
segment.cpp:871:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
871 | if (!ibd)
| ^~
segment.cpp:875:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
875 | SIBS << setw(10) << original[l] << " "
| ^~~~
segment.cpp: In member function ‘void Plink::testGenomeIBDByCovariate(Perm&)’:
segment.cpp:954:22: warning: unused variable ‘p1’ [-Wunused-variable]
954 | Individual * p1 = sample[i1];
| ^~
segment.cpp:955:22: warning: unused variable ‘p2’ [-Wunused-variable]
955 | Individual * p2 = sample[i2];
| ^~
segment.cpp:1027:26: warning: unused variable ‘p1’ [-Wunused-variable]
1027 | Individual * p1 = sample[i1];
| ^~
segment.cpp:1028:26: warning: unused variable ‘p2’ [-Wunused-variable]
1028 | Individual * p2 = sample[i2];
| ^~
segment.cpp:950:7: warning: unused variable ‘c’ [-Wunused-variable]
950 | int c=0;
| ^
segment.cpp: In member function ‘void Plink::summaryIBD()’:
segment.cpp:1529:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1529 | for (int i=0;i<pihat.size();i++)
| ~^~~~~~~~~~~~~
segment.cpp: In member function ‘void Plink::indivSegmentSummary()’:
segment.cpp:1855:21: warning: variable ‘p’ set but not used [-Wunused-but-set-variable]
1855 | indivPair p = ic->first;
| ^
segment.cpp: In member function ‘void Plink::displaySegmentsLong()’:
segment.cpp:2003:12: warning: unused variable ‘nseg’ [-Wunused-variable]
2003 | int nseg = smap.size();
| ^~~~
segment.cpp: In member function ‘void Plink::displaySegmentsBED()’:
segment.cpp:2378:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
2378 | else if ( par::cnv_col = 1 )
| ~~~~~~~~~~~~~^~~
segment.cpp:2380:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
2380 | else if ( par::cnv_col = 2 )
| ~~~~~~~~~~~~~^~~
segment.cpp:2382:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
2382 | else if ( par::cnv_col = 3 )
| ~~~~~~~~~~~~~^~~
segment.cpp:2412:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
2412 | else if ( par::cnv_col = 1 )
| ~~~~~~~~~~~~~^~~
segment.cpp:2414:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
2414 | else if ( par::cnv_col = 2 )
| ~~~~~~~~~~~~~^~~
segment.cpp:2416:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
2416 | else if ( par::cnv_col = 3 )
| ~~~~~~~~~~~~~^~~
segment.cpp:2443:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
2443 | else if ( par::cnv_col = 1 )
| ~~~~~~~~~~~~~^~~
segment.cpp:2445:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
2445 | else if ( par::cnv_col = 2 )
| ~~~~~~~~~~~~~^~~
segment.cpp:2447:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
2447 | else if ( par::cnv_col = 3 )
| ~~~~~~~~~~~~~^~~
segment.cpp:2474:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
2474 | else if ( par::cnv_col = 1 )
| ~~~~~~~~~~~~~^~~
segment.cpp:2476:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
2476 | else if ( par::cnv_col = 2 )
| ~~~~~~~~~~~~~^~~
segment.cpp:2478:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
2478 | else if ( par::cnv_col = 3 )
| ~~~~~~~~~~~~~^~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c model.cpp
In file included from model.cpp:15:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from model.cpp:17:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
model.cpp: In member function ‘void Model::setMissing(std::vector<bool>&)’:
model.cpp:132:23: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
132 | if ( include.size() != P->n )
| ~~~~~~~~~~~~~~~^~~~~~~
model.cpp: In member function ‘void Model::buildDesignMatrix()’:
model.cpp:354:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
354 | for (int i=0; i< par::parameter_list.size(); i++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:367:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
367 | for ( int i = 0 ; i < X.size() ; i++)
| ~~^~~~~~~~~~
model.cpp:374:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
374 | for ( int j = 0 ; j < par::parameter_list.size() ; j++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp: In member function ‘bool Model::checkVIF()’:
model.cpp:613:10: warning: unused variable ‘maxVIF’ [-Wunused-variable]
613 | double maxVIF = 0;
| ^~~~~~
model.cpp: In member function ‘double Model::buildQFAM(Individual*)’:
model.cpp:849:10: warning: control reaches end of non-void function [-Wreturn-type]
849 | error("Internal problem with QFAM model specification");
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c logistic.cpp
In file included from helper.h:24,
from logistic.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
logistic.cpp: In member function ‘virtual void LogisticModel::pruneY()’:
logistic.cpp:66:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
66 | for (int i=0; i<Y.size(); i++)
| ~^~~~~~~~~
logistic.cpp: In member function ‘double LogisticModel::getPValue()’:
logistic.cpp:327:8: warning: unused variable ‘okay’ [-Wunused-variable]
327 | bool okay = var[testParameter] < 1e-20 || !realnum(var[testParameter]) ? false : all_valid;
| ^~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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;
| ^~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dcdflib.cpp
dcdflib.cpp: In function ‘void cdfbin(int*, double*, double*, double*, double*, double*, double*, int*, double*)’:
dcdflib.cpp:1882:36: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
1882 | if(!(*s < 0.0e0 || *which != 3 && *s > *xn)) goto S160;
| ~~~~~~~~~~~~^~~~~~~~~~~
dcdflib.cpp: In function ‘void cdfgam(int*, double*, double*, double*, double*, double*, int*, double*)’:
dcdflib.cpp:3544:20: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
3544 | if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280;
| ~~~~~~^~~~~~~~~~~~~~
dcdflib.cpp: In function ‘void E0000(int, int*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*, double*, double*, double*)’:
dcdflib.cpp:6025:23: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
6025 | if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dcdflib.cpp:6088:17: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
6088 | qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0;
| ~~~~~~^~~~~~~~~~~~~
dcdflib.cpp:6112:18: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
6112 | qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0;
| ~~~~~~^~~~~~~~~~~~~~
dcdflib.cpp:6153:18: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
6153 | qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0;
| ~~~~~~^~~~~~~~~~~~~~
dcdflib.cpp:6020:56: warning: variable ‘qok’ set but not used [-Wunused-but-set-variable]
6020 | static unsigned long qbdd,qcond,qdum1,qdum2,qincr,qlim,qok,qup;
| ^~~
dcdflib.cpp: In function ‘double dlanor(double*)’:
dcdflib.cpp:6401:28: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
6401 | if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dcdflib.cpp: In function ‘double dstrem(double*)’:
dcdflib.cpp:6782:29: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
6782 | if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dcdflib.cpp: In function ‘void E0001(int, int*, double*, double*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*)’:
dcdflib.cpp:6996:26: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
6996 | qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0;
| ~~~~~~~~~~~~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c elf.cpp
In file included from helper.h:24,
from elf.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
elf.cpp: In function ‘void displayScoresRegion(std::ofstream&, RCount&)’:
elf.cpp:493:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
493 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
elf.cpp: In member function ‘void Plink::permTestRareDistribution(Perm&)’:
elf.cpp:609:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
609 | for (int l=0; l< original.size(); l++)
| ~^~~~~~~~~~~~~~~~~
elf.cpp: In member function ‘vector_t Plink::testRareDistribution(Perm&, bool, std::map<Range, int2>&)’:
elf.cpp:654:16: warning: unused variable ‘pthresh’ [-Wunused-variable]
654 | const double pthresh = 0.01;
| ^~~~~~~
elf.cpp:655:8: warning: unused variable ‘one_sided’ [-Wunused-variable]
655 | bool one_sided = true;
| ^~~~~~~~~
elf.cpp:707:7: warning: unused variable ‘srange_cnt’ [-Wunused-variable]
707 | int srange_cnt = 0;
| ^~~~~~~~~~
elf.cpp:708:8: warning: unused variable ‘inRange’ [-Wunused-variable]
708 | bool inRange = false;
| ^~~~~~~
elf.cpp: In member function ‘void Plink::displayRareRange()’:
elf.cpp:895:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
895 | for (int i = 0 ; i < tokens.size() ; i++)
| ~~^~~~~~~~~~~~~~~
elf.cpp:939:26: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
939 | if ( tokens.size() != ncol )
| ~~~~~~~~~~~~~~^~~~~~~
elf.cpp: In member function ‘bool RCount::addSNP(int)’:
elf.cpp:374:10: warning: ‘wt’ may be used uninitialized [-Wmaybe-uninitialized]
374 | double wt;
| ^~
elf.cpp: In member function ‘void Plink::elfBaseline()’:
elf.cpp: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:1153:18: warning: ‘p_gcnt’ may be used uninitialized [-Wmaybe-uninitialized]
1153 | ++(*p_gcnt);
| ~^~~~~~~~
elf.cpp:1112:13: note: ‘p_gcnt’ was declared here
1112 | int * p_gcnt;
| ^~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dfam.cpp
In file included from dfam.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
dfam.cpp: In member function ‘std::vector<double> Plink::testSibTDT(bool, bool, Perm&, std::vector<bool>&, std::vector<bool>&)’:
dfam.cpp:76:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
76 | for (int f=0; f<family.size(); f++)
| ~^~~~~~~~~~~~~~
dfam.cpp:86:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
86 | for ( int k=0; k<fam->kid.size(); k++)
| ~^~~~~~~~~~~~~~~~
dfam.cpp:96:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
96 | for ( int k=0; k<fam->kid.size(); k++)
| ~^~~~~~~~~~~~~~~~
dfam.cpp:106:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
106 | for (int c=0; c<klist[k]->person.size(); c++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~
dfam.cpp:157:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
157 | for (int f=0; f<family.size(); f++)
| ~^~~~~~~~~~~~~~
dfam.cpp:239:25: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
239 | if ( pat1 && (!pat2) ||
| ~~~~~^~~~~~~~~~
dfam.cpp:271:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
271 | for (int c=0; c<family[f]->kid.size(); c++)
| ~^~~~~~~~~~~~~~~~~~~~~~
dfam.cpp:378:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
378 | for (int c=0; c<family[f]->kid.size(); c++)
| ~^~~~~~~~~~~~~~~~~~~~~~
dfam.cpp:218:16: warning: unused variable ‘informative’ [-Wunused-variable]
218 | bool informative = false;
| ^~~~~~~~~~~
dfam.cpp:504:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
504 | for (int c=0; c<klist[k]->person.size(); c++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~
dfam.cpp:151:11: warning: unused variable ‘totalInformative’ [-Wunused-variable]
151 | int totalInformative = 0;
| ^~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c fisher.cpp
In file included from helper.h:24,
from fisher.cpp:17:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
fisher.cpp: In function ‘void fexact(int*, int*, double*, int*, double*, double*, double*, double*, double*, int*)’:
fisher.cpp:261:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
261 | prterr(1, "NROW must be less than or equal to LDTABL.");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:267:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
267 | prterr(2, "All elements of TABLE must be positive.");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:272:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
272 | prterr(3, "All elements of TABLE are zero.\n"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
273 | "PRT and PRE are set to missing values.");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp: In function ‘void f2xact(int*, int*, double*, int*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, double*, double*, int*, int*, double*)’:
fisher.cpp:448:15: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
448 | prterr(1, "NROW must be less than or equal to LDTABL.");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:450:15: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
450 | prterr(4, "NCOL must be at least 2");
| ^~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:449:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
449 | if (*ncol <= 1)
| ^~
fisher.cpp:453:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
453 | for (i = 1; i <= *ldkey << 1; ++i) {
| ^~~
fisher.cpp:501:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
501 | prterr(2, "All elements of TABLE must be positive.");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:508:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
508 | prterr(3, "All elements of TABLE are zero.\n"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
509 | "PRT and PRE are set to missing values.");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:559:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
559 | prterr(5, "The hash table key cannot be computed because "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
560 | "the largest key\n"
| ~~~~~~~~~~~~~~~~~~~
561 | "is larger than the largest representable int.\n"
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
562 | "The algorithm cannot proceed.\n"
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
563 | "Reduce the workspace size, or use `exact = FALSE'.");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:750:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
750 | prterr(6, "LDKEY is too small for this problem.\n"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
751 | "Try increasing the size of the workspace.");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp: In function ‘void f5xact(double*, const double*, int*, int*, int*, int*, double*, int*, int*, int*, int*, int*, int*, int*, int*)’:
fisher.cpp:1538:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
1538 | prterr(6, "LDKEY is too small for this problem.\n"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1539 | "Try increasing the size of the workspace.");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:1554:23: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
1554 | prterr(7, "LDSTP is too small for this problem.\n"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1555 | "Try increasing the size of the workspace.");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:1596:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
1596 | prterr(7, "LDSTP is too small for this problem.\n"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1597 | "Try increasing the size of the workspace.");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp: In function ‘int iwork(int, int*, int, int)’:
fisher.cpp:2001:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
2001 | prterr(40, "Out of workspace.");
| ^~~~~~~~~~~~~~~~~~~
fisher.cpp: In function ‘void isort(int*, int*)’:
fisher.cpp:2078:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
2078 | prterr(20, "This should never occur.");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linput.cpp
In file included from linput.cpp:25:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
linput.cpp: In member function ‘void Plink::readDataLongFormat()’:
linput.cpp:68:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for (int l=0; l< locus.size(); l++)
| ~^~~~~~~~~~~~~~
linput.cpp:128:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
128 | for (int i=0; i<sample.size(); i++)
| ~^~~~~~~~~~~~~~
linput.cpp:136:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CSNP*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
136 | for (int l=0; l<SNP.size(); l++)
| ~^~~~~~~~~~~
linput.cpp:146:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
146 | for (int l=0; l< locus.size(); l++)
| ~^~~~~~~~~~~~~~
linput.cpp:164:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
164 | for (int i=0; i<sample.size(); i++)
| ~^~~~~~~~~~~~~~
linput.cpp:200:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
200 | for (int i=0; i<include.size(); i++)
| ~^~~~~~~~~~~~~~~
linput.cpp:209:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
209 | for (int i=0; i<sample.size(); i++)
| ~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sockets.cpp
In file included from helper.h:24,
from sockets.cpp:18:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
sockets.cpp: In function ‘std::vector<std::__cxx11::basic_string<char> > socketConnection(Plink*, std::string, int, std::string)’:
sockets.cpp:78:24: warning: unused variable ‘out_buf’ [-Wunused-variable]
78 | char out_buf[BUF_SIZE+1]; // Output buffer for GET request
| ^~~~~~~
sockets.cpp:79:24: warning: unused variable ‘in_buf’ [-Wunused-variable]
79 | char in_buf[BUF_SIZE+1]; // Input buffer for response
| ^~~~~~
sockets.cpp:81:24: warning: unused variable ‘i’ [-Wunused-variable]
81 | unsigned int i; // Loop counter
| ^
sockets.cpp:119:7: warning: unused variable ‘echoStringLen’ [-Wunused-variable]
119 | int echoStringLen = 100;
| ^~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup.cpp
In file included from helper.h:24,
from lookup.cpp:18:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
lookup.cpp: In member function ‘void Plink::lookup()’:
lookup.cpp:206:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
206 | for (int i=25; i<tokens.size()-1; i++)
| ~^~~~~~~~~~~~~~~~
lookup.cpp:203:15: warning: unused variable ‘totalSNPs’ [-Wunused-variable]
203 | int totalSNPs = 0;
| ^~~~~~~~~
lookup.cpp:204:15: warning: unused variable ‘gcount’ [-Wunused-variable]
204 | int gcount = 0;
| ^~~~~~
lookup.cpp:272:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
272 | for (int i=25; i<tokens.size()-1; i++)
| ~^~~~~~~~~~~~~~~~
lookup.cpp:289:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
289 | for (int i=25; i<tokens.size()-1; i++)
| ~^~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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;
| ^~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c pdriver.cpp
In file included from pdriver.cpp:16:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from pdriver.cpp:18:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
pdriver.cpp: In member function ‘void Plink::proxyWrapper()’:
pdriver.cpp:266:11: warning: unused variable ‘similar’ [-Wunused-variable]
266 | int similar = 0;
| ^~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploQTL.cpp
In file included from haploQTL.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from haploQTL.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
haploQTL.cpp: In member function ‘void HaploPhase::haplotypicQTL(std::map<int, int>&, int, bool)’:
haploQTL.cpp:83:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
83 | for (int z = 0 ; z < hap1[i].size(); z++)
| ~~^~~~~~~~~~~~~~~~
haploQTL.cpp:145:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
145 | for (int z = 0 ; z < hap1[i].size(); z++)
| ~~^~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp
In file included from haplohelper.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from haplohelper.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
In file included from haplohelper.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
34 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
haplohelper.cpp: In member function ‘void HaploPhase::imputeAllHaplotypes()’:
haplohelper.cpp:104:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
104 | for (int l=0; l<new_one[i].size(); l++)
| ~^~~~~~~~~~~~~~~~~~
haplohelper.cpp:134:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
134 | for (int l=0; l < actual_map.size(); l++)
| ~~^~~~~~~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘std::vector<std::__cxx11::basic_string<char> > HaploPhase::returnHaplotypes(std::vector<int>&)’:
haplohelper.cpp:297:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
297 | for (int h=0; h<hap.size(); h++)
| ~^~~~~~~~~~~
haplohelper.cpp: In member function ‘void HaploPhase::setTestHaplotype(std::string)’:
haplohelper.cpp:337:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
337 | for (int h=0; h<hap.size(); h++)
| ~^~~~~~~~~~~
haplohelper.cpp: In member function ‘void HaploPhase::reportPhase()’:
haplohelper.cpp:396:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
396 | for (int z = 0; z < hap1[i].size(); z++)
| ~~^~~~~~~~~~~~~~~~
haplohelper.cpp:413:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
413 | for (int z2=0; z2<hap1[i].size(); z2++)
| ~~^~~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘void HaploPhase::reportPhaseWideFormat()’:
haplohelper.cpp:487:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
487 | for (int z = 0; z < hap1[i].size(); z++)
| ~~^~~~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘vector_t HaploPhase::imputeGenotype(int, int)’:
haplohelper.cpp:655:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
655 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘double HaploPhase::imputeHaplotypes(int, bool&, bool&)’:
haplohelper.cpp:754:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
754 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
haplohelper.cpp:802:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
802 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘double HaploPhase::rsq_internal(boolvec_t&, boolvec_t&, boolvec_t&, boolvec_t&)’:
haplohelper.cpp:850:20: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
850 | if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns
| ~~~~~~~~~~~~~^~~~~
haplohelper.cpp:850:41: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
850 | if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns
| ~~~~~~~~~~~~~^~~~~
haplohelper.cpp:850:65: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
850 | if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns
| ~~~~~~~~~~~~~~~~^~~~~
haplohelper.cpp:851:25: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
851 | ||alleles2.size() != ns )
| ~~~~~~~~~~~~~~~~^~~~~
haplohelper.cpp: In member function ‘double HaploPhase::freq(boolvec_t&, boolvec_t&)’:
haplohelper.cpp:957:20: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
957 | if (mask1.size() != ns ||alleles1.size() != ns )
| ~~~~~~~~~~~~~^~~~~
haplohelper.cpp:957:44: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
957 | if (mask1.size() != ns ||alleles1.size() != ns )
| ~~~~~~~~~~~~~~~~^~~~~
haplohelper.cpp: In member function ‘void HaploPhase::trackThisSegment()’:
haplohelper.cpp:1225:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1225 | for (int z = 0; z < hap1[p1].size(); z++)
| ~~^~~~~~~~~~~~~~~~~
haplohelper.cpp:1251:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1251 | for (int z1 = 0; z1 < hap1[p1].size(); z1++)
| ~~~^~~~~~~~~~~~~~~~~
haplohelper.cpp:1252:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1252 | for (int z2 = 0; z2 < hap1[p2].size(); z2++)
| ~~~^~~~~~~~~~~~~~~~~
haplohelper.cpp:1250:11: warning: unused variable ‘j’ [-Wunused-variable]
1250 | int j=0;
| ^
haplohelper.cpp: In member function ‘void HaploPhase::calculateEmpiricalVariance(std::set<int>&)’:
haplohelper.cpp:1419:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1419 | for( int z = 0; z < pp[i].size(); z++ )
| ~~^~~~~~~~~~~~~~
haplohelper.cpp:1477:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1477 | for( int z = 0; z < pp[i].size(); z++ )
| ~~^~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘void HaploPhase::verboseDisplayWindows(int, bool)’:
haplohelper.cpp:1666:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1666 | for (int z = 0; z < windows[w]->hap1[r].size(); z++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplowindow.cpp
In file included from haplowindow.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from haplowindow.cpp:27:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
In file included from haplowindow.cpp:28:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
34 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
haplowindow.cpp: In function ‘void verboseDisplayWindows2(HaploPhase*, int, bool)’:
haplowindow.cpp:48:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
48 | for (int z = 0; z < haplo->windows[w]->hap1[r].size(); z++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
haplowindow.cpp: In member function ‘void HaploWindow::enumerateHaplotypes(intvec_t&)’:
haplowindow.cpp:183:11: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
183 | while (h<nh)
| ~^~~
haplowindow.cpp: In member function ‘void HaploWindow::prunePhase(int, double)’:
haplowindow.cpp:558:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
558 | for (int z=0; z < hap1[i].size(); z++)
| ~~^~~~~~~~~~~~~~~~
haplowindow.cpp:574:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
574 | for (int z=0; z < new_pp.size(); z++)
| ~~^~~~~~~~~~~~~~~
haplowindow.cpp: In member function ‘void HaploWindow::performEM()’:
haplowindow.cpp:683:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
683 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
haplowindow.cpp:691:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
691 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
haplowindow.cpp:751:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
751 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
haplowindow.cpp:791:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
791 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
haplowindow.cpp:798:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
798 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
haplowindow.cpp:868:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
868 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
haplowindow.cpp:872:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
872 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
haplowindow.cpp: In member function ‘void HaploWindow::reportPhase()’:
haplowindow.cpp:949:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
949 | for (int z = 0; z < hap1[i].size(); z++)
| ~~^~~~~~~~~~~~~~~~
haplowindow.cpp:966:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
966 | for (int z2=0; z2<hap1[i].size(); z2++)
| ~~^~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.cpp
In file included from genogroup.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from genogroup.cpp:24:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
In file included from genogroup.cpp:28:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
34 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nonfounderphasing.cpp
In file included from nonfounderphasing.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from nonfounderphasing.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
34 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
In file included from nonfounderphasing.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
nonfounderphasing.cpp: In member function ‘void HaploPhase::phaseAndScoreNonfounder(int)’:
nonfounderphasing.cpp:668:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
668 | for (int z=0; z < pp[i].size(); z++)
| ~~^~~~~~~~~~~~~~
nonfounderphasing.cpp:360:7: warning: unused variable ‘pcnt’ [-Wunused-variable]
360 | int pcnt=1;
| ^~~~
nonfounderphasing.cpp: In member function ‘void HaploPhase::transmissionCount(int, std::map<FamilyTransmissions, double>&)’:
nonfounderphasing.cpp:715:14: warning: unused variable ‘posterior’ [-Wunused-variable]
715 | double posterior = ip->second;
| ^~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c clumpld.cpp
In file included from helper.h:24,
from clumpld.h:21,
from clumpld.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from clumpld.cpp:21:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
clumpld.cpp: In member function ‘std::vector<ResultTrio> clump_LD::read_assoc_file(std::string)’:
clumpld.cpp:92:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
92 | for (int f=0; f<filename.size(); f++)
| ~^~~~~~~~~~~~~~~~
clumpld.cpp:128:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
128 | for (int i=0; i<tokens.size(); i++)
| ~^~~~~~~~~~~~~~
clumpld.cpp:137:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
137 | for ( int f=0; f<tok_annot.size(); f++)
| ~^~~~~~~~~~~~~~~~~
clumpld.cpp:173:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
173 | if ( tokens.size() <= snp_column ||
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~
clumpld.cpp:174:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
174 | tokens.size() <= pval_column )
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
clumpld.cpp:201:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
201 | for (int f=0; f<annot_field.size(); f++)
| ~^~~~~~~~~~~~~~~~~~~
clumpld.cpp:204:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
204 | if ( f < annot_field.size() - 1 )
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
clumpld.cpp: In member function ‘void clump_LD::clump()’:
clumpld.cpp:368:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResultTrio>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
368 | for (int i = 0; i < sp.size(); i++)
| ~~^~~~~~~~~~~
clumpld.cpp:480:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
480 | if( l1 < P->locus.size()-1 )
| ~~~^~~~~~~~~~~~~~~~~~~
clumpld.cpp:520:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
520 | for (int f=1; f<=filename.size(); f++)
| ~^~~~~~~~~~~~~~~~~
clumpld.cpp:611:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
611 | for (int f=1; f<=filename.size(); f++)
| ~^~~~~~~~~~~~~~~~~
clumpld.cpp:1097:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<int2, double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1097 | if( j < grouped_snps.size()-1)
| ~~^~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp
In file included from genoerr.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from genoerr.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
34 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
In file included from genoerr.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
genoerr.cpp: In member function ‘void HaploPhase::queryThisGenotype(int, int, int, vector_t&)’:
genoerr.cpp:157:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
157 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
genoerr.cpp:189:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
189 | for( int a = 0; a < posshap1.size(); a++ )
| ~~^~~~~~~~~~~~~~~~~
genoerr.cpp:190:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
190 | for( int b = 0; b < posshap2.size(); b++ )
| ~~^~~~~~~~~~~~~~~~~
genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
225 | for (int z = 0; z < new_hap1.size(); z++)
| ~~^~~~~~~~~~~~~~~~~
genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
315 | for (int z = 0; z < hap1[i].size(); z++)
| ~~^~~~~~~~~~~~~~~~
genoerr.cpp:328:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
328 | for (int z2=0; z2<hap1[i].size(); z2++)
| ~~^~~~~~~~~~~~~~~
genoerr.cpp:347:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
347 | for (int z = 0; z < new_hap1.size(); z++)
| ~~^~~~~~~~~~~~~~~~~
genoerr.cpp:358:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
358 | for (int z2=0; z2<new_hap1.size(); z2++)
| ~~^~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c em.cpp
In file included from em.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from em.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
34 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
In file included from em.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
em.cpp: In member function ‘void HaploPhase::performEM_original()’:
em.cpp:89:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
89 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
em.cpp:97:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
97 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
em.cpp:106:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
106 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
em.cpp:128:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
128 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
em.cpp:132:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
132 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
em.cpp:162:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
162 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
em.cpp:166:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
166 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c impute.cpp
In file included from impute.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from impute.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
34 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
In file included from impute.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
impute.cpp: In constructor ‘probabilisticGenotype::probabilisticGenotype()’:
impute.cpp:40:23: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
40 | phased = genotype = false;
| ~~~~~~~~~^~~~~~~
impute.cpp: In member function ‘void HaploPhase::updateForImputation()’:
impute.cpp:105:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
105 | for (int z=0; z<hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~
impute.cpp:144:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
144 | for (int z=0; z< currentWindow->hap1[i].size(); z++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
impute.cpp:161:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
161 | for (int z=0; z< currentWindow->pp[i].size(); z++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
impute.cpp: In member function ‘void HaploPhase::mainImputation()’:
impute.cpp:263:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
263 | for ( int z = 0 ; z < currentWindow->hap1[i].size(); z++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
impute.cpp:313:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<probabilisticGenotype>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
313 | for (int s=0; s < g.size(); s++)
| ~~^~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaem.cpp
In file included from metaem.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from metaem.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
34 | for (int i=0; i<g.size(); i++)
| ~^~~~~~~~~
In file included from metaem.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
metaem.cpp: In member function ‘void HaploPhase::enumeratePhasedWindows(int)’:
metaem.cpp:239:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
239 | while (h<nperm)
| ~^~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c profile.cpp
In file included from profile.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
profile.cpp: In member function ‘void Plink::scoreIndividuals()’:
profile.cpp:303:12: warning: unused variable ‘OLD_assoc_glm_without_main_snp’ [-Wunused-variable]
303 | bool OLD_assoc_glm_without_main_snp = par::assoc_glm_without_main_snp;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profile.cpp:304:12: warning: unused variable ‘OLD_clist’ [-Wunused-variable]
304 | bool OLD_clist = par::clist;
| ^~~~~~~~~
profile.cpp:350:14: warning: unused variable ‘statistic’ [-Wunused-variable]
350 | double statistic = valid ? model->getStatistic() : 0;
| ^~~~~~~~~
profile.cpp:351:14: warning: unused variable ‘pvalue’ [-Wunused-variable]
351 | double pvalue = pval[ pval.size()-1 ];
| ^~~~~~
profile.cpp:352:14: warning: unused variable ‘beta’ [-Wunused-variable]
352 | double beta = b[ b.size()-1 ];
| ^~~~
profile.cpp:390:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
390 | for (int s=0; s<snpset.size(); s++)
| ~^~~~~~~~~~~~~~
profile.cpp:402:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
402 | for (int s=0; s<snpset.size(); s++)
| ~^~~~~~~~~~~~~~
profile.cpp:421:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
421 | if ( qcnt == qlabel.size() )
| ~~~~~^~~~~~~~~~~~~~~~
profile.cpp: In member function ‘void Plink::calculateProfile(std::map<int, double>&, std::map<int, bool>&, vector_t&, matrix_t&, std::vector<int>&, std::vector<int>&)’:
profile.cpp:480:16: warning: unused variable ‘a1’ [-Wunused-variable]
480 | bool a1 = i2->second;
| ^~
profile.cpp:525:16: warning: variable ‘sawNamedAllele’ set but not used [-Wunused-but-set-variable]
525 | bool sawNamedAllele = false;
| ^~~~~~~~~~~~~~
profile.cpp:629:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
629 | for (int j=0; j<snpset.size(); j++)
| ~^~~~~~~~~~~~~~
profile.cpp: In function ‘void scoreRanges(int, std::vector<int>&, std::map<int, std::set<Range*> >&, std::map<Range*, int>&, std::ofstream&)’:
profile.cpp:667:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
667 | for (int l=0; l<f.size(); l++)
| ~^~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nlist.cpp
In file included from helper.h:24,
from nlist.h:21,
from nlist.cpp:17:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
nlist.cpp: In member function ‘std::vector<int> NList::deparseNumberList(std::string)’:
nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
38 | for (int i=0; i<tok.size(); i++)
| ~^~~~~~~~~~~
nlist.cpp: In member function ‘std::vector<int> NList::deparseStringList(std::string, std::map<std::__cxx11::basic_string<char>, int>*)’:
nlist.cpp:83:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
83 | for (int i=0; i<tok.size(); i++)
| ~^~~~~~~~~~~
nlist.cpp: In member function ‘std::vector<int> NList::expandNumberList(std::vector<int>&)’:
nlist.cpp:107:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
107 | for (int i=0; i<nlist.size(); i++)
| ~^~~~~~~~~~~~~
nlist.cpp:124:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
124 | for (int i=0; i<nlist.size(); i++)
| ~^~~~~~~~~~~~~
nlist.cpp:151:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
151 | for (int i=0; i<n.size(); i++)
| ~^~~~~~~~~
nlist.cpp:160:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
160 | for (int i=0; i<n.size(); i++)
| ~^~~~~~~~~
nlist.cpp: In member function ‘std::vector<std::__cxx11::basic_string<char> > NList::tokenize(std::string)’:
nlist.cpp:189:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
189 | for (int i=0; i<s.length(); i++)
| ~^~~~~~~~~~~
nlist.cpp:239:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
239 | if ( s[i]== range_char && i == s.length()-1 )
| ~~^~~~~~~~~~~~~~~
nlist.cpp:253:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
253 | else if ( i == s.length()-1 )
| ~~^~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c whap.cpp
In file included from helper.h:24,
from whap.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from whap.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
whap.cpp: In member function ‘vector_t Plink::conditionalHaplotypeTest(bool, Perm&)’:
whap.cpp:334:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
334 | for (int g = 0; g < nullModel.group.size(); g++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
whap.cpp:393:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
393 | for (int g=0; g<subnullModel.group.size(); g++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~
whap.cpp:454:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
454 | for (int h=0; h<coeff1.size(); h++)
| ~^~~~~~~~~~~~~~
whap.cpp:456:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
456 | for (int h=0; h<coeff0.size(); h++)
| ~^~~~~~~~~~~~~~
whap.cpp:508:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
508 | for ( int g=0; g<nullModel.group.size(); g++ )
| ~^~~~~~~~~~~~~~~~~~~~~~~
whap.cpp:511:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
511 | for ( int g2=0; g2<alternateModel.group.size(); g2++ )
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
whap.cpp:619:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
619 | if ( g < nullModel.group.size() - 1 )
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
whap.cpp:670:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
670 | for (int s=0; s < conditioner.size(); s++)
| ~~^~~~~~~~~~~~~~~~~~~~
whap.cpp:793:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
793 | if ( p1 != coeff1.size() || p0 != coeff0.size() )
| ~~~^~~~~~~~~~~~~~~~
whap.cpp:793:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
793 | if ( p1 != coeff1.size() || p0 != coeff0.size() )
| ~~~^~~~~~~~~~~~~~~~
whap.cpp: In member function ‘void Chap::build(ChapModel&)’:
whap.cpp:962:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
962 | for (int h=0; h<tok.size(); h++)
| ~^~~~~~~~~~~
whap.cpp:986:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
986 | for (int i=0; i<tok.size(); i++)
| ~^~~~~~~~~~~
whap.cpp:1015:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1015 | for (int i=0; i< tok.size(); i++)
| ~^~~~~~~~~~~~
whap.cpp:1048:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1048 | for ( int i = 0 ; i < tok.size() ; i++ )
| ~~^~~~~~~~~~~~
whap.cpp:1118:27: warning: comparison of integer expressions of different signedness: ‘std::map<std::__cxx11::basic_string<char>, int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
1118 | if ( mapping.size() != H->ns + H->nh )
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
whap.cpp:1129:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1129 | for (int i=0; i< lst.size(); i++)
| ~^~~~~~~~~~~~
whap.cpp:1142:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1142 | for (int i=0; i<lst.size(); i++)
| ~^~~~~~~~~~~
whap.cpp:1162:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1162 | for (int i=0; i<lst.size(); i++)
| ~^~~~~~~~~~~
whap.cpp:1197:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1197 | for (int i=0; i<snplist.size(); i++)
| ~^~~~~~~~~~~~~~~
whap.cpp:1231:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1231 | for (int i=0; i<lst.size(); i++)
| ~^~~~~~~~~~~
whap.cpp:1290:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1290 | for (int g=0; g< model.group.size(); g++)
| ~^~~~~~~~~~~~~~~~~~~~
whap.cpp:1326:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1326 | for (int c=0; c < P->conditioner.size(); c++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~
whap.cpp:1334:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1334 | for (int l=0; l<lst.size(); l++)
| ~^~~~~~~~~~~
whap.cpp: In member function ‘void Chap::setSNPList(std::vector<int>&, ChapModel&)’:
whap.cpp:1389:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1389 | for (int l=0;l<snplist.size(); l++)
| ~^~~~~~~~~~~~~~~
whap.cpp: In function ‘void displayHaploGroups(std::ofstream&, ChapModel&, HaploPhase*)’:
whap.cpp:1425:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1425 | for (int h=0; h < m.group.size(); h++)
| ~~^~~~~~~~~~~~~~~~
whap.cpp:1434:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::set<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1434 | if ( cnt>0 && cnt2 < m.group[h].size() )
| ~~~~~^~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c simul.cpp
In file included from helper.h:24,
from simul.cpp:16:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
simul.cpp: In function ‘vector_t instanceSNP(SimParameters&)’:
simul.cpp:172:10: warning: unused variable ‘gh_11_12’ [-Wunused-variable]
172 | double gh_11_12 = h11*h12;
| ^~~~~~~~
simul.cpp: In member function ‘void Plink::simulateSNPs()’:
simul.cpp:635:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimParameters>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
635 | for (int s=0; s<sp.size(); s++)
| ~^~~~~~~~~~
simul.cpp:679:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimParameters>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
679 | for (int s=0; s<sp.size(); s++)
| ~^~~~~~~~~~
simul.cpp: In member function ‘void Plink::simulateSNPs_QT()’:
simul.cpp:1146:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimParametersQT>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1146 | for (int s=0; s<sp.size(); s++)
| ~^~~~~~~~~~
simul.cpp:1211:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimParametersQT>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1211 | for (int s=0; s<sp.size(); s++)
| ~^~~~~~~~~~
simul.cpp:1358:30: warning: unused variable ‘cumU’ [-Wunused-variable]
1358 | double cumA = 0, cumU = 0;
| ^~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gvar.cpp
In file included from helper.h:24,
from gvar.cpp:15:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
gvar.cpp: In member function ‘void Plink::readGenericVariantData()’:
gvar.cpp:125:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
125 | for (int l=0; l<locus.size(); l++)
| ~^~~~~~~~~~~~~
gvar.cpp:192:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
192 | for (int l=0; l<locus.size(); l++)
| ~^~~~~~~~~~~~~
gvar.cpp:247:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
247 | for (int i=0; i<sample.size(); i++)
| ~^~~~~~~~~~~~~~
gvar.cpp:298:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
298 | for (int i=0; i<sample.size(); i++)
| ~^~~~~~~~~~~~~~
gvar.cpp:381:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
381 | for (int i=0; i<include.size(); i++)
| ~^~~~~~~~~~~~~~~
gvar.cpp:395:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
395 | for (int i=0; i<include.size(); i++)
| ~^~~~~~~~~~~~~~~
gvar.cpp:403:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
403 | for (int i=0; i<sample.size(); i++)
| ~^~~~~~~~~~~~~~
gvar.cpp:471:11: warning: unused variable ‘ip’ [-Wunused-variable]
471 | int ip = peri->second;
| ^~
gvar.cpp:414:8: warning: unused variable ‘fatal’ [-Wunused-variable]
414 | bool fatal = false;
| ^~~~~
gvar.cpp:549:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
549 | for (int l=0; l<locus.size(); l++)
| ~^~~~~~~~~~~~~
gvar.cpp:553:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CSNP*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
553 | for (int l=0; l<SNP.size(); l++)
| ~^~~~~~~~~~~
gvar.cpp:556:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
556 | for (int i=0; i<sample.size(); i++)
| ~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnv.cpp
In file included from helper.h:24,
from cnv.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
cnv.cpp: In member function ‘void Plink::readCNVList()’:
cnv.cpp:247:15: warning: unused variable ‘p1’ [-Wunused-variable]
247 | int p1,p2;
| ^~
cnv.cpp:247:18: warning: unused variable ‘p2’ [-Wunused-variable]
247 | int p1,p2;
| ^~
cnv.cpp:332:19: warning: unused variable ‘p1’ [-Wunused-variable]
332 | int p1,p2;
| ^~
cnv.cpp:332:22: warning: unused variable ‘p2’ [-Wunused-variable]
332 | int p1,p2;
| ^~
cnv.cpp:678:43: warning: variable ‘is’ set but not used [-Wunused-but-set-variable]
678 | map<Range,string>::iterator is = idescription.find(*ir);
| ^~
cnv.cpp:815:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Segment>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
815 | for (int s1=0; s1<segment.size(); s1++)
| ~~^~~~~~~~~~~~~~~
cnv.cpp:825:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Segment>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
825 | for (int s2=s1+1; s2<segment.size(); s2++)
| ~~^~~~~~~~~~~~~~~
cnv.cpp:916:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
916 | if ( par::cnv_freq_include )
| ^~
cnv.cpp:922:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
922 | isection.clear();
| ^~~~~~~~
cnv.cpp:1031:32: warning: variable ‘i2’ set but not used [-Wunused-but-set-variable]
1031 | set<Range>::iterator i2 = isection.begin();
| ^~
cnv.cpp:1103:43: warning: variable ‘il’ set but not used [-Wunused-but-set-variable]
1103 | map<indivPair,double>::iterator il = segmentLength.find(t);
| ^~
cnv.cpp:1414:11: warning: unused variable ‘nseg’ [-Wunused-variable]
1414 | int nseg = 1;
| ^~~~
cnv.cpp:412:7: warning: unused variable ‘nseg’ [-Wunused-variable]
412 | int nseg=0;
| ^~~~
cnv.cpp: In function ‘double weighted_count_intersects(std::set<Range>&, int, int, int)’:
cnv.cpp:1749:7: warning: unused variable ‘cnt’ [-Wunused-variable]
1749 | int cnt = 0;
| ^~~
cnv.cpp: In member function ‘void Plink::positionPermuteSegments()’:
cnv.cpp:2013:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<int, CInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2013 | for (int c = 0 ; c < scaffold.size(); c++)
| ~~^~~~~~~~~~~~~~~~~
cnv.cpp: In member function ‘vector_t Plink::glmCNVBurdenModel(Perm&, bool)’:
cnv.cpp:2098:13: warning: statement has no effect [-Wunused-value]
2098 | noCovar == true;
| ~~~~~~~~^~~~~~~
cnv.cpp:2202:17: warning: variable ‘p’ set but not used [-Wunused-but-set-variable]
2202 | indivPair p = ic->first;
| ^
cnv.cpp:2288:10: warning: unused variable ‘statistic’ [-Wunused-variable]
2288 | double statistic = valid ? model->getStatistic() : 0;
| ^~~~~~~~~
cnv.cpp:2289:10: warning: unused variable ‘pvalue’ [-Wunused-variable]
2289 | double pvalue = pval[ pval.size()-1 ];
| ^~~~~~
cnv.cpp:2290:10: warning: unused variable ‘beta’ [-Wunused-variable]
2290 | double beta = b[ b.size()-1 ];
| ^~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c step.cpp
In file included from helper.h:24,
from step.cpp:18:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c greport.cpp
In file included from greport.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
greport.cpp: In member function ‘void Plink::displayGeneReport()’:
greport.cpp:78:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
78 | for (int i=0; i<tokens.size(); i++)
| ~^~~~~~~~~~~~~~
greport.cpp:147:26: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
147 | if ( tokens.size() <= chr_column ||
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~
greport.cpp:148:26: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
148 | tokens.size() <= bp_column )
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
greport.cpp:156:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
156 | if ( tokens.size() <= pval_column )
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
greport.cpp:169:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
169 | if ( tokens.size() <= snp_column )
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~
greport.cpp:240:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
240 | for (int l=0; l< ari->second.size(); l+=2)
| ~^~~~~~~~~~~~~~~~~~~~
greport.cpp:125:7: warning: unused variable ‘cnt’ [-Wunused-variable]
125 | int cnt = 0;
| ^~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c flip.cpp
In file included from helper.h:24,
from flip.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qualscores.cpp
In file included from helper.h:24,
from qualscores.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
qualscores.cpp: In member function ‘void Plink::filterQualGenotypes()’:
qualscores.cpp:122:12: warning: unused variable ‘nfound’ [-Wunused-variable]
122 | long int nfound = 0;
| ^~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnvqt.cpp
In file included from helper.h:24,
from cnvqt.cpp:22:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp
In file included from cfamily.cpp:18:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
cfamily.cpp: In function ‘int mCount(Individual*, Individual*)’:
cfamily.cpp:205:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
205 | for (int i = 0 ; i < inds.size() ; i++)
| ~~^~~~~~~~~~~~~
cfamily.cpp:221:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
221 | for (int j = 0 ; j < inds[i]->kids.size() ; j++)
| ~~^~~~~~~~~~~~~~~~~~~~~~
cfamily.cpp:237:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
237 | for (int i = 0 ; i < inds.size() ; i++)
| ~~^~~~~~~~~~~~~
cfamily.cpp: In function ‘bool isAncestorOf(Individual*, Individual*)’:
cfamily.cpp:263:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
263 | for (int i = 0 ; i < inds.size() ; i++)
| ~~^~~~~~~~~~~~~
cfamily.cpp:276:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
276 | for (int j = 0 ; j < inds[i]->kids.size() ; j++)
| ~~^~~~~~~~~~~~~~~~~~~~~~
cfamily.cpp:288:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
288 | for (int i = 0 ; i < inds.size() ; i++)
| ~~^~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c setscreen.cpp
In file included from setscreen.cpp:21:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
setscreen.cpp: In member function ‘void Plink::setAssocSummary()’:
setscreen.cpp:80:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
80 | for (int i=0; i<tokens.size(); i++)
| ~^~~~~~~~~~~~~~
setscreen.cpp:110:26: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
110 | if ( tokens.size() != cols )
| ~~~~~~~~~~~~~~^~~~~~~
setscreen.cpp:188:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
188 | for ( int j = 0; j < pS->snpset.size(); j++ )
| ~~^~~~~~~~~~~~~~~~~~~
setscreen.cpp:196:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
196 | for (int i=0; i < snpset[j].size(); i++)
| ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c idhelp.cpp
In file included from idhelp.cpp:18:
idhelp.h: In member function ‘void IDGroup::display()’:
idhelp.h:196:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
196 | for (int k=0; k<values.size(); k++)
| ~^~~~~~~~~~~~~~
In file included from idhelp.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
idhelp.cpp: In member function ‘std::map<IDField*, std::set<IDValue> > IDHelper::parseQuery(std::string)’:
idhelp.cpp:40:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
40 | for ( int i = 0 ; i < ids.size() ; i++)
| ~~^~~~~~~~~~~~
idhelp.cpp:63:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
63 | for (int i=0; i<flist.size(); i++)
| ~^~~~~~~~~~~~~
idhelp.cpp: In member function ‘bool IDHelper::matchIndividual(IDGroup*, std::map<IDField*, std::set<IDValue> >&)’:
idhelp.cpp:136:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
136 | for (int g=0; g<group->values.size(); g++)
| ~^~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:169:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<IDField*, std::set<IDValue> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
169 | if ( found != matchTemplate.size() )
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:128:8: warning: unused variable ‘match’ [-Wunused-variable]
128 | bool match = true;
| ^~~~~
idhelp.cpp: In member function ‘void IDHelper::setJointValues(IDGroup*)’:
idhelp.cpp:210:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<IDField*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
210 | for (int j = 0 ; j < jointField.size(); j++ )
| ~~^~~~~~~~~~~~~~~~~~~
idhelp.cpp:221:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
221 | for (int j = 0 ; j < group->values.size(); j++)
| ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:296:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
296 | for ( int i = 0 ; i < mask.size() ; i++)
| ~~^~~~~~~~~~~~~
idhelp.cpp:214:26: warning: unused variable ‘jo’ [-Wunused-variable]
214 | vector<IDField*> & jo = jointOrder[j];
| ^~
idhelp.cpp: In member function ‘std::set<IDGroup*> IDHelper::findAllIndividuals(std::map<IDField*, std::set<IDValue> >&)’:
idhelp.cpp:346:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
346 | for ( int g = 0 ; g < idgroup.size(); g++ )
| ~~^~~~~~~~~~~~~~~~
idhelp.cpp: In member function ‘void IDHelper::idHelp()’:
idhelp.cpp:502:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
502 | if ( ++p == tokens.size() )
| ~~~~^~~~~~~~~~~~~~~~
idhelp.cpp:510:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
510 | if ( p < tokens.size() )
| ~~^~~~~~~~~~~~~~~
idhelp.cpp:542:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
542 | for (int i = 0 ; i < ids.size() ; i++)
| ~~^~~~~~~~~~~~
idhelp.cpp:547:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
547 | for (int i = 0 ; i < ids.size() ; i++)
| ~~^~~~~~~~~~~~
idhelp.cpp:553:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
553 | for (int i = 0 ; i < ids.size() ; i++)
| ~~^~~~~~~~~~~~
idhelp.cpp:529:24: warning: unused variable ‘seenJoint’ [-Wunused-variable]
529 | bool seenJoint = true;
| ^~~~~~~~~
idhelp.cpp:584:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
584 | for (int i = 0 ; i < ids.size() ; i++)
| ~~^~~~~~~~~~~~
idhelp.cpp:594:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
594 | for (int i = 0 ; i < ids.size() ; i++)
| ~~^~~~~~~~~~~~
idhelp.cpp:678:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
678 | if ( ++p == tokens.size() )
| ~~~~^~~~~~~~~~~~~~~~
idhelp.cpp:727:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDFile>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
727 | for ( int f = 0 ; f < files.size() ; f++ )
| ~~^~~~~~~~~~~~~~
idhelp.cpp:742:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<IDField*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
742 | for (int j = 0 ; j < jointField.size(); j++ )
| ~~^~~~~~~~~~~~~~~~~~~
idhelp.cpp:745:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDFile>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
745 | for ( int f = 0 ; f < files.size() ; f++ )
| ~~^~~~~~~~~~~~~~
idhelp.cpp:747:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDField*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
747 | for ( int j = 0; j < files[f].fields.size(); j++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:757:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDField*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
757 | for ( int j = 0; j < files[f].fields.size(); j++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:744:23: warning: unused variable ‘jf’ [-Wunused-variable]
744 | set<IDField*> & jf = jointField[j];
| ^~
idhelp.cpp:772:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<IDField*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
772 | for (int j = 0 ; j < jointField.size(); j++ )
| ~~^~~~~~~~~~~~~~~~~~~
idhelp.cpp:790:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDFile>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
790 | for ( int f = 0 ; f < files.size() ; f++ )
| ~~^~~~~~~~~~~~~~
idhelp.cpp:794:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDField*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
794 | for ( int j = 0 ; j < files[f].fields.size(); j++ )
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:808:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDField*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
808 | for ( int j = 0 ; j < files[f].fields.size(); j++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:836:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
836 | for (int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
idhelp.cpp:888:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
888 | if ( tokens.size() != file->uniqFieldCount )
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:894:38: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
894 | int mx = tokens.size() > file->uniqFieldCount ? tokens.size() : file->uniqFieldCount ;
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:903:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
903 | if ( j < tokens.size() )
| ~~^~~~~~~~~~~~~~~
idhelp.cpp:922:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDField*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
922 | for ( int j = 0 ; j < files[f].fields.size(); j++ )
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:950:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
950 | for ( int i=0; i<atoken.size(); i++)
| ~^~~~~~~~~~~~~~
idhelp.cpp:975:44: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
975 | if ( v->value.size() + 3 > myField->width )
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
idhelp.cpp:1000:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1000 | for ( int g = 0 ; g < idgroup.size(); g++ )
| ~~^~~~~~~~~~~~~~~~
idhelp.cpp:1003:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1003 | for (int j = 0 ; j < group->values.size(); j++)
| ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1013:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1013 | for ( int g = 0 ; g < idgroup.size(); g++ )
| ~~^~~~~~~~~~~~~~~~
idhelp.cpp:1015:17: warning: unused variable ‘group’ [-Wunused-variable]
1015 | IDGroup * group = idgroup[g];
| ^~~~~
idhelp.cpp:1025:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1025 | for ( int g = 0 ; g < idgroup.size(); g++ )
| ~~^~~~~~~~~~~~~~~~
idhelp.cpp:1028:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1028 | for (int j = 0 ; j < group->values.size(); j++)
| ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1031:21: warning: unused variable ‘v’ [-Wunused-variable]
1031 | IDValue & v = *(group->values[j]);
| ^
idhelp.cpp:1070:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1070 | for ( int g = 0 ; g < idgroup.size(); g++ )
| ~~^~~~~~~~~~~~~~~~
idhelp.cpp:1085:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1085 | for (int j = 0 ; j < group->values.size(); j++)
| ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1110:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1110 | for ( int j = 0; j < group->values.size(); j++ )
| ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1128:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1128 | for ( int k = 0; k < (*i0)->values.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1183:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1183 | for (int z=0; z<group->values.size(); z++)
| ~^~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1189:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1189 | for (int z=0; z<(*i0)->values.size(); z++)
| ~^~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1236:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1236 | for ( int g = 0 ; g < idgroup.size(); g++ )
| ~~^~~~~~~~~~~~~~~~
idhelp.cpp:1242:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1242 | for (int j = 0 ; j < group->values.size(); j++)
| ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1245:21: warning: unused variable ‘v’ [-Wunused-variable]
1245 | IDValue & v = *(group->values[j]);
| ^
idhelp.cpp:1346:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1346 | for (int i=0; i<ids.size(); i++)
| ~^~~~~~~~~~~
idhelp.cpp:1424:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1424 | for ( int g = 0 ; g < idgroup.size(); g++ )
| ~~^~~~~~~~~~~~~~~~
idhelp.cpp:1440:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1440 | for ( int j = 0; j < group->values.size(); j++ )
| ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp: In member function ‘void IDHelper::idReplace()’:
idhelp.cpp:1551:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1551 | for ( int i=0; i<targetFields.size(); i++)
| ~^~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1631:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1631 | for (int i=0; i<ids.size(); i++)
| ~^~~~~~~~~~~
idhelp.cpp:1648:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1648 | for (int f = 0 ; f < targetFields.size(); f++)
| ~~^~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1649:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1649 | for (int i = 0 ; i < tokens.size(); i++)
| ~~^~~~~~~~~~~~~~~
idhelp.cpp:1654:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1654 | for (int i=0; i<rep_field.size(); i++)
| ~^~~~~~~~~~~~~~~~~
idhelp.cpp:1675:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1675 | for (int i=0; i<rep_field.size(); i++)
| ~^~~~~~~~~~~~~~~~~
idhelp.cpp:1684:26: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
1684 | if ( tokens.size() <= maxfield )
| ~~~~~~~~~~~~~~^~~~~~~~~~~
idhelp.cpp:1692:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1692 | for (int i=0; i<rep_field.size(); i++)
| ~^~~~~~~~~~~~~~~~~
idhelp.cpp:1710:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1710 | for (int i=0; i<rep_field.size(); i++)
| ~^~~~~~~~~~~~~~~~~
idhelp.cpp:1733:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1733 | for (int f=0; f<targetFields.size(); f++)
| ~^~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1735:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1735 | for (int i = 0 ; i < thisGroup->values.size(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1770:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1770 | for (int i=0; i<rep_field.size(); i++)
| ~^~~~~~~~~~~~~~~~~
idhelp.cpp:1784:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1784 | for (int f=0; f<targetFields.size(); f++)
| ~^~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1801:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1801 | for (int i = 0 ; i < tokens.size() ; i++ )
| ~~^~~~~~~~~~~~~~~
idhelp.cpp: In member function ‘void IDHelper::idMatch()’:
idhelp.cpp:1856:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1856 | for (int s=0; s< par::idhelp_match_string.size(); s+=2)
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1903:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1903 | for (int i=0; i<fstr.size(); i++)
| ~^~~~~~~~~~~~
idhelp.cpp:1937:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1937 | for (int k=0; k<h.size(); k++)
| ~^~~~~~~~~
idhelp.cpp:1957:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1957 | for (int f = 0; f<fieldNames.size(); f++)
| ~^~~~~~~~~~~~~~~~~~
idhelp.cpp:1964:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1964 | for (int i=0; i<header.size(); i++)
| ~^~~~~~~~~~~~~~
idhelp.cpp:1986:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1986 | for (int f = 0 ; f < fieldNames.size(); f++)
| ~~^~~~~~~~~~~~~~~~~~~
idhelp.cpp:2018:29: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’} [-Wsign-compare]
2018 | if ( tok.size() != tableSize[t] )
idhelp.cpp:2024:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2024 | for (int k=0; k<tok.size(); k++)
| ~^~~~~~~~~~~
idhelp.cpp:2030:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2030 | if ( maxF >= tok.size() )
| ~~~~~^~~~~~~~~~~~~
idhelp.cpp:2034:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2034 | for (int f=0; f<fieldCodes.size(); f++)
| ~^~~~~~~~~~~~~~~~~~
idhelp.cpp:2070:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2070 | for (int v=0; v<g->values.size(); v++)
| ~^~~~~~~~~~~~~~~~~
idhelp.cpp:1889:12: warning: unused variable ‘jointQuery’ [-Wunused-variable]
1889 | bool jointQuery = id.find("+") != string::npos;
| ^~~~~~~~~~
idhelp.cpp:2167:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2167 | for (int k=0; k<headers.size(); k++)
| ~^~~~~~~~~~~~~~~
idhelp.cpp:2168:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2168 | for (int j=0; j<headers[k].size(); j++)
| ~^~~~~~~~~~~~~~~~~~
idhelp.cpp:2201:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2201 | for (int k = 0 ; k < thisLine.size() ; k++ )
| ~~^~~~~~~~~~~~~~~~~
idhelp.cpp: In member function ‘void IDHelper::idDump()’:
idhelp.cpp:2229:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2229 | for ( int g = 0 ; g < idgroup.size(); g++ )
| ~~^~~~~~~~~~~~~~~~
idhelp.cpp:2234:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2234 | for (int j = 0 ; j < group->values.size(); j++ )
| ~~^~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tag.cpp
In file included from helper.h:24,
from tag.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hapglm.cpp
In file included from helper.h:24,
from hapglm.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from hapglm.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup2.cpp
In file included from helper.h:24,
from lookup2.cpp:18:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
lookup2.cpp: In member function ‘void Plink::lookup2()’:
lookup2.cpp:163:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
163 | for (int i = 0 ; i < ids.size(); i++)
| ~~^~~~~~~~~~~~
lookup2.cpp:203:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
203 | for (int i = 0 ; i < ids.size(); i++)
| ~~^~~~~~~~~~~~
lookup2.cpp:280:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
280 | for (int i = 0 ; i < ids.size(); i++)
| ~~^~~~~~~~~~~~
lookup2.cpp:325:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
325 | for (int t = 0 ; t < tokens.size() ; t++)
| ~~^~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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;
| ^~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zed.cpp
In file included from helper.h:24,
from zed.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dosage.cpp
In file included from dosage.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
In file included from dosage.cpp:23:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int i=0; i<hap.size(); i++)
| ~^~~~~~~~~~~
dosage.cpp: In member function ‘void Plink::processDosageFile()’:
dosage.cpp:110:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double2>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
110 | for ( int q = 0 ; q < qthresh.size() ; q++)
| ~~^~~~~~~~~~~~~~~~
dosage.cpp:513:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
513 | for (int i=0; i<dosageFilename_all.size(); i++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~
dosage.cpp:548:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ZInput*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
548 | for (int f = 0 ; f < vzin.size() ; f++ )
| ~~^~~~~~~~~~~~~
dosage.cpp:581:27: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
581 | if ( tok.size() < firstCol )
| ~~~~~~~~~~~^~~~~~~~~~
dosage.cpp:601:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
601 | for (int i=firstCol; i<tok.size(); i+= 2 )
| ~^~~~~~~~~~~
dosage.cpp:695:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
695 | for (int i = 0; i < personMap[f].size(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~
dosage.cpp:750:31: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’} [-Wsign-compare]
750 | if ( tok.size() != expected[f] )
dosage.cpp:989:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
989 | for (int q=0; q<inQ.size(); q++)
| ~^~~~~~~~~~~
dosage.cpp:1170:18: warning: unused variable ‘statistic’ [-Wunused-variable]
1170 | double statistic = valid ? model->getStatistic() : 0;
| ^~~~~~~~~
dosage.cpp:1252:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1252 | if ( o->second != dosageFilename_all.size() )
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
dosage.cpp:1310:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double2>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1310 | if ( ++qq == qthresh.size() )
| ~~~~~^~~~~~~~~~~~~~~~~
dosage.cpp:190:7: warning: unused variable ‘geno_field’ [-Wunused-variable]
190 | int geno_field = a2_field + skip2 + 1;
| ^~~~~~~~~~
In file included from /usr/aarch64-linux-gnu/include/c++/14/vector:66,
from options.h:18:
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = CSNP*; _Alloc = std::allocator<CSNP*>]’,
inlined from ‘void Plink::processDosageFile()’ at dosage.cpp:915:21:
/usr/aarch64-linux-gnu/include/c++/14/bits/stl_vector.h:1131:41: warning: ‘snp_code’ may be used uninitialized [-Wmaybe-uninitialized]
1131 | return *(this->_M_impl._M_start + __n);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
dosage.cpp: In member function ‘void Plink::processDosageFile()’:
dosage.cpp:725:15: note: ‘snp_code’ was declared here
725 | int snp_code;
| ^~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c annot.cpp
In file included from annot.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
annot.cpp: In member function ‘void Plink::annotateFile()’:
annot.cpp:83:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
83 | for (int j=1; j<tok.size(); j++)
| ~^~~~~~~~~~~
annot.cpp:149:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
149 | for (int i=0; i<tokens.size(); i++)
| ~^~~~~~~~~~~~~~
annot.cpp:250:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
250 | if ( tokens.size() <= chr_column ||
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~
annot.cpp:251:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
251 | tokens.size() <= bp_column )
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
annot.cpp:260:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
260 | if ( tokens.size() <= pval_column )
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
annot.cpp:275:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
275 | if ( tokens.size() <= snp_column )
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~
annot.cpp:300:16: warning: unused variable ‘include’ [-Wunused-variable]
300 | bool include = false;
| ^~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.cpp
In file included from metaanal.cpp:21:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for ( int k = 0 ; k < i->second.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~
metaanal.cpp: In constructor ‘Alleles::Alleles(std::string, int, int, std::string, std::string)’:
metaanal.cpp:47:7: warning: ‘Alleles::bp’ will be initialized after [-Wreorder]
47 | int bp;
| ^~
metaanal.cpp:44:10: warning: ‘std::string Alleles::a1’ [-Wreorder]
44 | string a1;
| ^~
metaanal.cpp:61:3: warning: when initialized here [-Wreorder]
61 | Alleles(string name, int chr, int bp, string a1, string a2)
| ^~~~~~~
metaanal.cpp: In member function ‘void Plink::metaAnalysis()’:
metaanal.cpp:159:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
159 | for (int f=0; f<ns.size(); f++)
| ~^~~~~~~~~~
metaanal.cpp:182:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
182 | for (int f=0; f<ns.size(); f++)
| ~^~~~~~~~~~
metaanal.cpp:203:18: warning: statement has no effect [-Wunused-value]
203 | par::run_chr == -1;
| ~~~~~~~~~~~~~^~~~~
metaanal.cpp:213:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
213 | for (int i=0; i<tok.size(); i++)
| ~^~~~~~~~~~~
metaanal.cpp:235:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
235 | for (int f = 0 ; f < par::meta_files.size() ; f++ )
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
metaanal.cpp:261:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
261 | for (int i=0; i<tokens.size(); i++)
| ~^~~~~~~~~~~~~~
metaanal.cpp:300:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
300 | if ( tokens.size() != fsize )
| ~~~~~~~~~~~~~~^~~~~~~~
metaanal.cpp:253:11: warning: variable ‘pval_column’ set but not used [-Wunused-but-set-variable]
253 | int pval_column = -1;
| ^~~~~~~~~~~
metaanal.cpp:482:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
482 | for (int f=0; f<par::meta_files.size(); f++)
| ~^~~~~~~~~~~~~~~~~~~~~~~
metaanal.cpp:637:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
637 | for (int f=0; f<par::meta_files.size(); f++)
| ~^~~~~~~~~~~~~~~~~~~~~~~
metaanal.cpp:680:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
680 | for (int f=0; f<par::meta_files.size(); f++)
| ~^~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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;
| ^~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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;
| ^~~~
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp
aarch64-linux-gnu-g++ -Wall -g -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.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_arm64.deb'.
dpkg-deb: building package 'plink-dbgsym' in '../plink-dbgsym_1.07+dfsg-4_arm64.deb'.
dpkg-genbuildinfo --build=any -O../plink_1.07+dfsg-4_arm64.buildinfo
dpkg-genchanges --build=any -O../plink_1.07+dfsg-4_arm64.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2025-03-13T22:00:36Z
+------------------------------------------------------------------------------+
| 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_arm64.changes:
--------------------------------
Format: 1.8
Date: Sun, 31 Oct 2021 21:01:46 +0530
Source: plink
Binary: plink plink-dbgsym
Built-For-Profiles: cross nocheck
Architecture: arm64
Version: 1.07+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Description:
plink - whole-genome association analysis toolset
Closes: 984293
Changes:
plink (1.07+dfsg-4) unstable; urgency=medium
.
* Team upload.
* Add patch to fix FTBFS with gcc-11 (Closes: #984293)
* Bump Standards-Version to 4.6.0 (no changes needed)
* Bump debhelper compatibility level to 13
* Replace ADTTMP with AUTOPKGTEST_TMP
* Add "Rules-Requires-Root: no"
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Build-Origin: Debian
Build-Architecture: amd64
Build-Date: Thu, 13 Mar 2025 22:00:35 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.72-3),
automake (= 1:1.17-3),
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autotools-dev (= 20220109.1),
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cpp-14-x86-64-linux-gnu (= 14.2.0-18),
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diffutils (= 1:3.10-2),
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g++-14 (= 14.2.0-18),
g++-14-x86-64-linux-gnu (= 14.2.0-18),
g++-x86-64-linux-gnu (= 4:14.2.0-1),
gcc (= 4:14.2.0-1),
gcc-14 (= 14.2.0-18),
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gcc-14-x86-64-linux-gnu (= 14.2.0-18),
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perl (= 5.40.1-2),
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rpcsvc-proto (= 1.4.3-1),
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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_arm64.deb
----------------------------------
new Debian package, version 2.0.
size 25079576 bytes: control archive=536 bytes.
372 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: plink-dbgsym
Source: plink
Version: 1.07+dfsg-4
Auto-Built-Package: debug-symbols
Architecture: arm64
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 28088
Depends: plink (= 1.07+dfsg-4)
Section: debug
Priority: optional
Description: debug symbols for plink
Build-Ids: 355315a4e84d7d0770cc3031434038f5a17798ec
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/35/
-rw-r--r-- root/root 28751680 2021-10-31 15:31 ./usr/lib/debug/.build-id/35/5315a4e84d7d0770cc3031434038f5a17798ec.debug
drwxr-xr-x root/root 0 2021-10-31 15:31 ./usr/share/
drwxr-xr-x root/root 0 2021-10-31 15:31 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-31 15:31 ./usr/share/doc/plink-dbgsym -> plink
plink_1.07+dfsg-4_arm64.deb
---------------------------
new Debian package, version 2.0.
size 1107588 bytes: control archive=1300 bytes.
1096 bytes, 26 lines control
915 bytes, 13 lines md5sums
Package: plink
Version: 1.07+dfsg-4
Architecture: arm64
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3379
Depends: libc6 (>= 2.38), libcrypt1 (>= 1:4.1.0), libgcc-s1 (>= 3.0), 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 3412120 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/
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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 [1308 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [1387 B]
Fetched 3310 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...
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libb-hooks-op-check-perl libberkeleydb-perl libbrotli1 libcapture-tiny-perl
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libcurl3t64-gnutls libdata-dpath-perl libdata-messagepack-perl
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libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl
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libgnutls30t64 libgpg-error0 libgssapi-krb5-2 libhtml-form-perl
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apt-config-icons isoquery libxml-parser-perl rng-tools low-memory-monitor
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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 libgpg-error-l10n
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
libcom-err2 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
libffi8 libfile-basedir-perl libfile-find-rule-perl libfile-listing-perl
libfile-sharedir-perl libfont-ttf-perl libgcrypt20 libglib2.0-0t64
libgnutls30t64 libgpg-error0 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 libidn2-0
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
libldap2 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 libp11-kit0
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 libtasn1-6 libterm-readkey-perl
libtext-charwidth-perl libtext-glob-perl libtext-levenshteinxs-perl
libtext-markdown-discount-perl libtext-wrapi18n-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:arm64 shared-mime-info
t1utils ucf unzip
0 upgraded, 173 newly installed, 0 to remove and 0 not upgraded.
Need to get 23.1 MB of archives.
After this operation, 87.7 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B]
Get:2 http://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+20250216-2 [135 kB]
Get:4 http://localhost:3142/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB]
Get:5 http://localhost:3142/debian unstable/main amd64 procps amd64 2:4.0.4-7 [878 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 3.4.1-1 [1427 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 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B]
Get:10 http://localhost:3142/debian unstable/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B]
Get:11 http://localhost:3142/debian unstable/main amd64 ucf all 3.0050 [42.7 kB]
Get:12 http://localhost:3142/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get:13 http://localhost:3142/debian unstable/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1514 kB]
Get:14 http://localhost:3142/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b2 [760 kB]
Get:15 http://localhost:3142/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB]
Get:16 http://localhost:3142/debian unstable/main amd64 libidn2-0 amd64 2.3.8-1 [109 kB]
Get:17 http://localhost:3142/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get:18 http://localhost:3142/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get:19 http://localhost:3142/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get:20 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB]
Get:21 http://localhost:3142/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get:22 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB]
Get:23 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get:24 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB]
Get:25 http://localhost:3142/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB]
Get:26 http://localhost:3142/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB]
Get:27 http://localhost:3142/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB]
Get:28 http://localhost:3142/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB]
Get:29 http://localhost:3142/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get:30 http://localhost:3142/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB]
Get:31 http://localhost:3142/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB]
Get:32 http://localhost:3142/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB]
Get:33 http://localhost:3142/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get:34 http://localhost:3142/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get:35 http://localhost:3142/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get:36 http://localhost:3142/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.12.1-3 [365 kB]
Get:37 http://localhost:3142/debian unstable/main amd64 libstemmer0d amd64 2.2.0-4+b2 [119 kB]
Get:38 http://localhost:3142/debian unstable/main amd64 libxmlb2 amd64 0.3.21-1 [63.0 kB]
Get:39 http://localhost:3142/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB]
Get:40 http://localhost:3142/debian unstable/main amd64 libappstream5 amd64 1.0.4-1 [225 kB]
Get:41 http://localhost:3142/debian unstable/main amd64 appstream amd64 1.0.4-1 [523 kB]
Get:42 http://localhost:3142/debian unstable/main amd64 diffstat amd64 1.67-1 [35.5 kB]
Get:43 http://localhost:3142/debian unstable/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB]
Get:44 http://localhost:3142/debian unstable/main amd64 libassuan9 amd64 3.0.2-2 [61.5 kB]
Get:45 http://localhost:3142/debian unstable/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB]
Get:46 http://localhost:3142/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get:47 http://localhost:3142/debian unstable/main amd64 gpgconf amd64 2.2.46-5 [122 kB]
Get:48 http://localhost:3142/debian unstable/main amd64 libsqlite3-0 amd64 3.46.1-2 [913 kB]
Get:49 http://localhost:3142/debian unstable/main amd64 gpg amd64 2.2.46-5 [533 kB]
Get:50 http://localhost:3142/debian unstable/main amd64 iso-codes all 4.17.0-1 [3055 kB]
Get:51 http://localhost:3142/debian unstable/main amd64 libaliased-perl all 0.34-3 [13.5 kB]
Get:52 http://localhost:3142/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.41 [68.3 kB]
Get:53 http://localhost:3142/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB]
Get:54 http://localhost:3142/debian unstable/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB]
Get:55 http://localhost:3142/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.2 kB]
Get:56 http://localhost:3142/debian unstable/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB]
Get:57 http://localhost:3142/debian unstable/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get:58 http://localhost:3142/debian unstable/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB]
Get:59 http://localhost:3142/debian unstable/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB]
Get:60 http://localhost:3142/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B]
Get:61 http://localhost:3142/debian unstable/main amd64 libvariable-magic-perl amd64 0.64-1+b1 [44.9 kB]
Get:62 http://localhost:3142/debian unstable/main amd64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB]
Get:63 http://localhost:3142/debian unstable/main amd64 libberkeleydb-perl amd64 0.66-1 [121 kB]
Get:64 http://localhost:3142/debian unstable/main amd64 libcapture-tiny-perl all 0.50-1 [24.6 kB]
Get:65 http://localhost:3142/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB]
Get:66 http://localhost:3142/debian unstable/main amd64 liburi-perl all 5.30-1 [105 kB]
Get:67 http://localhost:3142/debian unstable/main amd64 libhtml-parser-perl amd64 3.83-1+b2 [99.7 kB]
Get:68 http://localhost:3142/debian unstable/main amd64 libcgi-pm-perl all 4.67-1 [217 kB]
Get:69 http://localhost:3142/debian unstable/main amd64 libclass-data-inheritable-perl all 0.10-1 [8632 B]
Get:70 http://localhost:3142/debian unstable/main amd64 libclass-inspector-perl all 1.36-3 [17.5 kB]
Get:71 http://localhost:3142/debian unstable/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB]
Get:72 http://localhost:3142/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b5 [36.1 kB]
Get:73 http://localhost:3142/debian unstable/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB]
Get:74 http://localhost:3142/debian unstable/main amd64 libconfig-tiny-perl all 2.30-1 [18.9 kB]
Get:75 http://localhost:3142/debian unstable/main amd64 libparams-util-perl amd64 1.102-3+b1 [24.4 kB]
Get:76 http://localhost:3142/debian unstable/main amd64 libsub-install-perl all 0.929-1 [10.5 kB]
Get:77 http://localhost:3142/debian unstable/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB]
Get:78 http://localhost:3142/debian unstable/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB]
Get:79 http://localhost:3142/debian unstable/main amd64 libconst-fast-perl all 0.014-2 [8792 B]
Get:80 http://localhost:3142/debian unstable/main amd64 libcpanel-json-xs-perl amd64 4.39-1 [130 kB]
Get:81 http://localhost:3142/debian unstable/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB]
Get:82 http://localhost:3142/debian unstable/main amd64 libexception-class-perl all 1.45-1 [34.6 kB]
Get:83 http://localhost:3142/debian unstable/main amd64 libiterator-perl all 0.03+ds1-2 [18.8 kB]
Get:84 http://localhost:3142/debian unstable/main amd64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB]
Get:85 http://localhost:3142/debian unstable/main amd64 libdata-dpath-perl all 0.60-1 [41.8 kB]
Get:86 http://localhost:3142/debian unstable/main amd64 libdata-messagepack-perl amd64 1.02-1+b4 [32.8 kB]
Get:87 http://localhost:3142/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-4 [31.5 kB]
Get:88 http://localhost:3142/debian unstable/main amd64 libdata-validate-domain-perl all 0.15-1 [11.9 kB]
Get:89 http://localhost:3142/debian unstable/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB]
Get:90 http://localhost:3142/debian unstable/main amd64 libnet-netmask-perl all 2.0002-2 [28.6 kB]
Get:91 http://localhost:3142/debian unstable/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2+b5 [98.1 kB]
Get:92 http://localhost:3142/debian unstable/main amd64 libdata-validate-ip-perl all 0.31-1 [20.6 kB]
Get:93 http://localhost:3142/debian unstable/main amd64 libdata-validate-uri-perl all 0.07-3 [11.0 kB]
Get:94 http://localhost:3142/debian unstable/main amd64 libdevel-size-perl amd64 0.84-1+b1 [24.2 kB]
Get:95 http://localhost:3142/debian unstable/main amd64 libemail-address-xs-perl amd64 1.05-1+b4 [29.4 kB]
Get:96 http://localhost:3142/debian unstable/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB]
Get:97 http://localhost:3142/debian unstable/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB]
Get:98 http://localhost:3142/debian unstable/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB]
Get:99 http://localhost:3142/debian unstable/main amd64 libnumber-compare-perl all 0.03-3 [6332 B]
Get:100 http://localhost:3142/debian unstable/main amd64 libtext-glob-perl all 0.11-3 [7676 B]
Get:101 http://localhost:3142/debian unstable/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB]
Get:102 http://localhost:3142/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB]
Get:103 http://localhost:3142/debian unstable/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB]
Get:104 http://localhost:3142/debian unstable/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB]
Get:105 http://localhost:3142/debian unstable/main amd64 libfile-sharedir-perl all 1.118-3 [16.0 kB]
Get:106 http://localhost:3142/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB]
Get:107 http://localhost:3142/debian unstable/main amd64 libfont-ttf-perl all 1.06-2 [318 kB]
Get:108 http://localhost:3142/debian unstable/main amd64 libio-html-perl all 1.004-3 [16.2 kB]
Get:109 http://localhost:3142/debian unstable/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get:110 http://localhost:3142/debian unstable/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB]
Get:111 http://localhost:3142/debian unstable/main amd64 libhtml-form-perl all 6.12-1 [32.3 kB]
Get:112 http://localhost:3142/debian unstable/main amd64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB]
Get:113 http://localhost:3142/debian unstable/main amd64 libhtml-tree-perl all 5.07-3 [211 kB]
Get:114 http://localhost:3142/debian unstable/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB]
Get:115 http://localhost:3142/debian unstable/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB]
Get:116 http://localhost:3142/debian unstable/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B]
Get:117 http://localhost:3142/debian unstable/main amd64 libnet-ssleay-perl amd64 1.94-3 [339 kB]
Get:118 http://localhost:3142/debian unstable/main amd64 libio-socket-ssl-perl all 2.089-1 [223 kB]
Get:119 http://localhost:3142/debian unstable/main amd64 libnet-http-perl all 6.23-1 [23.9 kB]
Get:120 http://localhost:3142/debian unstable/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB]
Get:121 http://localhost:3142/debian unstable/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB]
Get:122 http://localhost:3142/debian unstable/main amd64 libwww-perl all 6.78-1 [183 kB]
Get:123 http://localhost:3142/debian unstable/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB]
Get:124 http://localhost:3142/debian unstable/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB]
Get:125 http://localhost:3142/debian unstable/main amd64 libio-interactive-perl all 1.026-1 [11.7 kB]
Get:126 http://localhost:3142/debian unstable/main amd64 libipc-run3-perl all 0.049-1 [31.5 kB]
Get:127 http://localhost:3142/debian unstable/main amd64 libjson-maybexs-perl all 1.004008-1 [12.9 kB]
Get:128 http://localhost:3142/debian unstable/main amd64 liblist-compare-perl all 0.55-2 [65.7 kB]
Get:129 http://localhost:3142/debian unstable/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB]
Get:130 http://localhost:3142/debian unstable/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB]
Get:131 http://localhost:3142/debian unstable/main amd64 liblz1 amd64 1.15-2 [38.9 kB]
Get:132 http://localhost:3142/debian unstable/main amd64 liblzo2-2 amd64 2.10-3+b1 [55.1 kB]
Get:133 http://localhost:3142/debian unstable/main amd64 libmarkdown2 amd64 2.2.7-2.1 [36.0 kB]
Get:134 http://localhost:3142/debian unstable/main amd64 libmldbm-perl all 2.05-4 [16.8 kB]
Get:135 http://localhost:3142/debian unstable/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB]
Get:136 http://localhost:3142/debian unstable/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB]
Get:137 http://localhost:3142/debian unstable/main amd64 libmoo-perl all 2.005005-1 [58.0 kB]
Get:138 http://localhost:3142/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB]
Get:139 http://localhost:3142/debian unstable/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B]
Get:140 http://localhost:3142/debian unstable/main amd64 libmouse-perl amd64 2.5.11-1+b1 [144 kB]
Get:141 http://localhost:3142/debian unstable/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB]
Get:142 http://localhost:3142/debian unstable/main amd64 libsub-identify-perl amd64 0.14-3+b3 [11.3 kB]
Get:143 http://localhost:3142/debian unstable/main amd64 libsub-name-perl amd64 0.28-1 [12.2 kB]
Get:144 http://localhost:3142/debian unstable/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB]
Get:145 http://localhost:3142/debian unstable/main amd64 libpath-tiny-perl all 0.146-1 [56.2 kB]
Get:146 http://localhost:3142/debian unstable/main amd64 libperlio-gzip-perl amd64 0.20-1+b4 [17.5 kB]
Get:147 http://localhost:3142/debian unstable/main amd64 libperlio-utf8-strict-perl amd64 0.010-1+b3 [11.4 kB]
Get:148 http://localhost:3142/debian unstable/main amd64 libproc-processtable-perl amd64 0.636-1+b3 [42.3 kB]
Get:149 http://localhost:3142/debian unstable/main amd64 libregexp-wildcards-perl all 1.05-3 [14.1 kB]
Get:150 http://localhost:3142/debian unstable/main amd64 libsereal-decoder-perl amd64 5.004+ds-1+b3 [100 kB]
Get:151 http://localhost:3142/debian unstable/main amd64 libsereal-encoder-perl amd64 5.004+ds-1+b3 [104 kB]
Get:152 http://localhost:3142/debian unstable/main amd64 libsort-versions-perl all 1.62-3 [8928 B]
Get:153 http://localhost:3142/debian unstable/main amd64 libxs-parse-keyword-perl amd64 0.48-2 [65.7 kB]
Get:154 http://localhost:3142/debian unstable/main amd64 libsyntax-keyword-try-perl amd64 0.30-1+b1 [27.4 kB]
Get:155 http://localhost:3142/debian unstable/main amd64 libterm-readkey-perl amd64 2.38-2+b4 [24.6 kB]
Get:156 http://localhost:3142/debian unstable/main amd64 libtext-levenshteinxs-perl amd64 0.03-5+b4 [8720 B]
Get:157 http://localhost:3142/debian unstable/main amd64 libtext-markdown-discount-perl amd64 0.18-1 [13.1 kB]
Get:158 http://localhost:3142/debian unstable/main amd64 libtext-xslate-perl amd64 3.5.9-2+b1 [174 kB]
Get:159 http://localhost:3142/debian unstable/main amd64 libtime-duration-perl all 1.21-2 [13.1 kB]
Get:160 http://localhost:3142/debian unstable/main amd64 libtime-moment-perl amd64 0.44-2+b4 [73.2 kB]
Get:161 http://localhost:3142/debian unstable/main amd64 libunicode-utf8-perl amd64 0.62-2+b3 [20.4 kB]
Get:162 http://localhost:3142/debian unstable/main amd64 libwww-mechanize-perl all 2.19-1 [114 kB]
Get:163 http://localhost:3142/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB]
Get:164 http://localhost:3142/debian unstable/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB]
Get:165 http://localhost:3142/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-4 [53.4 kB]
Get:166 http://localhost:3142/debian unstable/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-5+b2 [314 kB]
Get:167 http://localhost:3142/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.903.0+ds-1 [35.4 kB]
Get:168 http://localhost:3142/debian unstable/main amd64 plzip amd64 1.12-2 [65.0 kB]
Get:169 http://localhost:3142/debian unstable/main amd64 lzop amd64 1.04-2 [84.2 kB]
Get:170 http://localhost:3142/debian unstable/main amd64 patchutils amd64 0.4.2-1 [77.5 kB]
Get:171 http://localhost:3142/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB]
Get:172 http://localhost:3142/debian unstable/main amd64 unzip amd64 6.0-29 [173 kB]
Get:173 http://localhost:3142/debian unstable/main amd64 lintian all 2.121.1+nmu1 [1059 kB]
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update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode
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update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version
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update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
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Setting up lintian (2.121.1+nmu1) ...
Setting up sbuild-build-depends-lintian-dummy:arm64 (0.invalid.0) ...
Processing triggers for libc-bin (2.41-4) ...
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: 411
Distribution: unstable
Foreign Architectures: arm64
Host Architecture: arm64
Install-Time: 10
Job: plink_1.07+dfsg-4
Lintian: pass
Machine Architecture: amd64
Package: plink
Package-Time: 432
Source-Version: 1.07+dfsg-4
Space: n/a
Status: successful
Version: 1.07+dfsg-4
--------------------------------------------------------------------------------
Finished at 2025-03-13T22:00:36Z
Build needed 00:07:12, no disk space