bedtools →
2.31.0+dfsg-2 →
armhf → 2023-11-21 05:44:51
sbuild (Debian sbuild) 0.85.0 (04 January 2023) on test2023
+==============================================================================+
| bedtools 2.31.0+dfsg-2 (armhf) Tue, 21 Nov 2023 05:41:58 +0000 |
+==============================================================================+
Package: bedtools
Version: 2.31.0+dfsg-2
Source Version: 2.31.0+dfsg-2
Distribution: trixie-staging
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-80165d5c-f423-402b-a9c0-f83efd783f7d' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/bedtools-DANbzL/resolver-lGfbod' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.3 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [14.9 MB]
Fetched 29.2 MB in 5s (5617 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/bedtools.git
Please use:
git clone https://salsa.debian.org/med-team/bedtools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 14.5 MB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main bedtools 2.31.0+dfsg-2 (dsc) [2230 B]
Get:2 http://172.17.4.1/private trixie-staging/main bedtools 2.31.0+dfsg-2 (tar) [14.5 MB]
Get:3 http://172.17.4.1/private trixie-staging/main bedtools 2.31.0+dfsg-2 (diff) [14.6 kB]
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Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bedtools-DANbzL/bedtools-2.31.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bedtools-DANbzL' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), python3:any, zlib1g-dev, libbz2-dev, liblzma-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), python3:any, zlib1g-dev, libbz2-dev, liblzma-dev, build-essential, fakeroot
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
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Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils bsdutils debhelper
dh-autoreconf dh-strip-nondeterminism dpkg-dev dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libblkid1 libbz2-dev
libdebhelper-perl libdpkg-perl libelf1 libexpat1
libfile-stripnondeterminism-perl libicu72 liblzma-dev libmagic-mgc libmagic1
libmount1 libpipeline1 libpython3-stdlib libpython3.11-minimal
libpython3.11-stdlib libsmartcols1 libsub-override-perl libtool libuchardet0
libuuid1 libxml2 m4 man-db media-types mount po-debconf python3
python3-minimal python3.11 python3.11-minimal sensible-utils util-linux
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make debian-keyring
gettext-doc libasprintf-dev libgettextpo-dev groff git bzr liblzma-doc
cryptsetup-bin libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc
apparmor less www-browser nfs-common libmail-box-perl python3-doc python3-tk
python3-venv python3.11-venv python3.11-doc binfmt-support dosfstools kbd
util-linux-extra util-linux-locales
Recommended packages:
libalgorithm-merge-perl curl | wget | lynx bzip2-doc libfile-fcntllock-perl
libarchive-cpio-perl libltdl-dev uuid-runtime libmail-sendmail-perl
ca-certificates
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbz2-dev libdebhelper-perl
libelf1 libexpat1 libfile-stripnondeterminism-perl libicu72 liblzma-dev
libmagic-mgc libmagic1 libpipeline1 libpython3-stdlib libpython3.11-minimal
libpython3.11-stdlib libsub-override-perl libtool libuchardet0 libxml2 m4
man-db media-types po-debconf python3 python3-minimal python3.11
python3.11-minimal sbuild-build-depends-main-dummy sensible-utils zlib1g-dev
The following packages will be upgraded:
bsdutils dpkg-dev libblkid1 libdpkg-perl libmount1 libsmartcols1 libuuid1
mount util-linux
9 upgraded, 43 newly installed, 0 to remove and 20 not upgraded.
1 not fully installed or removed.
Need to get 26.1 MB/28.1 MB of archives.
After this operation, 92.8 MB of additional disk space will be used.
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Get:18 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.2-6 [81.2 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-1 [1358 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf sensible-utils all 0.0.20 [19.3 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
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Get:26 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-13 [156 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-13 [496 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.8 [82.1 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:40 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-13 [1201 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.8 [956 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf libbz2-dev armhf 1.0.8-5+b2 [26.8 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf liblzma-dev armhf 5.4.4-0.1 [269 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-3 [901 kB]
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Setting up mount (2.39.2-6) ...
Setting up sensible-utils (0.0.20) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
Setting up libpython3-stdlib:armhf (3.11.4-5) ...
Setting up libbz2-dev:armhf (1.0.8-5+b2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up python3.11 (3.11.6-3) ...
Setting up gettext (0.21-13) ...
Setting up libtool (2.4.7-7) ...
Setting up python3 (3.11.4-5) ...
Setting up dpkg-dev (1.22.1+rpi1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.23.0-3) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.12.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.11.8) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.37-12+rpi2) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.47-v8+ #1 SMP PREEMPT Fri Sep 1 07:05:33 BST 2023 arm64 (aarch64)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc-12_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 libc6-dev_2.37-12+rpi2 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 linux-libc-dev_6.5.6-1+rpi1
Package versions: adduser_3.137 apt_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.2 bash_5.2.15-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.2-6 bsdutils_1:2.39.2-6 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-10+rpi1 cpp-13_13.2.0-5+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.8 debianutils_5.14 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.1+rpi1 dpkg-dev_1.22.1+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.1-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc_4:13.2.0-1+rpi1 gcc-10-base_10.4.0-7+rpi1 gcc-12_12.3.0-10+rpi1 gcc-12-base_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 gcc-13-base_13.2.0-5+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-13 gettext-base_0.21-13 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libasan8_13.2.0-5+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-5+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.41-6+rpi1 libblkid1_2.39.2-6 libbz2-1.0_1.0.8-5+b2 libbz2-dev_1.0.8-5+b2 libc-bin_2.37-12+rpi2 libc-dev-bin_2.37-12+rpi2 libc6_2.37-12+rpi2 libc6-dev_2.37-12+rpi2 libcap-ng0_0.8.3-1+b1 libcap2_1:2.66-4 libcc1-0_13.2.0-5+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libdb5.3_5.3.28+dfsg2-2 libdebconfclient0_0.271 libdebhelper-perl_13.11.8 libdpkg-perl_1.22.1+rpi1 libelf1_0.188-2.1+rpi1 libexpat1_2.5.0-2 libext2fs2_1.47.0-2 libfakeroot_1.32.1-1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-10+rpi1 libgcc-13-dev_13.2.0-5+rpi1 libgcc-s1_13.2.0-5+rpi1 libgcrypt20_1.10.2-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.1-4 libgomp1_13.2.0-5+rpi1 libgpg-error0_1.47-2 libgssapi-krb5-2_1.20.1-4 libhogweed6_3.9.1-2 libicu72_72.1-4 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libk5crypto3_1.20.1-4 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-4 libkrb5support0_1.20.1-4 libksba8_1.6.4-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 liblocale-gettext-perl_1.07-6 liblz4-1_1.9.4-1+rpi1+b1 liblzma-dev_5.4.4-0.1 liblzma5_5.4.4-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.2-6 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20231016-1 libnettle8_3.9.1-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.25.0-5 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpcre2-8-0_10.42-4 libperl5.36_5.36.0-9 libpipeline1_1.5.7-1 libpython3-stdlib_3.11.4-5 libpython3.11-minimal_3.11.6-3 libpython3.11-stdlib_3.11.6-3 libreadline8_8.2-1.3 libsasl2-2_2.1.28+dfsg1-3 libsasl2-modules-db_2.1.28+dfsg1-3 libseccomp2_2.5.4-1+rpi1+b1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol2_3.5-1 libsframe1_2.41-6+rpi1 libsmartcols1_2.39.2-6 libsqlite3-0_3.43.2-1 libss2_1.47.0-2 libssl3_3.0.11-1 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 libsub-override-perl_0.09-4 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11 libtext-iconv-perl_1.7-8 libtinfo6_6.4+20231016-1 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libubsan1_13.2.0-5+rpi1 libuchardet0_0.0.7-1 libudev1_254.5-1+rpi1 libunistring5_1.1-2 libuuid1_2.39.2-6 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-1 mawk_1.3.4.20230808-1 media-types_10.1.0 mount_2.39.2-6 ncurses-base_6.4+20231016-1 ncurses-bin_6.4+20231016-1 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-9 perl-base_5.36.0-9 perl-modules-5.36_5.36.0-9 pinentry-curses_1.2.1-1 po-debconf_1.0.21+nmu1 python3_3.11.4-5 python3-minimal_3.11.4-5 python3.11_3.11.6-3 python3.11-minimal_3.11.6-3 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sysvinit-utils_3.08-3 tar_1.34+dfsg-1.2 tzdata_2023c-10 usr-is-merged_37 util-linux_2.39.2-6 xz-utils_5.4.4-0.1 zlib1g_1:1.2.13.dfsg-3 zlib1g-dev_1:1.2.13.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: bedtools
Binary: bedtools, bedtools-test
Architecture: any all
Version: 2.31.0+dfsg-2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>, Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://github.com/arq5x/bedtools2
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/bedtools
Vcs-Git: https://salsa.debian.org/med-team/bedtools.git
Testsuite: autopkgtest
Testsuite-Triggers: tabix
Build-Depends: debhelper-compat (= 13), python3:any, zlib1g-dev, libbz2-dev, liblzma-dev
Package-List:
bedtools deb science optional arch=any
bedtools-test deb science optional arch=all
Checksums-Sha1:
c633231ea43281518fc661bb308ff531c0e93f4e 14483704 bedtools_2.31.0+dfsg.orig.tar.xz
ffc64ee2b9dc7aad78ab729e21dc245bb2bc330c 14612 bedtools_2.31.0+dfsg-2.debian.tar.xz
Checksums-Sha256:
c2317d520716a21881ebce5beda510b084d04865f559fcaec53795edfa5e9c15 14483704 bedtools_2.31.0+dfsg.orig.tar.xz
a11c7ff99c891175178ce7f79b3a5efd2e71885565d8a931ec09c82f3e924c50 14612 bedtools_2.31.0+dfsg-2.debian.tar.xz
Files:
a9a31dad279a48f81a0a6db088372e2e 14483704 bedtools_2.31.0+dfsg.orig.tar.xz
9e47e14001ed5d267fd182cf1a56890a 14612 bedtools_2.31.0+dfsg-2.debian.tar.xz
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-----END PGP SIGNATURE-----
gpgv: Signature made Sat Nov 18 16:01:55 2023 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./bedtools_2.31.0+dfsg-2.dsc: no acceptable signature found
dpkg-source: info: extracting bedtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking bedtools_2.31.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking bedtools_2.31.0+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying gzstream.h.patch
dpkg-source: info: applying remove_barski_binding_site.png.patch
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying hardening
dpkg-source: info: applying htsutil
dpkg-source: info: applying no_ulimit.patch
dpkg-source: info: applying gcc-13.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=124
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-80165d5c-f423-402b-a9c0-f83efd783f7d
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mRaspbian pi5 test autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package bedtools
dpkg-buildpackage: info: source version 2.31.0+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from bedtools-2.31.0+dfsg/debian/source/options: --single-debian-patch
debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
* Cleaning up.
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/bedtools.substvars debian/bedtools-test.substvars debian/files
rm -fr -- debian/bedtools/ debian/tmp/ debian/bedtools-test/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
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 -- VERBOSE=1
make -j4 "INSTALL=install --strip-program=true" VERBOSE=1
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Building BEDTools:
cd src/utils/htslib && make config.h
=========================================================
DETECTED_VERSION = v2.31.0
CURRENT_VERSION =
Updating version file.
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/utils/htslib'
CXXFLAGS is [-g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security]
* compiling src/bedtools.cpp
* compiling src/htsutil.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedtools.o -MMD -MP -MF obj/bedtools.Td -c -o obj/bedtools.o src/bedtools.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/htsutil.o -MMD -MP -MF obj/htsutil.Td -c -o obj/htsutil.o src/htsutil.cpp
* compiling src/annotateBed/annotateMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/annotateMain.o -MMD -MP -MF obj/annotateMain.Td -c -o obj/annotateMain.o src/annotateBed/annotateMain.cpp
echo '/* Default config.h generated by Makefile */' > config.h
echo '#define HAVE_LIBBZ2 1' >> config.h
echo '#define HAVE_LIBLZMA 1' >> config.h
echo '#ifndef __APPLE__' >> config.h
echo '#define HAVE_LZMA_H 1' >> config.h
echo '#endif' >> config.h
echo '#define HAVE_FSEEKO 1' >> config.h
echo '#define HAVE_DRAND48 1' >> config.h
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/utils/htslib'
* compiling src/annotateBed/annotateBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/annotateBed.o -MMD -MP -MF obj/annotateBed.Td -c -o obj/annotateBed.o src/annotateBed/annotateBed.cpp
* compiling src/bamToBed/bamToBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bamToBed.o -MMD -MP -MF obj/bamToBed.Td -c -o obj/bamToBed.o src/bamToBed/bamToBed.cpp
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/driver/BedtoolsDriver.h:1,
from src/bedtools.cpp:21:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/bamToFastq/bamToFastqMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bamToFastqMain.o -MMD -MP -MF obj/bamToFastqMain.Td -c -o obj/bamToFastqMain.o src/bamToFastq/bamToFastqMain.cpp
src/bamToBed/bamToBed.cpp: In function ‘int bamtobed_main(int, char**)’:
src/bamToBed/bamToBed.cpp:88:10: warning: variable ‘useAlignmentScore’ set but not used [-Wunused-but-set-variable]
88 | bool useAlignmentScore = false;
| ^~~~~~~~~~~~~~~~~
* compiling src/bamToFastq/bamToFastq.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bamToFastq.o -MMD -MP -MF obj/bamToFastq.Td -c -o obj/bamToFastq.o src/bamToFastq/bamToFastq.cpp
In file included from src/utils/BamTools/include/api/BamReader.h:1,
from src/bamToBed/bamToBed.cpp:12:
src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’:
src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
32 | sam_hdr_write(fp, hdr);
| ~~~~~~~~~~~~~^~~~~~~~~
* compiling src/bedToBam/bedToBam.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedToBam.o -MMD -MP -MF obj/bedToBam.Td -c -o obj/bedToBam.o src/bedToBam/bedToBam.cpp
src/bamToFastq/bamToFastqMain.cpp: In function ‘int bamtofastq_main(int, char**)’:
src/bamToFastq/bamToFastqMain.cpp:38:10: warning: variable ‘haveFastq2’ set but not used [-Wunused-but-set-variable]
38 | bool haveFastq2 = false;
| ^~~~~~~~~~
* compiling src/bedpeToBam/bedpeToBam.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedpeToBam.o -MMD -MP -MF obj/bedpeToBam.Td -c -o obj/bedpeToBam.o src/bedpeToBam/bedpeToBam.cpp
In file included from src/utils/BamTools/include/api/BamReader.h:1,
from src/bamToFastq/bamToFastq.h:15,
from src/bamToFastq/bamToFastq.cpp:15:
src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’:
src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
32 | sam_hdr_write(fp, hdr);
| ~~~~~~~~~~~~~^~~~~~~~~
src/bedToBam/bedToBam.cpp: In function ‘int bedtobam_main(int, char**)’:
src/bedToBam/bedToBam.cpp:60:10: warning: variable ‘haveMapQual’ set but not used [-Wunused-but-set-variable]
60 | bool haveMapQual = false;
| ^~~~~~~~~~~
src/bedpeToBam/bedpeToBam.cpp: In function ‘int bedpetobam_main(int, char**)’:
src/bedpeToBam/bedpeToBam.cpp:61:10: warning: variable ‘haveMapQual’ set but not used [-Wunused-but-set-variable]
61 | bool haveMapQual = false;
| ^~~~~~~~~~~
* compiling src/bedToIgv/bedToIgv.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedToIgv.o -MMD -MP -MF obj/bedToIgv.Td -c -o obj/bedToIgv.o src/bedToIgv/bedToIgv.cpp
In file included from /usr/include/c++/13/vector:72,
from src/utils/BamTools/include/SamHeader.hpp:6:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BamTools::BamAlignment&}; _Tp = BamTools::BamAlignment; _Alloc = std::allocator<BamTools::BamAlignment>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<BamTools::BamAlignment>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::BamAlignment; _Alloc = std::allocator<BamTools::BamAlignment>]’,
inlined from ‘void BamToFastq::PairedFastq()’ at src/bamToFastq/bamToFastq.cpp:99:33:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BamTools::BamAlignment*, std::vector<BamTools::BamAlignment> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::BamAlignment; _Alloc = std::allocator<BamTools::BamAlignment>]’,
inlined from ‘void BamToFastq::PairedFastq()’ at src/bamToFastq/bamToFastq.cpp:104:37:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BamTools::BamAlignment*, std::vector<BamTools::BamAlignment> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
* compiling src/bed12ToBed6/bed12ToBed6.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bed12ToBed6.o -MMD -MP -MF obj/bed12ToBed6.Td -c -o obj/bed12ToBed6.o src/bed12ToBed6/bed12ToBed6.cpp
* compiling src/closestFile/closestHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/closestHelp.o -MMD -MP -MF obj/closestHelp.Td -c -o obj/closestHelp.o src/closestFile/closestHelp.cpp
* compiling src/closestFile/closestFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/closestFile.o -MMD -MP -MF obj/closestFile.Td -c -o obj/closestFile.o src/closestFile/closestFile.cpp
* compiling src/clusterBed/clusterMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/clusterMain.o -MMD -MP -MF obj/clusterMain.Td -c -o obj/clusterMain.o src/clusterBed/clusterMain.cpp
* compiling src/clusterBed/clusterBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/clusterBed.o -MMD -MP -MF obj/clusterBed.Td -c -o obj/clusterBed.o src/clusterBed/clusterBed.cpp
In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12,
from src/utils/ToolBase/ToolBase.h:11,
from src/intersectFile/intersectFile.h:15,
from src/closestFile/closestFile.h:11,
from src/closestFile/closestFile.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/RecordOutputMgr/RecordOutputMgr.h:11,
from src/utils/ToolBase/ToolBase.h:12:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
src/clusterBed/clusterMain.cpp: In function ‘int cluster_main(int, char**)’:
src/clusterBed/clusterMain.cpp:38:10: warning: variable ‘haveMaxDistance’ set but not used [-Wunused-but-set-variable]
38 | bool haveMaxDistance = false;
| ^~~~~~~~~~~~~~~
* compiling src/complementFile/complementHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/complementHelp.o -MMD -MP -MF obj/complementHelp.Td -c -o obj/complementHelp.o src/complementFile/complementHelp.cpp
* compiling src/complementFile/complementFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/complementFile.o -MMD -MP -MF obj/complementFile.Td -c -o obj/complementFile.o src/complementFile/complementFile.cpp
* compiling src/coverageFile/coverageHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/coverageHelp.o -MMD -MP -MF obj/coverageHelp.Td -c -o obj/coverageHelp.o src/coverageFile/coverageHelp.cpp
* compiling src/coverageFile/coverageFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/coverageFile.o -MMD -MP -MF obj/coverageFile.Td -c -o obj/coverageFile.o src/coverageFile/coverageFile.cpp
In file included from /usr/include/c++/13/vector:65,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/clusterBed/clusterBed.cpp:12:
/usr/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const BED*, vector<BED> >; _ForwardIterator = BED*]’:
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >’ changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >’ changed in GCC 7.1
* compiling src/expand/expand.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/expand.o -MMD -MP -MF obj/expand.Td -c -o obj/expand.o src/expand/expand.cpp
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >; _ForwardIterator = BED*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const BED*, vector<BED> >; _ForwardIterator = BED*]’ at /usr/include/c++/13/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 BED*, vector<BED> >; _ForwardIterator = BED*; _Tp = BED]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = BED; _Alloc = std::allocator<BED>]’ at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from ‘void BedCluster::ClusterBedStranded()’ at src/clusterBed/clusterBed.cpp:84:34:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12,
from src/utils/ToolBase/ToolBase.h:11,
from src/complementFile/complementFile.h:11,
from src/complementFile/complementFile.cpp:1:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/RecordOutputMgr/RecordOutputMgr.h:11,
from src/utils/ToolBase/ToolBase.h:12:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/fastaFromBed/fastaFromBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fastaFromBedMain.o -MMD -MP -MF obj/fastaFromBedMain.Td -c -o obj/fastaFromBedMain.o src/fastaFromBed/fastaFromBedMain.cpp
In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12,
from src/utils/ToolBase/ToolBase.h:11,
from src/intersectFile/intersectFile.h:15,
from src/coverageFile/coverageFile.h:12,
from src/coverageFile/coverageFile.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/RecordOutputMgr/RecordOutputMgr.h:11,
from src/utils/ToolBase/ToolBase.h:12:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/fastaFromBed/fastaFromBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fastaFromBed.o -MMD -MP -MF obj/fastaFromBed.Td -c -o obj/fastaFromBed.o src/fastaFromBed/fastaFromBed.cpp
src/coverageFile/coverageFile.cpp: In member function ‘virtual void CoverageFile::giveFinalReport(RecordOutputMgr*)’:
src/coverageFile/coverageFile.cpp:100:25: warning: ignoring return value of ‘int asprintf(char**, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
100 | asprintf(&depthPctString, "%0.7f", depthPct);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/coverageFile/coverageFile.cpp: In member function ‘void CoverageFile::doMean(RecordOutputMgr*, RecordKeyVector&)’:
src/coverageFile/coverageFile.cpp:181:17: warning: ignoring return value of ‘int asprintf(char**, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
181 | asprintf(&meanString, "%0.7f", mean);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/coverageFile/coverageFile.cpp: In member function ‘void CoverageFile::doHist(RecordOutputMgr*, RecordKeyVector&)’:
src/coverageFile/coverageFile.cpp:210:25: warning: ignoring return value of ‘int asprintf(char**, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
210 | asprintf(&coveredFractionString, "%0.7f", coveredFraction);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/coverageFile/coverageFile.cpp: In member function ‘void CoverageFile::doDefault(RecordOutputMgr*, RecordKeyVector&)’:
src/coverageFile/coverageFile.cpp:230:17: warning: ignoring return value of ‘int asprintf(char**, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
230 | asprintf(&coveredFractionString, "%0.7f", coveredFraction);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/flankBed/flankBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/flankBedMain.o -MMD -MP -MF obj/flankBedMain.Td -c -o obj/flankBedMain.o src/flankBed/flankBedMain.cpp
* compiling src/flankBed/flankBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/flankBed.o -MMD -MP -MF obj/flankBed.Td -c -o obj/flankBed.o src/flankBed/flankBed.cpp
* compiling src/genomeCoverageBed/genomeCoverageMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/genomeCoverageMain.o -MMD -MP -MF obj/genomeCoverageMain.Td -c -o obj/genomeCoverageMain.o src/genomeCoverageBed/genomeCoverageMain.cpp
* compiling src/genomeCoverageBed/genomeCoverageBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/genomeCoverageBed.o -MMD -MP -MF obj/genomeCoverageBed.Td -c -o obj/genomeCoverageBed.o src/genomeCoverageBed/genomeCoverageBed.cpp
* compiling src/getOverlap/getOverlap.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/getOverlap.o -MMD -MP -MF obj/getOverlap.Td -c -o obj/getOverlap.o src/getOverlap/getOverlap.cpp
* compiling src/groupBy/groupByHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/groupByHelp.o -MMD -MP -MF obj/groupByHelp.Td -c -o obj/groupByHelp.o src/groupBy/groupByHelp.cpp
src/getOverlap/getOverlap.cpp: In function ‘int getoverlap_main(int, char**)’:
src/getOverlap/getOverlap.cpp:44:10: warning: variable ‘haveColumns’ set but not used [-Wunused-but-set-variable]
44 | bool haveColumns = false;
| ^~~~~~~~~~~
* compiling src/groupBy/groupBy.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/groupBy.o -MMD -MP -MF obj/groupBy.Td -c -o obj/groupBy.o src/groupBy/groupBy.cpp
* compiling src/intersectFile/intersectHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/intersectHelp.o -MMD -MP -MF obj/intersectHelp.Td -c -o obj/intersectHelp.o src/intersectFile/intersectHelp.cpp
In file included from src/utils/BamTools/include/api/BamReader.h:1,
from src/utils/GenomeFile/NewGenomeFile.h:20,
from src/genomeCoverageBed/genomeCoverageBed.h:13,
from src/genomeCoverageBed/genomeCoverageBed.cpp:13:
src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’:
src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
32 | sam_hdr_write(fp, hdr);
| ~~~~~~~~~~~~~^~~~~~~~~
* compiling src/intersectFile/intersectFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/intersectFile.o -MMD -MP -MF obj/intersectFile.Td -c -o obj/intersectFile.o src/intersectFile/intersectFile.cpp
* compiling src/fisher/fisherHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fisherHelp.o -MMD -MP -MF obj/fisherHelp.Td -c -o obj/fisherHelp.o src/fisher/fisherHelp.cpp
In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12,
from src/utils/ToolBase/ToolBase.h:11,
from src/groupBy/groupBy.h:10,
from src/groupBy/groupBy.cpp:7:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/RecordOutputMgr/RecordOutputMgr.h:11,
from src/utils/ToolBase/ToolBase.h:12:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/fisher/fisher.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fisher.o -MMD -MP -MF obj/fisher.Td -c -o obj/fisher.o src/fisher/fisher.cpp
In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12,
from src/utils/ToolBase/ToolBase.h:11,
from src/intersectFile/intersectFile.h:15,
from src/intersectFile/intersectFile.cpp:13:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/RecordOutputMgr/RecordOutputMgr.h:11,
from src/utils/ToolBase/ToolBase.h:12:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/istream:40,
from /usr/include/c++/13/sstream:40,
from src/utils/lineFileUtilities/lineFileUtilities.h:8,
from src/genomeCoverageBed/genomeCoverageBed.cpp:12:
In member function ‘std::streamsize std::ios_base::precision(std::streamsize)’,
inlined from ‘void BedGenomeCoverage::ReportChromCoverageBedGraph(const std::vector<DEPTH>&, const CHRPOS&, const std::string&)’ at src/genomeCoverageBed/genomeCoverageBed.cpp:541:23:
/usr/include/c++/13/bits/ios_base.h:744:20: warning: ‘prec’ may be used uninitialized [-Wmaybe-uninitialized]
744 | _M_precision = __prec;
| ~~~~~~~~~~~~~^~~~~~~~
src/genomeCoverageBed/genomeCoverageBed.cpp: In member function ‘void BedGenomeCoverage::ReportChromCoverageBedGraph(const std::vector<DEPTH>&, const CHRPOS&, const std::string&)’:
src/genomeCoverageBed/genomeCoverageBed.cpp:491:16: note: ‘prec’ was declared here
491 | streamsize prec;
| ^~~~
In function ‘constexpr std::_Ios_Fmtflags std::operator|(_Ios_Fmtflags, _Ios_Fmtflags)’,
inlined from ‘const std::_Ios_Fmtflags& std::operator|=(_Ios_Fmtflags&, _Ios_Fmtflags)’ at /usr/include/c++/13/bits/ios_base.h:100:22,
inlined from ‘std::ios_base::fmtflags std::ios_base::setf(fmtflags)’ at /usr/include/c++/13/bits/ios_base.h:692:19,
inlined from ‘void BedGenomeCoverage::ReportChromCoverageBedGraph(const std::vector<DEPTH>&, const CHRPOS&, const std::string&)’ at src/genomeCoverageBed/genomeCoverageBed.cpp:542:18:
/usr/include/c++/13/bits/ios_base.h:88:71: warning: ‘fflags’ may be used uninitialized [-Wmaybe-uninitialized]
88 | { return _Ios_Fmtflags(static_cast<int>(__a) | static_cast<int>(__b)); }
| ^
src/genomeCoverageBed/genomeCoverageBed.cpp: In member function ‘void BedGenomeCoverage::ReportChromCoverageBedGraph(const std::vector<DEPTH>&, const CHRPOS&, const std::string&)’:
src/genomeCoverageBed/genomeCoverageBed.cpp:492:29: note: ‘fflags’ was declared here
492 | std::ios_base::fmtflags fflags;
| ^~~~~~
* compiling src/fisher/kfunc.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/kfunc.o -MMD -MP -MF obj/kfunc.Td -c -o obj/kfunc.o src/fisher/kfunc.cpp
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextIntersect.h:11,
from src/utils/Contexts/ContextJaccard.h:11,
from src/jaccard/jaccard.h:11,
from src/fisher/fisher.h:11,
from src/fisher/fisher.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
* compiling src/jaccard/jaccardHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/jaccardHelp.o -MMD -MP -MF obj/jaccardHelp.Td -c -o obj/jaccardHelp.o src/jaccard/jaccardHelp.cpp
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/jaccard/jaccard.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/jaccard.o -MMD -MP -MF obj/jaccard.Td -c -o obj/jaccard.o src/jaccard/jaccard.cpp
In member function ‘std::streamsize std::ios_base::precision(std::streamsize)’,
inlined from ‘void BedGenomeCoverage::ReportChromCoverage(const std::vector<DEPTH>&, const CHRPOS&, const std::string&, chromHistMap&)’ at src/genomeCoverageBed/genomeCoverageBed.cpp:401:27:
/usr/include/c++/13/bits/ios_base.h:744:20: warning: ‘prec’ may be used uninitialized [-Wmaybe-uninitialized]
744 | _M_precision = __prec;
| ~~~~~~~~~~~~~^~~~~~~~
src/genomeCoverageBed/genomeCoverageBed.cpp: In member function ‘void BedGenomeCoverage::ReportChromCoverage(const std::vector<DEPTH>&, const CHRPOS&, const std::string&, chromHistMap&)’:
src/genomeCoverageBed/genomeCoverageBed.cpp:381:20: note: ‘prec’ was declared here
381 | streamsize prec;
| ^~~~
In function ‘constexpr std::_Ios_Fmtflags std::operator|(_Ios_Fmtflags, _Ios_Fmtflags)’,
inlined from ‘const std::_Ios_Fmtflags& std::operator|=(_Ios_Fmtflags&, _Ios_Fmtflags)’ at /usr/include/c++/13/bits/ios_base.h:100:22,
inlined from ‘std::ios_base::fmtflags std::ios_base::setf(fmtflags)’ at /usr/include/c++/13/bits/ios_base.h:692:19,
inlined from ‘void BedGenomeCoverage::ReportChromCoverage(const std::vector<DEPTH>&, const CHRPOS&, const std::string&, chromHistMap&)’ at src/genomeCoverageBed/genomeCoverageBed.cpp:402:22:
/usr/include/c++/13/bits/ios_base.h:88:71: warning: ‘fflags’ may be used uninitialized [-Wmaybe-uninitialized]
88 | { return _Ios_Fmtflags(static_cast<int>(__a) | static_cast<int>(__b)); }
| ^
src/genomeCoverageBed/genomeCoverageBed.cpp: In member function ‘void BedGenomeCoverage::ReportChromCoverage(const std::vector<DEPTH>&, const CHRPOS&, const std::string&, chromHistMap&)’:
src/genomeCoverageBed/genomeCoverageBed.cpp:382:33: note: ‘fflags’ was declared here
382 | std::ios_base::fmtflags fflags;
| ^~~~~~
* compiling src/linksBed/linksMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/linksMain.o -MMD -MP -MF obj/linksMain.Td -c -o obj/linksMain.o src/linksBed/linksMain.cpp
* compiling src/linksBed/linksBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/linksBed.o -MMD -MP -MF obj/linksBed.Td -c -o obj/linksBed.o src/linksBed/linksBed.cpp
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextIntersect.h:11,
from src/utils/Contexts/ContextJaccard.h:11,
from src/jaccard/jaccard.h:11,
from src/jaccard/jaccard.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/maskFastaFromBed/maskFastaFromBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/maskFastaFromBedMain.o -MMD -MP -MF obj/maskFastaFromBedMain.Td -c -o obj/maskFastaFromBedMain.o src/maskFastaFromBed/maskFastaFromBedMain.cpp
* compiling src/maskFastaFromBed/maskFastaFromBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/maskFastaFromBed.o -MMD -MP -MF obj/maskFastaFromBed.Td -c -o obj/maskFastaFromBed.o src/maskFastaFromBed/maskFastaFromBed.cpp
* compiling src/mapFile/mapHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/mapHelp.o -MMD -MP -MF obj/mapHelp.Td -c -o obj/mapHelp.o src/mapFile/mapHelp.cpp
* compiling src/mapFile/mapFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/mapFile.o -MMD -MP -MF obj/mapFile.Td -c -o obj/mapFile.o src/mapFile/mapFile.cpp
* compiling src/mergeFile/mergeHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/mergeHelp.o -MMD -MP -MF obj/mergeHelp.Td -c -o obj/mergeHelp.o src/mergeFile/mergeHelp.cpp
* compiling src/mergeFile/mergeFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/mergeFile.o -MMD -MP -MF obj/mergeFile.Td -c -o obj/mergeFile.o src/mergeFile/mergeFile.cpp
In file included from /usr/include/c++/13/vector:65,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/maskFastaFromBed/maskFastaFromBed.cpp:12:
/usr/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const BED*, vector<BED> >; _ForwardIterator = BED*]’:
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >’ changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >; _ForwardIterator = BED*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const BED*, vector<BED> >; _ForwardIterator = BED*]’ at /usr/include/c++/13/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 BED*, vector<BED> >; _ForwardIterator = BED*; _Tp = BED]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = BED; _Alloc = std::allocator<BED>]’ at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from ‘void MaskFastaFromBed::MaskFasta()’ at src/maskFastaFromBed/maskFastaFromBed.cpp:82:66:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >; _ForwardIterator = BED*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const BED*, vector<BED> >; _ForwardIterator = BED*]’ at /usr/include/c++/13/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 BED*, vector<BED> >; _ForwardIterator = BED*; _Tp = BED]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = BED; _Alloc = std::allocator<BED>]’ at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from ‘void MaskFastaFromBed::MaskFasta()’ at src/maskFastaFromBed/maskFastaFromBed.cpp:123:58:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12,
from src/utils/ToolBase/ToolBase.h:11,
from src/intersectFile/intersectFile.h:15,
from src/mapFile/mapFile.h:11,
from src/mapFile/mapFile.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/RecordOutputMgr/RecordOutputMgr.h:11,
from src/utils/ToolBase/ToolBase.h:12:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12,
from src/utils/ToolBase/ToolBase.h:11,
from src/mergeFile/mergeFile.h:11,
from src/mergeFile/mergeFile.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/RecordOutputMgr/RecordOutputMgr.h:11,
from src/utils/ToolBase/ToolBase.h:12:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
* compiling src/multiBamCov/multiBamCovMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/multiBamCovMain.o -MMD -MP -MF obj/multiBamCovMain.Td -c -o obj/multiBamCovMain.o src/multiBamCov/multiBamCovMain.cpp
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/multiBamCov/multiBamCov.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/multiBamCov.o -MMD -MP -MF obj/multiBamCov.Td -c -o obj/multiBamCov.o src/multiBamCov/multiBamCov.cpp
* compiling src/multiIntersectBed/multiIntersectBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/multiIntersectBedMain.o -MMD -MP -MF obj/multiIntersectBedMain.Td -c -o obj/multiIntersectBedMain.o src/multiIntersectBed/multiIntersectBedMain.cpp
* compiling src/multiIntersectBed/multiIntersectBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/multiIntersectBed.o -MMD -MP -MF obj/multiIntersectBed.Td -c -o obj/multiIntersectBed.o src/multiIntersectBed/multiIntersectBed.cpp
src/multiBamCov/multiBamCovMain.cpp: In function ‘int multibamcov_main(int, char**)’:
src/multiBamCov/multiBamCovMain.cpp:38:10: warning: variable ‘haveBed’ set but not used [-Wunused-but-set-variable]
38 | bool haveBed = false;
| ^~~~~~~
src/multiBamCov/multiBamCovMain.cpp:39:10: warning: variable ‘haveBams’ set but not used [-Wunused-but-set-variable]
39 | bool haveBams = false;
| ^~~~~~~~
src/multiBamCov/multiBamCovMain.cpp:47:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable]
47 | bool haveFraction = false;
| ^~~~~~~~~~~~
src/multiIntersectBed/multiIntersectBedMain.cpp: In function ‘int multiintersect_main(int, char**)’:
src/multiIntersectBed/multiIntersectBedMain.cpp:45:10: warning: variable ‘haveFiles’ set but not used [-Wunused-but-set-variable]
45 | bool haveFiles = false;
| ^~~~~~~~~
src/multiIntersectBed/multiIntersectBedMain.cpp:47:10: warning: variable ‘haveGenome’ set but not used [-Wunused-but-set-variable]
47 | bool haveGenome = false;
| ^~~~~~~~~~
src/multiIntersectBed/multiIntersectBedMain.cpp:48:10: warning: variable ‘haveFiller’ set but not used [-Wunused-but-set-variable]
48 | bool haveFiller = true;
| ^~~~~~~~~~
In file included from src/utils/BamTools/include/BamReader.hpp:4,
from src/utils/BamTools/include/api/BamMultiReader.h:4,
from src/multiBamCov/multiBamCov.h:16,
from src/multiBamCov/multiBamCov.cpp:13:
src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’:
src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
32 | sam_hdr_write(fp, hdr);
| ~~~~~~~~~~~~~^~~~~~~~~
* compiling src/nucBed/nucBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/nucBedMain.o -MMD -MP -MF obj/nucBedMain.Td -c -o obj/nucBedMain.o src/nucBed/nucBedMain.cpp
* compiling src/nucBed/nucBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/nucBed.o -MMD -MP -MF obj/nucBed.Td -c -o obj/nucBed.o src/nucBed/nucBed.cpp
In file included from /usr/include/c++/13/bits/stl_algo.h:61,
from /usr/include/c++/13/algorithm:61,
from src/multiIntersectBed/multiIntersectBed.cpp:17:
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Point*, vector<Point, allocator<Point> > >; _Distance = int; _Tp = Point; _Compare = __gnu_cxx::__ops::_Iter_comp_val<less<Point> >]’:
/usr/include/c++/13/bits/stl_heap.h:135:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Point*, std::vector<Point, std::allocator<Point> > >’ changed in GCC 7.1
135 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Point*, vector<Point, allocator<Point> > >; _Distance = int; _Tp = Point; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<less<Point> >]’:
/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Point*, std::vector<Point, std::allocator<Point> > >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from src/utils/general/BedtoolsTypes.h:26,
from src/utils/bedFile/bedFile.h:16,
from src/multiIntersectBed/multiIntersectBed.cpp:19:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Point&}; _Tp = Point; _Alloc = std::allocator<Point>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<Point, std::allocator<Point> >::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
* compiling src/pairToBed/pairToBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/pairToBedMain.o -MMD -MP -MF obj/pairToBedMain.Td -c -o obj/pairToBedMain.o src/pairToBed/pairToBedMain.cpp
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Point; _Alloc = std::allocator<Point>]’,
inlined from ‘void std::priority_queue<_Tp, _Sequence, _Compare>::push(const value_type&) [with _Tp = Point; _Sequence = std::vector<Point, std::allocator<Point> >; _Compare = std::less<Point>]’ at /usr/include/c++/13/bits/stl_queue.h:740:13,
inlined from ‘void MultiIntersectBed::AddInterval(int)’ at src/multiIntersectBed/multiIntersectBed.cpp:77:15:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Point*, std::vector<Point, std::allocator<Point> > >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Point; _Alloc = std::allocator<Point>]’,
inlined from ‘void std::priority_queue<_Tp, _Sequence, _Compare>::push(const value_type&) [with _Tp = Point; _Sequence = std::vector<Point, std::allocator<Point> >; _Compare = std::less<Point>]’ at /usr/include/c++/13/bits/stl_queue.h:740:13,
inlined from ‘void MultiIntersectBed::AddInterval(int)’ at src/multiIntersectBed/multiIntersectBed.cpp:78:15:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Point*, std::vector<Point, std::allocator<Point> > >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
* compiling src/pairToBed/pairToBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/pairToBed.o -MMD -MP -MF obj/pairToBed.Td -c -o obj/pairToBed.o src/pairToBed/pairToBed.cpp
* compiling src/pairToPair/pairToPairMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/pairToPairMain.o -MMD -MP -MF obj/pairToPairMain.Td -c -o obj/pairToPairMain.o src/pairToPair/pairToPairMain.cpp
* compiling src/pairToPair/pairToPair.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/pairToPair.o -MMD -MP -MF obj/pairToPair.Td -c -o obj/pairToPair.o src/pairToPair/pairToPair.cpp
src/pairToBed/pairToBedMain.cpp: In function ‘int pairtobed_main(int, char**)’:
src/pairToBed/pairToBedMain.cpp:43:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable]
43 | bool haveFraction = false;
| ^~~~~~~~~~~~
src/pairToPair/pairToPairMain.cpp: In function ‘int pairtopair_main(int, char**)’:
src/pairToPair/pairToPairMain.cpp:44:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable]
44 | bool haveFraction = false;
| ^~~~~~~~~~~~
src/pairToBed/pairToBed.cpp: In member function ‘void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const std::string&)’:
src/pairToBed/pairToBed.cpp:257:12: warning: variable ‘spanLength’ set but not used [-Wunused-but-set-variable]
257 | CHRPOS spanLength = 0;
| ^~~~~~~~~~
src/pairToBed/pairToBed.cpp: In member function ‘bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const std::string&)’:
src/pairToBed/pairToBed.cpp:310:12: warning: variable ‘spanLength’ set but not used [-Wunused-but-set-variable]
310 | CHRPOS spanLength = 0;
| ^~~~~~~~~~
src/pairToPair/pairToPair.cpp: In member function ‘void PairToPair::FindOverlaps(const BEDPE&)’:
src/pairToPair/pairToPair.cpp:112:14: warning: variable ‘found1’ set but not used [-Wunused-but-set-variable]
112 | bool found1 = false;
| ^~~~~~
src/pairToPair/pairToPair.cpp:113:14: warning: variable ‘found2’ set but not used [-Wunused-but-set-variable]
113 | bool found2 = false;
| ^~~~~~
In file included from src/utils/BamTools/include/api/BamReader.h:1,
from src/pairToBed/pairToBed.h:15,
from src/pairToBed/pairToBed.cpp:13:
src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’:
src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
32 | sam_hdr_write(fp, hdr);
| ~~~~~~~~~~~~~^~~~~~~~~
* compiling src/randomBed/randomBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/randomBedMain.o -MMD -MP -MF obj/randomBedMain.Td -c -o obj/randomBedMain.o src/randomBed/randomBedMain.cpp
* compiling src/randomBed/randomBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/randomBed.o -MMD -MP -MF obj/randomBed.Td -c -o obj/randomBed.o src/randomBed/randomBed.cpp
In file included from /usr/include/c++/13/vector:72,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/pairToPair/pairToPair.cpp:12:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const MATE&}; _Tp = MATE; _Alloc = std::allocator<MATE>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<MATE>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MATE; _Alloc = std::allocator<MATE>]’,
inlined from ‘bool PairToPair::FindHitsOnBothEnds(const BEDPE&, const std::vector<MATE>&, const std::vector<MATE>&)’ at src/pairToPair/pairToPair.cpp:142:38:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MATE; _Alloc = std::allocator<MATE>]’,
inlined from ‘bool PairToPair::FindHitsOnBothEnds(const BEDPE&, const std::vector<MATE>&, const std::vector<MATE>&)’ at src/pairToPair/pairToPair.cpp:145:38:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MATE; _Alloc = std::allocator<MATE>]’,
inlined from ‘void PairToPair::FindHitsOnEitherEnd(const BEDPE&, const std::vector<MATE>&, const std::vector<MATE>&)’ at src/pairToPair/pairToPair.cpp:181:38:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MATE; _Alloc = std::allocator<MATE>]’,
inlined from ‘void PairToPair::FindHitsOnEitherEnd(const BEDPE&, const std::vector<MATE>&, const std::vector<MATE>&)’ at src/pairToPair/pairToPair.cpp:184:38:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
* compiling src/regressTest/regressTestMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/regressTestMain.o -MMD -MP -MF obj/regressTestMain.Td -c -o obj/regressTestMain.o src/regressTest/regressTestMain.cpp
* compiling src/regressTest/RegressTest.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RegressTest.o -MMD -MP -MF obj/RegressTest.Td -c -o obj/RegressTest.o src/regressTest/RegressTest.cpp
* compiling src/reldist/reldistMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/reldistMain.o -MMD -MP -MF obj/reldistMain.Td -c -o obj/reldistMain.o src/reldist/reldistMain.cpp
* compiling src/reldist/reldist.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/reldist.o -MMD -MP -MF obj/reldist.Td -c -o obj/reldist.o src/reldist/reldist.cpp
In file included from /usr/include/c++/13/vector:72,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/pairToBed/pairToBed.cpp:12:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator<BED>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<BED>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BED; _Alloc = std::allocator<BED>]’,
inlined from ‘void BedIntersectPE::FindOverlaps(const BEDPE&, std::vector<BED>&, std::vector<BED>&, const std::string&)’ at src/pairToBed/pairToBed.cpp:106:43:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BED; _Alloc = std::allocator<BED>]’,
inlined from ‘void BedIntersectPE::FindOverlaps(const BEDPE&, std::vector<BED>&, std::vector<BED>&, const std::string&)’ at src/pairToBed/pairToBed.cpp:137:43:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
src/regressTest/RegressTest.cpp: In member function ‘bool RegressTest::executeAndCompareCorrectness(const fileListType&)’:
src/regressTest/RegressTest.cpp:431:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
431 | system(diffCmd.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~
src/regressTest/RegressTest.cpp: In member function ‘bool RegressTest::startMemoryProfile(bool)’:
src/regressTest/RegressTest.cpp:573:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
573 | fgets(sLine, 4192, fp);
| ~~~~~^~~~~~~~~~~~~~~~~
src/regressTest/RegressTest.cpp: In member function ‘bool RegressTest::calcMemoryStats()’:
src/regressTest/RegressTest.cpp:622:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
622 | fgets(sLine, 4192, fp);
| ~~~~~^~~~~~~~~~~~~~~~~
src/reldist/reldist.cpp: In member function ‘void RelativeDistance::ReportDistanceSummary()’:
src/reldist/reldist.cpp:69:25: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘unsigned int’ [-Wformat=]
69 | printf("%.2f\t%lu\t%lu\t%.3lf\n",
| ~~^
| |
| long unsigned int
| %u
70 | freqItr->first,
71 | freqItr->second,
| ~~~~~~~~~~~~~~~
| |
| unsigned int
src/reldist/reldist.cpp:69:30: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
69 | printf("%.2f\t%lu\t%lu\t%.3lf\n",
| ~~^
| |
| long unsigned int
| %u
......
72 | _tot_queries,
| ~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
* compiling src/sampleFile/sampleHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sampleHelp.o -MMD -MP -MF obj/sampleHelp.Td -c -o obj/sampleHelp.o src/sampleFile/sampleHelp.cpp
In file included from /usr/include/c++/13/bits/stl_algo.h:61,
from /usr/include/c++/13/algorithm:61,
from src/utils/bedFile/bedFile.h:30,
from src/reldist/reldist.h:15,
from src/reldist/reldist.cpp:13:
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/sampleFile/sampleFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sampleFile.o -MMD -MP -MF obj/sampleFile.Td -c -o obj/sampleFile.o src/sampleFile/sampleFile.cpp
* compiling src/shiftBed/shiftBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/shiftBedMain.o -MMD -MP -MF obj/shiftBedMain.Td -c -o obj/shiftBedMain.o src/shiftBed/shiftBedMain.cpp
In file included from /usr/include/c++/13/vector:72,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/reldist/reldist.cpp:12:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘void RelativeDistance::LoadMidpoints()’ at src/reldist/reldist.cpp:45:43:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >]’ at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from ‘void RelativeDistance::LoadMidpoints()’ at src/reldist/reldist.cpp:52:13:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/13/bits/stl_algo.h:1950:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >]’ at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from ‘void RelativeDistance::LoadMidpoints()’ at src/reldist/reldist.cpp:52:13:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/shiftBed/shiftBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/shiftBed.o -MMD -MP -MF obj/shiftBed.Td -c -o obj/shiftBed.o src/shiftBed/shiftBed.cpp
In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12,
from src/utils/ToolBase/ToolBase.h:11,
from src/sampleFile/sampleFile.h:11,
from src/sampleFile/sampleFile.cpp:1:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/RecordOutputMgr/RecordOutputMgr.h:11,
from src/utils/ToolBase/ToolBase.h:12:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/shuffleBed/shuffleBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/shuffleBedMain.o -MMD -MP -MF obj/shuffleBedMain.Td -c -o obj/shuffleBedMain.o src/shuffleBed/shuffleBedMain.cpp
* compiling src/shuffleBed/shuffleBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/shuffleBed.o -MMD -MP -MF obj/shuffleBed.Td -c -o obj/shuffleBed.o src/shuffleBed/shuffleBed.cpp
* compiling src/slopBed/slopBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/slopBedMain.o -MMD -MP -MF obj/slopBedMain.Td -c -o obj/slopBedMain.o src/slopBed/slopBedMain.cpp
* compiling src/slopBed/slopBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/slopBed.o -MMD -MP -MF obj/slopBed.Td -c -o obj/slopBed.o src/slopBed/slopBed.cpp
* compiling src/sortBed/sortMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sortMain.o -MMD -MP -MF obj/sortMain.Td -c -o obj/sortMain.o src/sortBed/sortMain.cpp
* compiling src/sortBed/sortBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sortBed.o -MMD -MP -MF obj/sortBed.Td -c -o obj/sortBed.o src/sortBed/sortBed.cpp
* compiling src/spacingFile/spacingHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/spacingHelp.o -MMD -MP -MF obj/spacingHelp.Td -c -o obj/spacingHelp.o src/spacingFile/spacingHelp.cpp
* compiling src/spacingFile/spacingFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/spacingFile.o -MMD -MP -MF obj/spacingFile.Td -c -o obj/spacingFile.o src/spacingFile/spacingFile.cpp
* compiling src/split/splitBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/splitBedMain.o -MMD -MP -MF obj/splitBedMain.Td -c -o obj/splitBedMain.o src/split/splitBedMain.cpp
* compiling src/split/splitBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/splitBed.o -MMD -MP -MF obj/splitBed.Td -c -o obj/splitBed.o src/split/splitBed.cpp
In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12,
from src/utils/ToolBase/ToolBase.h:11,
from src/spacingFile/spacingFile.h:12,
from src/spacingFile/spacingFile.cpp:7:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/RecordOutputMgr/RecordOutputMgr.h:11,
from src/utils/ToolBase/ToolBase.h:12:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/subtractFile/subtractHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/subtractHelp.o -MMD -MP -MF obj/subtractHelp.Td -c -o obj/subtractHelp.o src/subtractFile/subtractHelp.cpp
In file included from /usr/include/c++/13/vector:72,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/sortBed/sortBed.cpp:13:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator<BED>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<BED>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
* compiling src/subtractFile/subtractFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/subtractFile.o -MMD -MP -MF obj/subtractFile.Td -c -o obj/subtractFile.o src/subtractFile/subtractFile.cpp
In file included from /usr/include/c++/13/algorithm:61,
from src/utils/bedFile/bedFile.h:30,
from src/sortBed/sortBed.h:12,
from src/sortBed/sortBed.cpp:14:
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1792 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
* compiling src/summaryFile/summaryHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/summaryHelp.o -MMD -MP -MF obj/summaryHelp.Td -c -o obj/summaryHelp.o src/summaryFile/summaryHelp.cpp
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1854 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algo.h:61:
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Distance = int; _Tp = BED; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
254 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’,
inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’ at /usr/include/c++/13/bits/stl_algo.h:1910:25,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’ at /usr/include/c++/13/bits/stl_algo.h:1926:27:
/usr/include/c++/13/bits/stl_algo.h:1635:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1635 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’,
inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’ at /usr/include/c++/13/bits/stl_algo.h:1911:23,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’ at /usr/include/c++/13/bits/stl_algo.h:1926:27:
/usr/include/c++/13/bits/stl_heap.h:425:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
425 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BED; _Alloc = std::allocator<BED>]’,
inlined from ‘void BedSort::SortBedBySizeDesc()’ at src/sortBed/sortBed.cpp:158:33:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = bool (*)(const BED&, const BED&)]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘void BedSort::SortBedBySizeDesc()’ at src/sortBed/sortBed.cpp:163:9:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1950 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = bool (*)(const BED&, const BED&)]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘void BedSort::SortBedByChromThenSizeDesc()’ at src/sortBed/sortBed.cpp:195:13:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1950 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = bool (*)(const BED&, const BED&)]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘void BedSort::SortBedByChromThenSizeAsc()’ at src/sortBed/sortBed.cpp:178:13:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1950 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = bool (*)(const BED&, const BED&)]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘void BedSort::SortBedByChromThenScoreAsc()’ at src/sortBed/sortBed.cpp:212:17:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1950 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = bool (*)(const BED&, const BED&)]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘void BedSort::SortBedByChromThenScoreDesc()’ at src/sortBed/sortBed.cpp:234:17:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1950 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/summaryFile/summaryFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/summaryFile.o -MMD -MP -MF obj/summaryFile.Td -c -o obj/summaryFile.o src/summaryFile/summaryFile.cpp
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BED; _Alloc = std::allocator<BED>]’,
inlined from ‘void BedSort::SortBedBySizeAsc()’ at src/sortBed/sortBed.cpp:131:33:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = bool (*)(const BED&, const BED&)]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘void BedSort::SortBedBySizeAsc()’ at src/sortBed/sortBed.cpp:136:9:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1950 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/split/splitBed.cpp:15:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator<BED>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<BED>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BED; _Alloc = std::allocator<BED>]’,
inlined from ‘void BedSplit::loadBed()’ at src/split/splitBed.cpp:193:26:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12,
from src/utils/ToolBase/ToolBase.h:11,
from src/intersectFile/intersectFile.h:15,
from src/subtractFile/subtractFile.h:12,
from src/subtractFile/subtractFile.cpp:1:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/RecordOutputMgr/RecordOutputMgr.h:11,
from src/utils/ToolBase/ToolBase.h:12:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/tagBam/tagBamMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/tagBamMain.o -MMD -MP -MF obj/tagBamMain.Td -c -o obj/tagBamMain.o src/tagBam/tagBamMain.cpp
In file included from /usr/include/c++/13/algorithm:61,
from src/utils/bedFile/bedFile.h:30,
from src/split/splitBed.h:10,
from src/split/splitBed.cpp:17:
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1792 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
In file included from /usr/include/c++/13/bits/stl_algo.h:61:
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Distance = int; _Tp = BED; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
254 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12,
from src/utils/ToolBase/ToolBase.h:11,
from src/summaryFile/summaryFile.h:12,
from src/summaryFile/summaryFile.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/RecordOutputMgr/RecordOutputMgr.h:11,
from src/utils/ToolBase/ToolBase.h:12:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’,
inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’ at /usr/include/c++/13/bits/stl_algo.h:1910:25,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’ at /usr/include/c++/13/bits/stl_algo.h:1926:27:
/usr/include/c++/13/bits/stl_algo.h:1635:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1635 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’,
inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’ at /usr/include/c++/13/bits/stl_algo.h:1911:23,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’ at /usr/include/c++/13/bits/stl_algo.h:1926:27:
/usr/include/c++/13/bits/stl_heap.h:425:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
425 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/tagBam/tagBam.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/tagBam.o -MMD -MP -MF obj/tagBam.Td -c -o obj/tagBam.o src/tagBam/tagBam.cpp
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = bool (*)(const BED&, const BED&)]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘int BedSplit::doEuristicSplitOnTotalSize()’ at src/split/splitBed.cpp:285:14:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’ at /usr/include/c++/13/bits/stl_algo.h:1950:31,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = bool (*)(const BED&, const BED&)]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘int BedSplit::doEuristicSplitOnTotalSize()’ at src/split/splitBed.cpp:285:14:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/unionBedGraphs/unionBedGraphsMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/unionBedGraphsMain.o -MMD -MP -MF obj/unionBedGraphsMain.Td -c -o obj/unionBedGraphsMain.o src/unionBedGraphs/unionBedGraphsMain.cpp
In file included from /usr/include/c++/13/vector:72,
from src/utils/general/BedtoolsTypes.h:26,
from src/utils/FileRecordTools/Records/Record.h:13:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Interval&}; _Tp = Interval; _Alloc = std::allocator<Interval>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<Interval>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/algorithm:61,
from src/utils/fileType/FileRecordTypeChecker.h:18,
from src/utils/FileRecordTools/Records/Record.h:16:
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval*, vector<Interval> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const Interval&, const Interval&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >’ changed in GCC 7.1
1792 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval*, vector<Interval> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const Interval&, const Interval&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >’ changed in GCC 7.1
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >’ changed in GCC 7.1
In file included from /usr/include/c++/13/bits/stl_algo.h:61:
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval*, vector<Interval> >; _Distance = int; _Tp = Interval; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const Interval&, const Interval&)>]’:
/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval*, vector<Interval> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const Interval&, const Interval&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >’ changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >’ changed in GCC 7.1
1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator<Interval>]’,
inlined from ‘virtual bool SummaryFile::findNext(RecordKeyVector&)’ at src/summaryFile/summaryFile.cpp:52:57:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval*, vector<Interval> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const Interval&, const Interval&)>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<Interval*, vector<Interval> >; _Compare = bool (*)(const Interval&, const Interval&)]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘virtual bool SummaryFile::findNext(RecordKeyVector&)’ at src/summaryFile/summaryFile.cpp:60:13:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval*, vector<Interval> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const Interval&, const Interval&)>]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval*, vector<Interval> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const Interval&, const Interval&)>]’ at /usr/include/c++/13/bits/stl_algo.h:1950:31,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<Interval*, vector<Interval> >; _Compare = bool (*)(const Interval&, const Interval&)]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘virtual bool SummaryFile::findNext(RecordKeyVector&)’ at src/summaryFile/summaryFile.cpp:60:13:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >’ changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >’ changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/utils/BamTools/include/api/BamReader.h:1,
from src/tagBam/tagBam.h:17,
from src/tagBam/tagBam.cpp:13:
src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’:
src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
32 | sam_hdr_write(fp, hdr);
| ~~~~~~~~~~~~~^~~~~~~~~
* compiling src/unionBedGraphs/unionBedGraphs.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/unionBedGraphs.o -MMD -MP -MF obj/unionBedGraphs.Td -c -o obj/unionBedGraphs.o src/unionBedGraphs/unionBedGraphs.cpp
src/unionBedGraphs/unionBedGraphsMain.cpp: In function ‘int unionbedgraphs_main(int, char**)’:
src/unionBedGraphs/unionBedGraphsMain.cpp:46:10: warning: variable ‘haveFiles’ set but not used [-Wunused-but-set-variable]
46 | bool haveFiles = false;
| ^~~~~~~~~
src/unionBedGraphs/unionBedGraphsMain.cpp:48:10: warning: variable ‘haveGenome’ set but not used [-Wunused-but-set-variable]
48 | bool haveGenome = false;
| ^~~~~~~~~~
src/unionBedGraphs/unionBedGraphsMain.cpp:49:10: warning: variable ‘haveFiller’ set but not used [-Wunused-but-set-variable]
49 | bool haveFiller = true;
| ^~~~~~~~~~
* compiling src/windowBed/windowMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/windowMain.o -MMD -MP -MF obj/windowMain.Td -c -o obj/windowMain.o src/windowBed/windowMain.cpp
* compiling src/windowBed/windowBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/windowBed.o -MMD -MP -MF obj/windowBed.Td -c -o obj/windowBed.o src/windowBed/windowBed.cpp
In file included from /usr/include/c++/13/bits/stl_algo.h:61,
from /usr/include/c++/13/algorithm:61,
from src/unionBedGraphs/unionBedGraphs.cpp:17:
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PointWithDepth*, vector<PointWithDepth, allocator<PointWithDepth> > >; _Distance = int; _Tp = PointWithDepth; _Compare = __gnu_cxx::__ops::_Iter_comp_val<less<PointWithDepth> >]’:
/usr/include/c++/13/bits/stl_heap.h:135:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PointWithDepth*, std::vector<PointWithDepth, std::allocator<PointWithDepth> > >’ changed in GCC 7.1
135 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/utils/bedGraphFile/bedGraphFile.h:16,
from src/unionBedGraphs/unionBedGraphs.cpp:19:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const PointWithDepth&}; _Tp = PointWithDepth; _Alloc = std::allocator<PointWithDepth>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<PointWithDepth, std::allocator<PointWithDepth> >::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
* compiling src/windowMaker/windowMakerMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/windowMakerMain.o -MMD -MP -MF obj/windowMakerMain.Td -c -o obj/windowMakerMain.o src/windowMaker/windowMakerMain.cpp
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = PointWithDepth; _Alloc = std::allocator<PointWithDepth>]’,
inlined from ‘void std::priority_queue<_Tp, _Sequence, _Compare>::push(const value_type&) [with _Tp = PointWithDepth; _Sequence = std::vector<PointWithDepth, std::allocator<PointWithDepth> >; _Compare = std::less<PointWithDepth>]’ at /usr/include/c++/13/bits/stl_queue.h:740:13,
inlined from ‘void UnionBedGraphs::AddInterval(int)’ at src/unionBedGraphs/unionBedGraphs.cpp:228:15:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PointWithDepth*, std::vector<PointWithDepth, std::allocator<PointWithDepth> > >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = PointWithDepth; _Alloc = std::allocator<PointWithDepth>]’,
inlined from ‘void std::priority_queue<_Tp, _Sequence, _Compare>::push(const value_type&) [with _Tp = PointWithDepth; _Sequence = std::vector<PointWithDepth, std::allocator<PointWithDepth> >; _Compare = std::less<PointWithDepth>]’ at /usr/include/c++/13/bits/stl_queue.h:740:13,
inlined from ‘void UnionBedGraphs::AddInterval(int)’ at src/unionBedGraphs/unionBedGraphs.cpp:229:15:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PointWithDepth*, std::vector<PointWithDepth, std::allocator<PointWithDepth> > >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from src/utils/BamTools/include/api/BamReader.h:1,
from src/windowBed/windowBed.h:15,
from src/windowBed/windowBed.cpp:13:
src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’:
src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
32 | sam_hdr_write(fp, hdr);
| ~~~~~~~~~~~~~^~~~~~~~~
* compiling src/windowMaker/windowMaker.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/windowMaker.o -MMD -MP -MF obj/windowMaker.Td -c -o obj/windowMaker.o src/windowMaker/windowMaker.cpp
* compiling src/utils/FileRecordTools/FileRecordMgr.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/FileRecordMgr.o -MMD -MP -MF obj/FileRecordMgr.Td -c -o obj/FileRecordMgr.o src/utils/FileRecordTools/FileRecordMgr.cpp
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMgr.cpp:2:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/utils/FileRecordTools/FileRecordMergeMgr.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/FileRecordMergeMgr.o -MMD -MP -MF obj/FileRecordMergeMgr.Td -c -o obj/FileRecordMergeMgr.o src/utils/FileRecordTools/FileRecordMergeMgr.cpp
* compiling src/utils/FileRecordTools/FileReaders/FileReader.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/FileReader.o -MMD -MP -MF obj/FileReader.Td -c -o obj/FileReader.o src/utils/FileRecordTools/FileReaders/FileReader.cpp
* compiling src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/SingleLineDelimTextFileReader.o -MMD -MP -MF obj/SingleLineDelimTextFileReader.Td -c -o obj/SingleLineDelimTextFileReader.o src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp
* compiling src/utils/FileRecordTools/FileReaders/BamFileReader.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BamFileReader.o -MMD -MP -MF obj/BamFileReader.Td -c -o obj/BamFileReader.o src/utils/FileRecordTools/FileReaders/BamFileReader.cpp
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/FileRecordTools/FileRecordMergeMgr.cpp:9:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BufferedStreamMgr.o -MMD -MP -MF obj/BufferedStreamMgr.Td -c -o obj/BufferedStreamMgr.o src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp
* compiling src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/InputStreamMgr.o -MMD -MP -MF obj/InputStreamMgr.Td -c -o obj/InputStreamMgr.o src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
In file included from /usr/include/c++/13/vector:72,
from src/utils/fileType/FileRecordTypeChecker.h:16,
from src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.h:13,
from src/utils/FileRecordTools/FileReaders/FileReader.h:10,
from src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:12,
from src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:1:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘void Tokenize(const std::string&, std::vector<long long int>&, char)’ at src/utils/lineFileUtilities/lineFileUtilities.h:47:24:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/utils/FileRecordTools/Records/Record.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Record.o -MMD -MP -MF obj/Record.Td -c -o obj/Record.o src/utils/FileRecordTools/Records/Record.cpp
src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp: In member function ‘bool BufferedStreamMgr::readFileChunk()’:
src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:148:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
148 | if (_mainBufCurrLen < _useBufSize) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from src/utils/BamTools/include/api/BamReader.h:1,
from src/utils/FileRecordTools/FileReaders/InputStreamMgr.h:14,
from src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:8:
src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’:
src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
32 | sam_hdr_write(fp, hdr);
| ~~~~~~~~~~~~~^~~~~~~~~
* compiling src/utils/FileRecordTools/Records/EmptyRecord.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/EmptyRecord.o -MMD -MP -MF obj/EmptyRecord.Td -c -o obj/EmptyRecord.o src/utils/FileRecordTools/Records/EmptyRecord.cpp
* compiling src/utils/FileRecordTools/Records/Bed3Interval.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed3Interval.o -MMD -MP -MF obj/Bed3Interval.Td -c -o obj/Bed3Interval.o src/utils/FileRecordTools/Records/Bed3Interval.cpp
In file included from src/utils/FileRecordTools/Records/EmptyRecord.h:11,
from src/utils/FileRecordTools/Records/EmptyRecord.cpp:9:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11,
from src/utils/FileRecordTools/Records/Bed3Interval.cpp:1:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
* compiling src/utils/FileRecordTools/Records/Bed4Interval.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed4Interval.o -MMD -MP -MF obj/Bed4Interval.Td -c -o obj/Bed4Interval.o src/utils/FileRecordTools/Records/Bed4Interval.cpp
* compiling src/utils/FileRecordTools/Records/BedGraphInterval.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BedGraphInterval.o -MMD -MP -MF obj/BedGraphInterval.Td -c -o obj/BedGraphInterval.o src/utils/FileRecordTools/Records/BedGraphInterval.cpp
* compiling src/utils/FileRecordTools/Records/Bed5Interval.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed5Interval.o -MMD -MP -MF obj/Bed5Interval.Td -c -o obj/Bed5Interval.o src/utils/FileRecordTools/Records/Bed5Interval.cpp
* compiling src/utils/FileRecordTools/Records/Bed6Interval.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed6Interval.o -MMD -MP -MF obj/Bed6Interval.Td -c -o obj/Bed6Interval.o src/utils/FileRecordTools/Records/Bed6Interval.cpp
In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11,
from src/utils/FileRecordTools/Records/Bed4Interval.h:13,
from src/utils/FileRecordTools/Records/Bed4Interval.cpp:1:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11,
from src/utils/FileRecordTools/Records/BedGraphInterval.h:12,
from src/utils/FileRecordTools/Records/BedGraphInterval.cpp:1:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11,
from src/utils/FileRecordTools/Records/Bed5Interval.h:12,
from src/utils/FileRecordTools/Records/Bed5Interval.cpp:1:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11,
from src/utils/FileRecordTools/Records/Bed6Interval.h:12,
from src/utils/FileRecordTools/Records/Bed6Interval.cpp:1:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
* compiling src/utils/FileRecordTools/Records/PlusFields.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/PlusFields.o -MMD -MP -MF obj/PlusFields.Td -c -o obj/PlusFields.o src/utils/FileRecordTools/Records/PlusFields.cpp
* compiling src/utils/FileRecordTools/Records/GffRecord.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/GffRecord.o -MMD -MP -MF obj/GffRecord.Td -c -o obj/GffRecord.o src/utils/FileRecordTools/Records/GffRecord.cpp
* compiling src/utils/FileRecordTools/Records/GffPlusRecord.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/GffPlusRecord.o -MMD -MP -MF obj/GffPlusRecord.Td -c -o obj/GffPlusRecord.o src/utils/FileRecordTools/Records/GffPlusRecord.cpp
* compiling src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/NoPosPlusRecord.o -MMD -MP -MF obj/NoPosPlusRecord.Td -c -o obj/NoPosPlusRecord.o src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp
In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11,
from src/utils/FileRecordTools/Records/Bed6Interval.h:12,
from src/utils/FileRecordTools/Records/GffRecord.h:11,
from src/utils/FileRecordTools/Records/GffRecord.cpp:1:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11,
from src/utils/FileRecordTools/Records/Bed6Interval.h:12,
from src/utils/FileRecordTools/Records/GffRecord.h:11,
from src/utils/FileRecordTools/Records/GffPlusRecord.h:11,
from src/utils/FileRecordTools/Records/GffPlusRecord.cpp:1:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/NoPosPlusRecord.h:11,
from src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp:1:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/utils/FileRecordTools/Records/BedPlusInterval.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BedPlusInterval.o -MMD -MP -MF obj/BedPlusInterval.Td -c -o obj/BedPlusInterval.o src/utils/FileRecordTools/Records/BedPlusInterval.cpp
* compiling src/utils/FileRecordTools/Records/Bed12Interval.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed12Interval.o -MMD -MP -MF obj/Bed12Interval.Td -c -o obj/Bed12Interval.o src/utils/FileRecordTools/Records/Bed12Interval.cpp
* compiling src/utils/FileRecordTools/Records/BamRecord.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BamRecord.o -MMD -MP -MF obj/BamRecord.Td -c -o obj/BamRecord.o src/utils/FileRecordTools/Records/BamRecord.cpp
In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11,
from src/utils/FileRecordTools/Records/BedPlusInterval.h:11,
from src/utils/FileRecordTools/Records/BedPlusInterval.cpp:1:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
* compiling src/utils/FileRecordTools/Records/VcfRecord.cpp
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/VcfRecord.o -MMD -MP -MF obj/VcfRecord.Td -c -o obj/VcfRecord.o src/utils/FileRecordTools/Records/VcfRecord.cpp
In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11,
from src/utils/FileRecordTools/Records/Bed6Interval.h:12,
from src/utils/FileRecordTools/Records/Bed12Interval.h:11,
from src/utils/FileRecordTools/Records/Bed12Interval.cpp:1:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11,
from src/utils/FileRecordTools/Records/Bed6Interval.h:12,
from src/utils/FileRecordTools/Records/BamRecord.h:11,
from src/utils/FileRecordTools/Records/BamRecord.cpp:9:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11,
from src/utils/FileRecordTools/Records/BedPlusInterval.h:11,
from src/utils/FileRecordTools/Records/VcfRecord.h:11,
from src/utils/FileRecordTools/Records/VcfRecord.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
* compiling src/utils/FileRecordTools/Records/BlockMgr.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BlockMgr.o -MMD -MP -MF obj/BlockMgr.Td -c -o obj/BlockMgr.o src/utils/FileRecordTools/Records/BlockMgr.cpp
In file included from /usr/include/c++/13/vector:72,
from src/utils/general/BedtoolsTypes.h:26,
from src/utils/FileRecordTools/Records/Record.h:13:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘void Tokenize(const std::string&, std::vector<long long int>&, char)’ at src/utils/lineFileUtilities/lineFileUtilities.h:47:24:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12,
from src/utils/FileRecordTools/Records/BlockMgr.h:17,
from src/utils/FileRecordTools/Records/BlockMgr.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13,
from src/utils/FileRecordTools/Records/BlockMgr.cpp:9:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
* compiling src/utils/FileRecordTools/Records/StrandQueue.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/StrandQueue.o -MMD -MP -MF obj/StrandQueue.Td -c -o obj/StrandQueue.o src/utils/FileRecordTools/Records/StrandQueue.cpp
* compiling src/utils/FileRecordTools/Records/RecordMgr.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordMgr.o -MMD -MP -MF obj/RecordMgr.Td -c -o obj/RecordMgr.o src/utils/FileRecordTools/Records/RecordMgr.cpp
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/BlockMgr.cpp: In member function ‘int BlockMgr::getNonRedundantOverlap()’:
src/utils/FileRecordTools/Records/BlockMgr.cpp:194:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<long long int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
194 | for (int i = 1; i < _overlapStarts.size(); ++i)
| ~~^~~~~~~~~~~~~~~~~~~~~~~
* compiling src/utils/FileRecordTools/Records/RecordList.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordList.o -MMD -MP -MF obj/RecordList.Td -c -o obj/RecordList.o src/utils/FileRecordTools/Records/RecordList.cpp
In file included from /usr/include/c++/13/bits/stl_algo.h:61,
from /usr/include/c++/13/algorithm:61,
from src/utils/fileType/FileRecordTypeChecker.h:18,
from src/utils/FileRecordTools/Records/BlockMgr.h:16:
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1854 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/Records/RecordMgr.cpp:1:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >]’ at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from ‘int BlockMgr::getNonRedundantOverlap()’ at src/utils/FileRecordTools/Records/BlockMgr.cpp:190:7:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1950 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<long long int*, vector<long long int> >]’ at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from ‘int BlockMgr::getNonRedundantOverlap()’ at src/utils/FileRecordTools/Records/BlockMgr.cpp:191:7:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1950 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from src/utils/FileRecordTools/Records/BlockMgr.h:11:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘int BlockMgr::findBlockedOverlaps(RecordKeyVector&, RecordKeyVector&, RecordKeyVector&, RecordKeyVector*)’ at src/utils/FileRecordTools/Records/BlockMgr.cpp:266:30:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘int BlockMgr::findBlockedOverlaps(RecordKeyVector&, RecordKeyVector&, RecordKeyVector&, RecordKeyVector*)’ at src/utils/FileRecordTools/Records/BlockMgr.cpp:267:28:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘int BlockMgr::findBlockedOverlaps(RecordKeyVector&, RecordKeyVector&, RecordKeyVector&, RecordKeyVector*)’ at src/utils/FileRecordTools/Records/BlockMgr.cpp:276:27:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/utils/FileRecordTools/Records/RecordKeyList.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordKeyList.o -MMD -MP -MF obj/RecordKeyList.Td -c -o obj/RecordKeyList.o src/utils/FileRecordTools/Records/RecordKeyList.cpp
* compiling src/utils/FileRecordTools/Records/RecordKeyVector.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordKeyVector.o -MMD -MP -MF obj/RecordKeyVector.Td -c -o obj/RecordKeyVector.o src/utils/FileRecordTools/Records/RecordKeyVector.cpp
* compiling src/utils/bedFile/bedFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedFile.o -MMD -MP -MF obj/bedFile.Td -c -o obj/bedFile.o src/utils/bedFile/bedFile.cpp
* compiling src/utils/BinTree/BinTree.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BinTree.o -MMD -MP -MF obj/BinTree.Td -c -o obj/BinTree.o src/utils/BinTree/BinTree.cpp
* compiling src/utils/version/version.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/version.o -MMD -MP -MF obj/version.Td -c -o obj/version.o src/utils/version/version.cpp
* compiling src/utils/bedGraphFile/bedGraphFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedGraphFile.o -MMD -MP -MF obj/bedGraphFile.Td -c -o obj/bedGraphFile.o src/utils/bedGraphFile/bedGraphFile.cpp
In file included from src/utils/FileRecordTools/Records/RecordKeyList.h:11,
from src/utils/BinTree/BinTree.h:19,
from src/utils/BinTree/BinTree.cpp:1:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextIntersect.h:11,
from src/utils/BinTree/BinTree.h:20:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/utils/chromsweep/chromsweep.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/chromsweep.o -MMD -MP -MF obj/chromsweep.Td -c -o obj/chromsweep.o src/utils/chromsweep/chromsweep.cpp
In file included from /usr/include/c++/13/set:62,
from src/utils/general/BedtoolsTypes.h:27,
from src/utils/bedFile/bedFile.h:16,
from src/utils/bedFile/bedFile.cpp:12:
/usr/include/c++/13/bits/stl_tree.h: In function ‘std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = long long int; _Val = std::pair<const long long int, DEPTH>; _KeyOfValue = std::_Select1st<std::pair<const long long int, DEPTH> >; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, DEPTH> >]’:
/usr/include/c++/13/bits/stl_tree.h:2210:5: note: parameter passing for argument of type ‘std::_Rb_tree<long long int, std::pair<const long long int, DEPTH>, std::_Select1st<std::pair<const long long int, DEPTH> >, std::less<long long int>, std::allocator<std::pair<const long long int, DEPTH> > >::const_iterator’ changed in GCC 7.1
2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<long long int&&>, std::tuple<>}; _Key = long long int; _Val = std::pair<const long long int, DEPTH>; _KeyOfValue = std::_Select1st<std::pair<const long long int, DEPTH> >; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, DEPTH> >]’:
/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree<long long int, std::pair<const long long int, DEPTH>, std::_Select1st<std::pair<const long long int, DEPTH> >, std::less<long long int>, std::allocator<std::pair<const long long int, DEPTH> > >::const_iterator’ changed in GCC 7.1
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/utils/Contexts/ContextBase.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextBase.o -MMD -MP -MF obj/ContextBase.Td -c -o obj/ContextBase.o src/utils/Contexts/ContextBase.cpp
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextBase.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/utils/Contexts/ContextIntersect.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextIntersect.o -MMD -MP -MF obj/ContextIntersect.Td -c -o obj/ContextIntersect.o src/utils/Contexts/ContextIntersect.cpp
In file included from /usr/include/c++/13/vector:72,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/utils/chromsweep/chromsweep.cpp:12:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator<BED>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<BED>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/map:63,
from src/utils/general/BedtoolsTypes.h:28:
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long int; _Tp = DEPTH; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, DEPTH> >]’,
inlined from ‘void BedFile::countListHits(const BED&, int, bool, bool)’ at src/utils/bedFile/bedFile.cpp:624:62:
/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree<long long int, std::pair<const long long int, DEPTH>, std::_Select1st<std::pair<const long long int, DEPTH> >, std::less<long long int>, std::allocator<std::pair<const long long int, DEPTH> > >::const_iterator’ changed in GCC 7.1
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long int; _Tp = DEPTH; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, DEPTH> >]’,
inlined from ‘void BedFile::countListHits(const BED&, int, bool, bool)’ at src/utils/bedFile/bedFile.cpp:630:62:
/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree<long long int, std::pair<const long long int, DEPTH>, std::_Select1st<std::pair<const long long int, DEPTH> >, std::less<long long int>, std::allocator<std::pair<const long long int, DEPTH> > >::const_iterator’ changed in GCC 7.1
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long int; _Tp = DEPTH; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, DEPTH> >]’,
inlined from ‘void BedFile::countListHits(const BED&, int, bool, bool)’ at src/utils/bedFile/bedFile.cpp:631:60:
/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree<long long int, std::pair<const long long int, DEPTH>, std::_Select1st<std::pair<const long long int, DEPTH> >, std::less<long long int>, std::allocator<std::pair<const long long int, DEPTH> > >::const_iterator’ changed in GCC 7.1
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BED; _Alloc = std::allocator<BED>]’,
inlined from ‘void ChromSweep::ScanCache()’ at src/utils/chromsweep/chromsweep.cpp:90:32:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:65:
/usr/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const BED*, vector<BED> >; _ForwardIterator = BED*]’:
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >’ changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >; _ForwardIterator = BED*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const BED*, vector<BED> >; _ForwardIterator = BED*]’ at /usr/include/c++/13/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 BED*, vector<BED> >; _ForwardIterator = BED*; _Tp = BED]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = BED; _Alloc = std::allocator<BED>]’ at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from ‘constexpr std::pair<_T1, _T2>::pair(_U1&&, _U2&&) [with _U1 = BED&; _U2 = std::vector<BED>&; typename std::enable_if<(std::_PCC<true, _T1, _T2>::_MoveConstructiblePair<_U1, _U2>() && std::_PCC<true, _T1, _T2>::_ImplicitlyMoveConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = BED; _T2 = std::vector<BED>]’ at /usr/include/c++/13/bits/stl_pair.h:688:35,
inlined from ‘constexpr std::pair<typename std::__strip_reference_wrapper<typename std::decay<_Tp>::type>::__type, typename std::__strip_reference_wrapper<typename std::decay<_Tp2>::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = BED&; _T2 = vector<BED>&]’ at /usr/include/c++/13/bits/stl_pair.h:927:72,
inlined from ‘bool ChromSweep::ChromChange()’ at src/utils/chromsweep/chromsweep.cpp:124:36:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >; _ForwardIterator = BED*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const BED*, vector<BED> >; _ForwardIterator = BED*]’ at /usr/include/c++/13/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 BED*, vector<BED> >; _ForwardIterator = BED*; _Tp = BED]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = BED; _Alloc = std::allocator<BED>]’ at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from ‘constexpr std::pair<_T1, _T2>::pair(_U1&&, _U2&&) [with _U1 = BED&; _U2 = std::vector<BED>&; typename std::enable_if<(std::_PCC<true, _T1, _T2>::_MoveConstructiblePair<_U1, _U2>() && std::_PCC<true, _T1, _T2>::_ImplicitlyMoveConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = BED; _T2 = std::vector<BED>]’ at /usr/include/c++/13/bits/stl_pair.h:688:35,
inlined from ‘constexpr std::pair<typename std::__strip_reference_wrapper<typename std::decay<_Tp>::type>::__type, typename std::__strip_reference_wrapper<typename std::decay<_Tp2>::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = BED&; _T2 = vector<BED>&]’ at /usr/include/c++/13/bits/stl_pair.h:927:72,
inlined from ‘bool ChromSweep::ChromChange()’ at src/utils/chromsweep/chromsweep.cpp:130:36:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextIntersect.h:11,
from src/utils/Contexts/ContextIntersect.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BED; _Alloc = std::allocator<BED>]’,
inlined from ‘bool ChromSweep::Next(std::pair<BED, std::vector<BED> >&)’ at src/utils/chromsweep/chromsweep.cpp:184:36:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >; _ForwardIterator = BED*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const BED*, vector<BED> >; _ForwardIterator = BED*]’ at /usr/include/c++/13/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 BED*, vector<BED> >; _ForwardIterator = BED*; _Tp = BED]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = BED; _Alloc = std::allocator<BED>]’ at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from ‘constexpr std::pair<_T1, _T2>::pair(_U1&&, _U2&&) [with _U1 = BED&; _U2 = std::vector<BED>&; typename std::enable_if<(std::_PCC<true, _T1, _T2>::_MoveConstructiblePair<_U1, _U2>() && std::_PCC<true, _T1, _T2>::_ImplicitlyMoveConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = BED; _T2 = std::vector<BED>]’ at /usr/include/c++/13/bits/stl_pair.h:688:35,
inlined from ‘constexpr std::pair<typename std::__strip_reference_wrapper<typename std::decay<_Tp>::type>::__type, typename std::__strip_reference_wrapper<typename std::decay<_Tp2>::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = BED&; _T2 = vector<BED>&]’ at /usr/include/c++/13/bits/stl_pair.h:927:72,
inlined from ‘bool ChromSweep::Next(std::pair<BED, std::vector<BED> >&)’ at src/utils/chromsweep/chromsweep.cpp:190:36:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >; _ForwardIterator = BED*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const BED*, vector<BED> >; _ForwardIterator = BED*]’ at /usr/include/c++/13/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 BED*, vector<BED> >; _ForwardIterator = BED*; _Tp = BED]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >; _Tp = BED; _Alloc = std::allocator<BED>]’ at /usr/include/c++/13/bits/stl_vector.h:1619:35,
inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = BED; _Alloc = std::allocator<BED>]’ at /usr/include/c++/13/bits/vector.tcc:238:44,
inlined from ‘std::pair<_T1, _T2>& std::pair<_T1, _T2>::operator=(std::__conditional_t<std::__and_<std::is_copy_assignable<_T1>, std::is_copy_assignable<_T2> >::value, const std::pair<_T1, _T2>&, const std::__nonesuch&>) [with _T1 = BED; _T2 = std::vector<BED>]’ at /usr/include/c++/13/bits/stl_pair.h:732:9,
inlined from ‘bool ChromSweep::Next(std::pair<BED, std::vector<BED> >&)’ at src/utils/chromsweep/chromsweep.cpp:199:31:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const BED*, std::vector<BED> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from src/utils/general/BedtoolsTypes.h:26:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BEDCOVLIST&}; _Tp = BEDCOVLIST; _Alloc = std::allocator<BEDCOVLIST>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<BEDCOVLIST>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator<BED>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<BED>::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BED; _Alloc = std::allocator<BED>]’,
inlined from ‘void BedFile::allHits(std::string, CHRPOS, CHRPOS, std::string, std::vector<BED>&, bool, bool, float, bool)’ at src/utils/bedFile/bedFile.cpp:385:43:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BED; _Alloc = std::allocator<BED>]’,
inlined from ‘void BedFile::allHits(std::string, CHRPOS, CHRPOS, std::string, std::vector<BED>&, bool, bool, float, bool)’ at src/utils/bedFile/bedFile.cpp:387:43:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
* compiling src/utils/Contexts/ContextFisher.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextFisher.o -MMD -MP -MF obj/ContextFisher.Td -c -o obj/ContextFisher.o src/utils/Contexts/ContextFisher.cpp
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BED; _Alloc = std::allocator<BED>]’,
inlined from ‘void BedFile::addBEDIntoMap(BED)’ at src/utils/bedFile/bedFile.cpp:689:42:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BEDCOV&}; _Tp = BEDCOV; _Alloc = std::allocator<BEDCOV>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<BEDCOV>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BEDCOV; _Alloc = std::allocator<BEDCOV>]’,
inlined from ‘void BedFile::loadBedCovFileIntoMap()’ at src/utils/bedFile/bedFile.cpp:714:53:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BEDCOV*, std::vector<BEDCOV> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
* compiling src/utils/Contexts/ContextMap.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextMap.o -MMD -MP -MF obj/ContextMap.Td -c -o obj/ContextMap.o src/utils/Contexts/ContextMap.cpp
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BEDCOVLIST; _Alloc = std::allocator<BEDCOVLIST>]’,
inlined from ‘void BedFile::loadBedCovListFileIntoMap()’ at src/utils/bedFile/bedFile.cpp:739:57:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BEDCOVLIST*, std::vector<BEDCOVLIST> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextIntersect.h:11,
from src/utils/Contexts/ContextJaccard.h:11,
from src/utils/Contexts/ContextFisher.h:11,
from src/utils/Contexts/ContextFisher.cpp:6:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BED; _Alloc = std::allocator<BED>]’,
inlined from ‘void BedFile::loadBedFileIntoVector()’ at src/utils/bedFile/bedFile.cpp:775:30:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/algorithm:61,
from src/utils/bedFile/bedFile.h:30:
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1792 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1854 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algo.h:61:
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Distance = int; _Tp = BED; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
254 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’,
inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’ at /usr/include/c++/13/bits/stl_algo.h:1910:25,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’ at /usr/include/c++/13/bits/stl_algo.h:1926:27:
/usr/include/c++/13/bits/stl_algo.h:1635:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1635 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’,
inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’ at /usr/include/c++/13/bits/stl_algo.h:1911:23,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’ at /usr/include/c++/13/bits/stl_algo.h:1926:27:
/usr/include/c++/13/bits/stl_heap.h:425:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
425 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = bool (*)(const BED&, const BED&)]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘void BedFile::assignWeightsBasedOnSize()’ at src/utils/bedFile/bedFile.cpp:783:9:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1950 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/utils/Contexts/ContextSample.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextSample.o -MMD -MP -MF obj/ContextSample.Td -c -o obj/ContextSample.o src/utils/Contexts/ContextSample.cpp
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BED; _Alloc = std::allocator<BED>]’,
inlined from ‘void BedFile::loadBedFileIntoMapNoBin()’ at src/utils/bedFile/bedFile.cpp:753:50:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<BED*, vector<BED> >; _Compare = bool (*)(const BED&, const BED&)]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘void BedFile::loadBedFileIntoMapNoBin()’ at src/utils/bedFile/bedFile.cpp:764:13:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1950 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextIntersect.h:11,
from src/utils/Contexts/ContextMap.h:11,
from src/utils/Contexts/ContextMap.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/utils/Contexts/ContextSpacing.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextSpacing.o -MMD -MP -MF obj/ContextSpacing.Td -c -o obj/ContextSpacing.o src/utils/Contexts/ContextSpacing.cpp
* compiling src/utils/Contexts/ContextMerge.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextMerge.o -MMD -MP -MF obj/ContextMerge.Td -c -o obj/ContextMerge.o src/utils/Contexts/ContextMerge.cpp
* compiling src/utils/Contexts/ContextJaccard.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextJaccard.o -MMD -MP -MF obj/ContextJaccard.Td -c -o obj/ContextJaccard.o src/utils/Contexts/ContextJaccard.cpp
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextSample.h:11,
from src/utils/Contexts/ContextSample.cpp:7:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextSpacing.h:11,
from src/utils/Contexts/ContextSpacing.cpp:7:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/utils/Contexts/ContextClosest.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextClosest.o -MMD -MP -MF obj/ContextClosest.Td -c -o obj/ContextClosest.o src/utils/Contexts/ContextClosest.cpp
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextMerge.h:11,
from src/utils/Contexts/ContextMerge.cpp:9:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextIntersect.h:11,
from src/utils/Contexts/ContextJaccard.h:11,
from src/utils/Contexts/ContextJaccard.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
* compiling src/utils/Contexts/ContextSubtract.cpp
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextSubtract.o -MMD -MP -MF obj/ContextSubtract.Td -c -o obj/ContextSubtract.o src/utils/Contexts/ContextSubtract.cpp
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/utils/Contexts/ContextCoverage.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextCoverage.o -MMD -MP -MF obj/ContextCoverage.Td -c -o obj/ContextCoverage.o src/utils/Contexts/ContextCoverage.cpp
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextIntersect.h:11,
from src/utils/Contexts/ContextClosest.h:12,
from src/utils/Contexts/ContextClosest.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextIntersect.h:11,
from src/utils/Contexts/ContextSubtract.h:12,
from src/utils/Contexts/ContextSubtract.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/utils/Contexts/ContextComplement.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextComplement.o -MMD -MP -MF obj/ContextComplement.Td -c -o obj/ContextComplement.o src/utils/Contexts/ContextComplement.cpp
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextIntersect.h:11,
from src/utils/Contexts/ContextCoverage.h:12,
from src/utils/Contexts/ContextCoverage.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/utils/Contexts/ContextGroupBy.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextGroupBy.o -MMD -MP -MF obj/ContextGroupBy.Td -c -o obj/ContextGroupBy.o src/utils/Contexts/ContextGroupBy.cpp
* compiling src/utils/Contexts/ContextSummary.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextSummary.o -MMD -MP -MF obj/ContextSummary.Td -c -o obj/ContextSummary.o src/utils/Contexts/ContextSummary.cpp
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextComplement.h:12,
from src/utils/Contexts/ContextComplement.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/utils/general/ParseTools.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ParseTools.o -MMD -MP -MF obj/ParseTools.Td -c -o obj/ParseTools.o src/utils/general/ParseTools.cpp
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextGroupBy.h:11,
from src/utils/Contexts/ContextGroupBy.cpp:9:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextSummary.h:11,
from src/utils/Contexts/ContextSummary.cpp:7:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/utils/general/PushBackStreamBuf.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/PushBackStreamBuf.o -MMD -MP -MF obj/PushBackStreamBuf.Td -c -o obj/PushBackStreamBuf.o src/utils/general/PushBackStreamBuf.cpp
* compiling src/utils/general/CompressionTools.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/CompressionTools.o -MMD -MP -MF obj/CompressionTools.Td -c -o obj/CompressionTools.o src/utils/general/CompressionTools.cpp
* compiling src/utils/general/Tokenizer.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Tokenizer.o -MMD -MP -MF obj/Tokenizer.Td -c -o obj/Tokenizer.o src/utils/general/Tokenizer.cpp
* compiling src/utils/general/CommonHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/CommonHelp.o -MMD -MP -MF obj/CommonHelp.Td -c -o obj/CommonHelp.o src/utils/general/CommonHelp.cpp
* compiling src/utils/general/ErrorMsg.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ErrorMsg.o -MMD -MP -MF obj/ErrorMsg.Td -c -o obj/ErrorMsg.o src/utils/general/ErrorMsg.cpp
* compiling src/utils/general/Random.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Random.o -MMD -MP -MF obj/Random.Td -c -o obj/Random.o src/utils/general/Random.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Isrc/utils/gzstream -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/gzstream.o src/utils/gzstream/gzstream.C
* compiling src/utils/fileType/fileType.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fileType.o -MMD -MP -MF obj/fileType.Td -c -o obj/fileType.o src/utils/fileType/fileType.cpp
* compiling src/utils/fileType/FileRecordTypeChecker.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/FileRecordTypeChecker.o -MMD -MP -MF obj/FileRecordTypeChecker.Td -c -o obj/FileRecordTypeChecker.o src/utils/fileType/FileRecordTypeChecker.cpp
* compiling src/utils/bedFilePE/bedFilePE.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedFilePE.o -MMD -MP -MF obj/bedFilePE.Td -c -o obj/bedFilePE.o src/utils/bedFilePE/bedFilePE.cpp
* compiling src/utils/KeyListOps/KeyListOps.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/KeyListOps.o -MMD -MP -MF obj/KeyListOps.Td -c -o obj/KeyListOps.o src/utils/KeyListOps/KeyListOps.cpp
* compiling src/utils/KeyListOps/KeyListOpsMethods.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/KeyListOpsMethods.o -MMD -MP -MF obj/KeyListOpsMethods.Td -c -o obj/KeyListOpsMethods.o src/utils/KeyListOps/KeyListOpsMethods.cpp
src/utils/fileType/FileRecordTypeChecker.cpp: In member function ‘bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)’:
src/utils/fileType/FileRecordTypeChecker.cpp:366:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
366 | for (int j=0; j < len; j++) {
| ~~^~~~~
In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12,
from src/utils/KeyListOps/KeyListOpsMethods.h:15,
from src/utils/KeyListOps/KeyListOps.h:11,
from src/utils/KeyListOps/KeyListOps.cpp:7:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/KeyListOps/KeyListOps.cpp:8:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algo.h:61,
from /usr/include/c++/13/algorithm:61,
from src/utils/fileType/FileRecordTypeChecker.h:18,
from src/utils/FileRecordTools/Records/Record.h:16,
from src/utils/FileRecordTools/Records/RecordKeyVector.h:12,
from src/utils/KeyListOps/KeyListOpsMethods.h:15,
from src/utils/KeyListOps/KeyListOpsMethods.cpp:8:
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<greater<double> >]’:
/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<less<double> >]’:
/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<greater<double> >]’:
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<less<double> >]’:
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<less<double> >]’:
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<greater<double> >]’:
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/utils/NewChromsweep/NewChromsweep.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/NewChromsweep.o -MMD -MP -MF obj/NewChromsweep.Td -c -o obj/NewChromsweep.o src/utils/NewChromsweep/NewChromsweep.cpp
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<less<double> >]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = less<double>]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘void KeyListOpsMethods::sortArray(bool, bool)’ at src/utils/KeyListOps/KeyListOpsMethods.cpp:390:8,
inlined from ‘void KeyListOpsMethods::sortArray(bool, bool)’ at src/utils/KeyListOps/KeyListOpsMethods.cpp:386:6:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<less<double> >]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<less<double> >]’ at /usr/include/c++/13/bits/stl_algo.h:1950:31,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = less<double>]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘void KeyListOpsMethods::sortArray(bool, bool)’ at src/utils/KeyListOps/KeyListOpsMethods.cpp:390:8,
inlined from ‘void KeyListOpsMethods::sortArray(bool, bool)’ at src/utils/KeyListOps/KeyListOpsMethods.cpp:386:6:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<greater<double> >]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = greater<double>]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘void KeyListOpsMethods::sortArray(bool, bool)’ at src/utils/KeyListOps/KeyListOpsMethods.cpp:392:8,
inlined from ‘void KeyListOpsMethods::sortArray(bool, bool)’ at src/utils/KeyListOps/KeyListOpsMethods.cpp:386:6:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<greater<double> >]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<greater<double> >]’ at /usr/include/c++/13/bits/stl_algo.h:1950:31,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = greater<double>]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘void KeyListOpsMethods::sortArray(bool, bool)’ at src/utils/KeyListOps/KeyListOpsMethods.cpp:392:8,
inlined from ‘void KeyListOpsMethods::sortArray(bool, bool)’ at src/utils/KeyListOps/KeyListOpsMethods.cpp:386:6:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from src/utils/bedFilePE/bedFilePE.h:4,
from src/utils/bedFilePE/bedFilePE.cpp:15:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const MATE&}; _Tp = MATE; _Alloc = std::allocator<MATE>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<MATE>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MATE; _Alloc = std::allocator<MATE>]’,
inlined from ‘void BedFilePE::FindOverlapsPerBin(int, std::string, CHRPOS, CHRPOS, std::string, std::string, std::vector<MATE>&, float, bool, bool)’ at src/utils/bedFilePE/bedFilePE.cpp:446:39:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MATE; _Alloc = std::allocator<MATE>]’,
inlined from ‘void BedFilePE::FindOverlapsPerBin(int, std::string, CHRPOS, CHRPOS, std::string, std::string, std::vector<MATE>&, float, bool, bool)’ at src/utils/bedFilePE/bedFilePE.cpp:450:43:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MATE; _Alloc = std::allocator<MATE>]’,
inlined from ‘void BedFilePE::FindOverlapsPerBin(int, std::string, CHRPOS, CHRPOS, std::string, std::string, std::vector<MATE>&, float, bool, bool)’ at src/utils/bedFilePE/bedFilePE.cpp:454:43:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MATE; _Alloc = std::allocator<MATE>]’,
inlined from ‘void BedFilePE::FindOverlapsPerBin(int, std::string, CHRPOS, CHRPOS, std::string, std::string, std::vector<MATE>&, float, bool, bool)’ at src/utils/bedFilePE/bedFilePE.cpp:458:43:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MATE; _Alloc = std::allocator<MATE>]’,
inlined from ‘void BedFilePE::loadBedPEFileIntoMap()’ at src/utils/bedFilePE/bedFilePE.cpp:490:67:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MATE; _Alloc = std::allocator<MATE>]’,
inlined from ‘void BedFilePE::loadBedPEFileIntoMap()’ at src/utils/bedFilePE/bedFilePE.cpp:494:67:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
* compiling src/utils/NewChromsweep/CloseSweep.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/CloseSweep.o -MMD -MP -MF obj/CloseSweep.Td -c -o obj/CloseSweep.o src/utils/NewChromsweep/CloseSweep.cpp
In file included from src/utils/FileRecordTools/Records/RecordKeyList.h:11,
from src/utils/NewChromsweep/NewChromsweep.h:17,
from src/utils/NewChromsweep/NewChromsweep.cpp:13:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextIntersect.h:11,
from src/utils/NewChromsweep/NewChromsweep.cpp:14:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/utils/sequenceUtilities/sequenceUtils.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sequenceUtils.o -MMD -MP -MF obj/sequenceUtils.Td -c -o obj/sequenceUtils.o src/utils/sequenceUtilities/sequenceUtils.cpp
* compiling src/utils/tabFile/tabFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/tabFile.o -MMD -MP -MF obj/tabFile.Td -c -o obj/tabFile.o src/utils/tabFile/tabFile.cpp
src/utils/NewChromsweep/NewChromsweep.h: In constructor ‘NewChromSweep::NewChromSweep(ContextIntersect*)’:
src/utils/NewChromsweep/NewChromsweep.h:124:10: warning: ‘NewChromSweep::_testLastQueryRec’ will be initialized after [-Wreorder]
124 | bool _testLastQueryRec;
| ^~~~~~~~~~~~~~~~~
src/utils/NewChromsweep/NewChromsweep.h:93:14: warning: ‘bool NewChromSweep::_runToDbEnd’ [-Wreorder]
93 | bool _runToDbEnd;
| ^~~~~~~~~~~
src/utils/NewChromsweep/NewChromsweep.cpp:17:1: warning: when initialized here [-Wreorder]
17 | NewChromSweep::NewChromSweep(ContextIntersect *context)
| ^~~~~~~~~~~~~
* compiling src/utils/BamTools-Ancillary/BamAncillary.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BamAncillary.o -MMD -MP -MF obj/BamAncillary.Td -c -o obj/BamAncillary.o src/utils/BamTools-Ancillary/BamAncillary.cpp
In file included from src/utils/FileRecordTools/Records/RecordKeyList.h:11,
from src/utils/NewChromsweep/NewChromsweep.h:17,
from src/utils/NewChromsweep/CloseSweep.h:11,
from src/utils/NewChromsweep/CloseSweep.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/Contexts/ContextIntersect.h:11,
from src/utils/Contexts/ContextClosest.h:12,
from src/utils/NewChromsweep/CloseSweep.h:15:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
* compiling src/utils/BlockedIntervals/BlockedIntervals.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BlockedIntervals.o -MMD -MP -MF obj/BlockedIntervals.Td -c -o obj/BlockedIntervals.o src/utils/BlockedIntervals/BlockedIntervals.cpp
* compiling src/utils/Fasta/Fasta.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Fasta.o -MMD -MP -MF obj/Fasta.Td -c -o obj/Fasta.o src/utils/Fasta/Fasta.cpp
In file included from /usr/include/c++/13/vector:72,
from src/utils/general/FreeList.h:13,
from src/utils/general/BTlist.h:28,
from src/utils/NewChromsweep/NewChromsweep.h:16:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘void CloseSweep::addSingleRec(Record*, CHRPOS, int&, RecordKeyVector&)’ at src/utils/NewChromsweep/CloseSweep.cpp:442:27:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘void CloseSweep::addSingleRec(Record*, CHRPOS, int&, RecordKeyVector&)’ at src/utils/NewChromsweep/CloseSweep.cpp:442:27,
inlined from ‘int CloseSweep::addRecsToRetList(RecDistList::elemsType*, CHRPOS, RecordKeyVector&)’ at src/utils/NewChromsweep/CloseSweep.cpp:424:15:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘void CloseSweep::addSingleRec(Record*, CHRPOS, int&, RecordKeyVector&)’ at src/utils/NewChromsweep/CloseSweep.cpp:442:27,
inlined from ‘int CloseSweep::addRecsToRetList(RecDistList::elemsType*, CHRPOS, RecordKeyVector&)’ at src/utils/NewChromsweep/CloseSweep.cpp:428:15:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘void CloseSweep::addSingleRec(Record*, CHRPOS, int&, RecordKeyVector&)’ at src/utils/NewChromsweep/CloseSweep.cpp:442:27,
inlined from ‘int CloseSweep::addRecsToRetList(RecDistList::elemsType*, CHRPOS, RecordKeyVector&)’ at src/utils/NewChromsweep/CloseSweep.cpp:434:16:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from src/utils/general/BedtoolsTypes.h:26,
from src/utils/bedFile/bedFile.h:16,
from src/utils/BamTools-Ancillary/BamAncillary.h:12,
from src/utils/BamTools-Ancillary/BamAncillary.cpp:12:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator<BED>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<BED>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator<BED>]’:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’:
/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
529 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘CloseSweep::CloseSweep(ContextClosest*)’ at src/utils/NewChromsweep/CloseSweep.cpp:172:34:
/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1034 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘CloseSweep::CloseSweep(ContextClosest*)’ at src/utils/NewChromsweep/CloseSweep.cpp:173:41:
/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1034 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from src/utils/BlockedIntervals/BlockedIntervals.h:12,
from src/utils/BlockedIntervals/BlockedIntervals.cpp:12:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘void Tokenize(const std::string&, std::vector<long long int>&, char)’ at src/utils/lineFileUtilities/lineFileUtilities.h:47:24:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘void CloseSweep::addSingleRec(Record*, CHRPOS, int&, RecordKeyVector&)’ at src/utils/NewChromsweep/CloseSweep.cpp:442:27,
inlined from ‘void CloseSweep::checkMultiDbs(RecordKeyVector&)’ at src/utils/NewChromsweep/CloseSweep.cpp:499:18:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘void CloseSweep::addSingleRec(Record*, CHRPOS, int&, RecordKeyVector&)’ at src/utils/NewChromsweep/CloseSweep.cpp:442:27,
inlined from ‘void CloseSweep::checkMultiDbs(RecordKeyVector&)’ at src/utils/NewChromsweep/CloseSweep.cpp:506:18:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘void CloseSweep::addSingleRec(Record*, CHRPOS, int&, RecordKeyVector&)’ at src/utils/NewChromsweep/CloseSweep.cpp:442:27,
inlined from ‘void CloseSweep::checkMultiDbs(RecordKeyVector&)’ at src/utils/NewChromsweep/CloseSweep.cpp:513:18:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘void CloseSweep::addSingleRec(Record*, CHRPOS, int&, RecordKeyVector&)’ at src/utils/NewChromsweep/CloseSweep.cpp:442:27,
inlined from ‘void CloseSweep::checkMultiDbs(RecordKeyVector&)’ at src/utils/NewChromsweep/CloseSweep.cpp:519:16:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator<BED>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<BED>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator<BED>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<BED>::iterator’ changed in GCC 7.1
* compiling src/utils/Fasta/split.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/split.o -MMD -MP -MF obj/split.Td -c -o obj/split.o src/utils/Fasta/split.cpp
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BED; _Alloc = std::allocator<BED>]’,
inlined from ‘void GetBedBlocks(const BED&, bedVector&)’ at src/utils/BlockedIntervals/BlockedIntervals.cpp:74:28:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BED; _Alloc = std::allocator<BED>]’,
inlined from ‘void GetBedBlocks(const BED&, bedVector&)’ at src/utils/BlockedIntervals/BlockedIntervals.cpp:104:32:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator<BED>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = BED; _Alloc = std::allocator<BED>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘void GetBamBlocks(const BamTools::BamAlignment&, const std::string&, bedVector&, bool, bool)’ at src/utils/BlockedIntervals/BlockedIntervals.cpp:44:40:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator<BED>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = BED; _Alloc = std::allocator<BED>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘void GetBamBlocks(const BamTools::BamAlignment&, const std::string&, bedVector&, bool, bool)’ at src/utils/BlockedIntervals/BlockedIntervals.cpp:54:40:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator<BED>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = BED; _Alloc = std::allocator<BED>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘void GetBamBlocks(const BamTools::BamAlignment&, const std::string&, bedVector&, bool, bool)’ at src/utils/BlockedIntervals/BlockedIntervals.cpp:65:24:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/utils/VectorOps/VectorOps.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/VectorOps.o -MMD -MP -MF obj/VectorOps.Td -c -o obj/VectorOps.o src/utils/VectorOps/VectorOps.cpp
* compiling src/utils/GenomeFile/NewGenomeFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/NewGenomeFile.o -MMD -MP -MF obj/NewGenomeFile.Td -c -o obj/NewGenomeFile.o src/utils/GenomeFile/NewGenomeFile.cpp
* compiling src/utils/GenomeFile/GenomeFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/GenomeFile.o -MMD -MP -MF obj/GenomeFile.Td -c -o obj/GenomeFile.o src/utils/GenomeFile/GenomeFile.cpp
* compiling src/utils/RecordOutputMgr/RecordOutputMgr.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordOutputMgr.o -MMD -MP -MF obj/RecordOutputMgr.Td -c -o obj/RecordOutputMgr.o src/utils/RecordOutputMgr/RecordOutputMgr.cpp
src/utils/GenomeFile/GenomeFile.cpp: In member function ‘void GenomeFile::loadGenomeFileIntoMap()’:
src/utils/GenomeFile/GenomeFile.cpp:60:26: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable]
60 | long c2;
| ^~
In file included from /usr/include/c++/13/bits/stl_algo.h:61,
from /usr/include/c++/13/algorithm:61,
from src/utils/VectorOps/VectorOps.h:21,
from src/utils/VectorOps/VectorOps.cpp:15:
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<greater<double> >]’:
/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<less<double> >]’:
/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<less<double> >]’:
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/RecordOutputMgr/RecordOutputMgr.h:11,
from src/utils/RecordOutputMgr/RecordOutputMgr.cpp:8:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<greater<double> >]’:
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
In file included from /usr/include/c++/13/vector:72,
from src/utils/general/BedtoolsTypes.h:26,
from src/utils/GenomeFile/NewGenomeFile.h:18,
from src/utils/GenomeFile/NewGenomeFile.cpp:12:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function ‘void RecordOutputMgr::printClosest(RecordKeyVector&, const std::vector<long long int>*)’:
src/utils/RecordOutputMgr/RecordOutputMgr.cpp:170:56: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
170 | if (context->getNumClosestHitsWanted() > keyList.size())
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function ‘void RecordOutputMgr::reportOverlapSummary(RecordKeyVector&)’:
src/utils/RecordOutputMgr/RecordOutputMgr.cpp:456:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
456 | for (size_t i = 0; i < _context->getNumInputFiles(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘void NewGenomeFile::loadGenomeFileIntoMap()’ at src/utils/GenomeFile/NewGenomeFile.cpp:90:26:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘void NewGenomeFile::loadGenomeFileIntoMap()’ at src/utils/GenomeFile/NewGenomeFile.cpp:105:25:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/utils/GenomeFile/GenomeFile.cpp:12:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]’,
inlined from ‘void GenomeFile::loadGenomeFileIntoMap()’ at src/utils/GenomeFile/GenomeFile.cpp:70:48:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
* compiling src/utils/ToolBase/ToolBase.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ToolBase.o -MMD -MP -MF obj/ToolBase.Td -c -o obj/ToolBase.o src/utils/ToolBase/ToolBase.cpp
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<less<double> >]’:
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/utils/driver/BedtoolsDriver.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BedtoolsDriver.o -MMD -MP -MF obj/BedtoolsDriver.Td -c -o obj/BedtoolsDriver.o src/utils/driver/BedtoolsDriver.cpp
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<greater<double> >]’:
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12,
from src/utils/ToolBase/ToolBase.h:11,
from src/utils/ToolBase/ToolBase.cpp:1:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/RecordOutputMgr/RecordOutputMgr.h:11,
from src/utils/ToolBase/ToolBase.h:12:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
cd src/utils/htslib && make lib-static
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/utils/htslib'
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c
In file included from /usr/include/c++/13/vector:72,
from src/utils/VectorOps/VectorOps.h:15:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘std::back_insert_iterator<_Container>& std::back_insert_iterator<_Container>::operator=(typename _Container::value_type&&) [with _Container = std::vector<double>]’ at /usr/include/c++/13/bits/stl_iterator.h:747:22,
inlined from ‘_OIter std::transform(_IIter, _IIter, _OIter, _UnaryOperation) [with _IIter = __gnu_cxx::__normal_iterator<__cxx11::basic_string<char>*, vector<__cxx11::basic_string<char> > >; _OIter = back_insert_iterator<vector<double> >; _UnaryOperation = double (*)(const __cxx11::basic_string<char>&)]’ at /usr/include/c++/13/bits/stl_algo.h:4309:12,
inlined from ‘std::string VectorOps::GetDistinctSortNum(bool)’ at src/utils/VectorOps/VectorOps.cpp:277:14:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<less<double> >]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = less<double>]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘std::string VectorOps::GetDistinctSortNum(bool)’ at src/utils/VectorOps/VectorOps.cpp:280:10:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<less<double> >]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<less<double> >]’ at /usr/include/c++/13/bits/stl_algo.h:1950:31,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = less<double>]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘std::string VectorOps::GetDistinctSortNum(bool)’ at src/utils/VectorOps/VectorOps.cpp:280:10:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<greater<double> >]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = greater<double>]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘std::string VectorOps::GetDistinctSortNum(bool)’ at src/utils/VectorOps/VectorOps.cpp:282:10:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<greater<double> >]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<greater<double> >]’ at /usr/include/c++/13/bits/stl_algo.h:1950:31,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = greater<double>]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘std::string VectorOps::GetDistinctSortNum(bool)’ at src/utils/VectorOps/VectorOps.cpp:282:10:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘std::back_insert_iterator<_Container>& std::back_insert_iterator<_Container>::operator=(typename _Container::value_type&&) [with _Container = std::vector<double>]’ at /usr/include/c++/13/bits/stl_iterator.h:747:22,
inlined from ‘_OIter std::transform(_IIter, _IIter, _OIter, _UnaryOperation) [with _IIter = __gnu_cxx::__normal_iterator<__cxx11::basic_string<char>*, vector<__cxx11::basic_string<char> > >; _OIter = back_insert_iterator<vector<double> >; _UnaryOperation = double (*)(const __cxx11::basic_string<char>&)]’ at /usr/include/c++/13/bits/stl_algo.h:4309:12,
inlined from ‘double VectorOps::GetSum()’ at src/utils/VectorOps/VectorOps.cpp:74:14:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘std::back_insert_iterator<_Container>& std::back_insert_iterator<_Container>::operator=(typename _Container::value_type&&) [with _Container = std::vector<double>]’ at /usr/include/c++/13/bits/stl_iterator.h:747:22,
inlined from ‘_OIter std::transform(_IIter, _IIter, _OIter, _UnaryOperation) [with _IIter = __gnu_cxx::__normal_iterator<__cxx11::basic_string<char>*, vector<__cxx11::basic_string<char> > >; _OIter = back_insert_iterator<vector<double> >; _UnaryOperation = double (*)(const __cxx11::basic_string<char>&)]’ at /usr/include/c++/13/bits/stl_algo.h:4309:12,
inlined from ‘double VectorOps::GetMean()’ at src/utils/VectorOps/VectorOps.cpp:81:14:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘std::back_insert_iterator<_Container>& std::back_insert_iterator<_Container>::operator=(typename _Container::value_type&&) [with _Container = std::vector<double>]’ at /usr/include/c++/13/bits/stl_iterator.h:747:22,
inlined from ‘_OIter std::transform(_IIter, _IIter, _OIter, _UnaryOperation) [with _IIter = __gnu_cxx::__normal_iterator<__cxx11::basic_string<char>*, vector<__cxx11::basic_string<char> > >; _OIter = back_insert_iterator<vector<double> >; _UnaryOperation = double (*)(const __cxx11::basic_string<char>&)]’ at /usr/include/c++/13/bits/stl_algo.h:4309:12,
inlined from ‘double VectorOps::GetMax()’ at src/utils/VectorOps/VectorOps.cpp:152:14:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘std::back_insert_iterator<_Container>& std::back_insert_iterator<_Container>::operator=(typename _Container::value_type&&) [with _Container = std::vector<double>]’ at /usr/include/c++/13/bits/stl_iterator.h:747:22,
inlined from ‘_OIter std::transform(_IIter, _IIter, _OIter, _UnaryOperation) [with _IIter = __gnu_cxx::__normal_iterator<__cxx11::basic_string<char>*, vector<__cxx11::basic_string<char> > >; _OIter = back_insert_iterator<vector<double> >; _UnaryOperation = double (*)(const __cxx11::basic_string<char>&)]’ at /usr/include/c++/13/bits/stl_algo.h:4309:12,
inlined from ‘double VectorOps::GetMin()’ at src/utils/VectorOps/VectorOps.cpp:138:14:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘std::back_insert_iterator<_Container>& std::back_insert_iterator<_Container>::operator=(typename _Container::value_type&&) [with _Container = std::vector<double>]’ at /usr/include/c++/13/bits/stl_iterator.h:747:22,
inlined from ‘_OIter std::transform(_IIter, _IIter, _OIter, _UnaryOperation) [with _IIter = __gnu_cxx::__normal_iterator<__cxx11::basic_string<char>*, vector<__cxx11::basic_string<char> > >; _OIter = back_insert_iterator<vector<double> >; _UnaryOperation = double (*)(const __cxx11::basic_string<char>&)]’ at /usr/include/c++/13/bits/stl_algo.h:4309:12,
inlined from ‘double VectorOps::GetAbsMax()’ at src/utils/VectorOps/VectorOps.cpp:159:14:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘std::back_insert_iterator<_Container>& std::back_insert_iterator<_Container>::operator=(typename _Container::value_type&&) [with _Container = std::vector<double>]’ at /usr/include/c++/13/bits/stl_iterator.h:747:22,
inlined from ‘_OIter std::transform(_IIter, _IIter, _OIter, _UnaryOperation) [with _IIter = __gnu_cxx::__normal_iterator<__cxx11::basic_string<char>*, vector<__cxx11::basic_string<char> > >; _OIter = back_insert_iterator<vector<double> >; _UnaryOperation = double (*)(const __cxx11::basic_string<char>&)]’ at /usr/include/c++/13/bits/stl_algo.h:4309:12,
inlined from ‘double VectorOps::GetAbsMin()’ at src/utils/VectorOps/VectorOps.cpp:145:14:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘std::back_insert_iterator<_Container>& std::back_insert_iterator<_Container>::operator=(typename _Container::value_type&&) [with _Container = std::vector<double>]’ at /usr/include/c++/13/bits/stl_iterator.h:747:22,
inlined from ‘_OIter std::transform(_IIter, _IIter, _OIter, _UnaryOperation) [with _IIter = __gnu_cxx::__normal_iterator<__cxx11::basic_string<char>*, vector<__cxx11::basic_string<char> > >; _OIter = back_insert_iterator<vector<double> >; _UnaryOperation = double (*)(const __cxx11::basic_string<char>&)]’ at /usr/include/c++/13/bits/stl_algo.h:4309:12,
inlined from ‘double VectorOps::GetMedian()’ at src/utils/VectorOps/VectorOps.cpp:116:14:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]’ at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from ‘double VectorOps::GetMedian()’ at src/utils/VectorOps/VectorOps.cpp:119:9:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/13/bits/stl_algo.h:1950:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]’ at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from ‘double VectorOps::GetMedian()’ at src/utils/VectorOps/VectorOps.cpp:119:9:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12,
from src/utils/FileRecordTools/FileRecordMgr.h:23,
from src/utils/FileRecordTools/FileRecordMergeMgr.h:11,
from src/utils/Contexts/ContextBase.h:23,
from src/utils/driver/BedtoolsDriver.h:1,
from src/utils/driver/BedtoolsDriver.cpp:1:
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13:
src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’
15 | class EmptyRecord : public Record {
| ^~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14:
src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’
19 | class Bed3Interval : public Record {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15:
src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’
17 | class Bed4Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16:
src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’
16 | class Bed5Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
16 | class BedGraphInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
16 | class Bed6Interval : public Bed3Interval {
| ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
16 | class BedPlusInterval : public Bed3Interval {
| ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
30 | const Bed12Interval &operator=(const Bed12Interval &other);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
25 | virtual const BamRecord &operator=(const BamRecord &);
| ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’
15 | class VcfRecord : public BedPlusInterval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
15 | class GffRecord : public Bed6Interval {
| ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
16 | class GffPlusRecord : public GffRecord {
| ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
76 | virtual const Record & operator=(const Record &);
| ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
16 | class NoPosPlusRecord : public Record {
| ^~~~~~~~~~~~~~~
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.9"' > version.h
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c
- Creating executables for old CLI.
done.
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_samtools.o cram/cram_samtools.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/files.o cram/files.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/rANS_static.o cram/rANS_static.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/sam_header.o cram/sam_header.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c
hts.c: In function ‘hts_idx_init’:
hts.c:1397:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ [-Woverflow]
1397 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu;
| ^~~
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
ranlib libhts.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/utils/htslib'
- Building main bedtools binary.
g++ -Wl,-z,relro -Wl,-z,now -o bin/bedtools obj/bedtools.o obj/htsutil.o obj/annotateMain.o obj/annotateBed.o obj/bamToBed.o obj/bamToFastqMain.o obj/bamToFastq.o obj/bedToBam.o obj/bedpeToBam.o obj/bedToIgv.o obj/bed12ToBed6.o obj/closestHelp.o obj/closestFile.o obj/clusterMain.o obj/clusterBed.o obj/complementHelp.o obj/complementFile.o obj/coverageHelp.o obj/coverageFile.o obj/expand.o obj/fastaFromBedMain.o obj/fastaFromBed.o obj/flankBedMain.o obj/flankBed.o obj/genomeCoverageMain.o obj/genomeCoverageBed.o obj/getOverlap.o obj/groupByHelp.o obj/groupBy.o obj/intersectHelp.o obj/intersectFile.o obj/fisherHelp.o obj/fisher.o obj/kfunc.o obj/jaccardHelp.o obj/jaccard.o obj/linksMain.o obj/linksBed.o obj/maskFastaFromBedMain.o obj/maskFastaFromBed.o obj/mapHelp.o obj/mapFile.o obj/mergeHelp.o obj/mergeFile.o obj/multiBamCovMain.o obj/multiBamCov.o obj/multiIntersectBedMain.o obj/multiIntersectBed.o obj/nucBedMain.o obj/nucBed.o obj/pairToBedMain.o obj/pairToBed.o obj/pairToPairMain.o obj/pairToPair.o obj/randomBedMain.o obj/randomBed.o obj/regressTestMain.o obj/RegressTest.o obj/reldistMain.o obj/reldist.o obj/sampleHelp.o obj/sampleFile.o obj/shiftBedMain.o obj/shiftBed.o obj/shuffleBedMain.o obj/shuffleBed.o obj/slopBedMain.o obj/slopBed.o obj/sortMain.o obj/sortBed.o obj/spacingHelp.o obj/spacingFile.o obj/splitBedMain.o obj/splitBed.o obj/subtractHelp.o obj/subtractFile.o obj/summaryHelp.o obj/summaryFile.o obj/tagBamMain.o obj/tagBam.o obj/unionBedGraphsMain.o obj/unionBedGraphs.o obj/windowMain.o obj/windowBed.o obj/windowMakerMain.o obj/windowMaker.o obj/FileRecordMgr.o obj/FileRecordMergeMgr.o obj/FileReader.o obj/SingleLineDelimTextFileReader.o obj/BamFileReader.o obj/BufferedStreamMgr.o obj/InputStreamMgr.o obj/Record.o obj/EmptyRecord.o obj/Bed3Interval.o obj/Bed4Interval.o obj/BedGraphInterval.o obj/Bed5Interval.o obj/Bed6Interval.o obj/PlusFields.o obj/GffRecord.o obj/GffPlusRecord.o obj/NoPosPlusRecord.o obj/BedPlusInterval.o obj/Bed12Interval.o obj/BamRecord.o obj/VcfRecord.o obj/BlockMgr.o obj/StrandQueue.o obj/RecordMgr.o obj/RecordList.o obj/RecordKeyList.o obj/RecordKeyVector.o obj/bedFile.o obj/BinTree.o obj/version.o obj/bedGraphFile.o obj/chromsweep.o obj/ContextBase.o obj/ContextIntersect.o obj/ContextFisher.o obj/ContextMap.o obj/ContextSample.o obj/ContextSpacing.o obj/ContextMerge.o obj/ContextJaccard.o obj/ContextClosest.o obj/ContextSubtract.o obj/ContextCoverage.o obj/ContextComplement.o obj/ContextGroupBy.o obj/ContextSummary.o obj/ParseTools.o obj/PushBackStreamBuf.o obj/CompressionTools.o obj/Tokenizer.o obj/CommonHelp.o obj/ErrorMsg.o obj/Random.o obj/gzstream.o obj/fileType.o obj/FileRecordTypeChecker.o obj/bedFilePE.o obj/KeyListOps.o obj/KeyListOpsMethods.o obj/NewChromsweep.o obj/CloseSweep.o obj/sequenceUtils.o obj/tabFile.o obj/BamAncillary.o obj/BlockedIntervals.o obj/Fasta.o obj/split.o obj/VectorOps.o obj/NewGenomeFile.o obj/GenomeFile.o obj/RecordOutputMgr.o obj/ToolBase.o obj/BedtoolsDriver.o src/utils/htslib/libhts.a -lz -lm -lbz2 -llzma -lpthread
done.
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f debian/bedtools.debhelper.log
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mv test/shuffle debian/
htsutil="../../bin/bedtools htsutil" \
dh_auto_test
make -j4 test
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Testing bedtools bamtobed:
bamtobed.t1...ok
bamtobed.t2...ok
bamtobed.t3...ok
bamtobed.t4...ok
bamtobed.t5...ok
bamtobed.t6...ok
bamtobed.t7...ok
bamtobed.t8...ok
bamtobed.t9...ok
bamtobed.t10...ok
bamtobed.t9...ok
bamtobed.t11...ok
bamtobed.t12..ok
bamtobed.t13..ok
Testing bedtools bamtofastq:
ok
ok
Testing bedtools bed12tobed6:
bed12tobed6.t1...ok
bed12tobed6.t2...ok
bed12tobed6.t3...ok
bed12tobed6.t4...ok
bed12tobed6.t5...ok
Testing bedtools bedtobam:
bedtobam.t1...ok
Testing bedtools bigchroms:
bigchroms.t01...ok
bigchroms.t02...ok
bigchroms.t03... skip set env var 'BT_NO_BIG_FILES' to run this test
bigchroms.t04... merge ok
bigchroms.t05... closest ok
Testing bedtools closest:
closest.t1...ok
closest.t2...ok
closest.t3...ok
closest.t4...ok
closest.t5...ok
closest.t6...ok
closest.t7...ok
closest.t8...ok
closest.t9...ok
closest.t10...ok
closest.t11...ok
closest.t13...ok
closest.t14...ok
closest.t15...ok
closest.t16...ok
closest.t17...ok
closest.t18...ok
closest.t19...ok
closest.t20...ok
closest.t21...ok
closest.t22...ok
closest.t23...ok
closest.t24...ok
closest.t25...ok
closest.t26...ok
closest.t27...ok
closest.t28...ok
closest.t29...ok
closest.t30...ok
closest.t31...ok
closest.t32...ok
closest.t33...ok
closest.t34...ok
closest.t35...ok
closest.t36...ok
closest.t37...ok
closest.t38...ok
closest.t39...ok
closest.t40...ok
closest.t41...ok
closest.t42...ok
closest.t43...ok
closest.t44...ok
closest.t45...ok
closest.t46...ok
closest.t47...ok
closest.t48...ok
closest.t49...ok
closest.t50...ok
closest.t51...ok
closest.t52...ok
closest.t53...ok
closest.t54...ok
closest.t55...ok
closest.t56...ok
closest.t57...ok
closest.t58...ok
closest.t59...ok
closest.t60...ok
closest.t61...ok
closest.t62...ok
closest.t63...ok
closest.t64...ok
closest.t65...ok
closest.t66...ok
closest.t67...ok
closest.t68...ok
closest.t69...ok
closest.t70...ok
closest.t71...ok
###########################################################
#
# CHROMOSOME SORT ORDER AND NAMING CONVENTIONS
#
###########################################################
closest.t01...ok
closest.t02...ok
closest.t03...ok
closest.t04...ok
closest.t05...ok
closest.t06...ok
closest.t07...ok
closest.t08...ok
closest.t09...ok
closest.t10...ok
closest.t11...ok
closest.t12...ok
closest.t13...ok
closest.t14...ok
closest.t15...ok
closest.t16...ok
closest.t17...ok
closest.t18...ok
closest.t19...ok
closest.20...ok
closest.21...ok
closest.22...ok
closest.23...ok
###########################################################
#
# K CLOSEST HITS TESTS
#
###########################################################
kclosest.t1...ok
kclosest.t2...ok
kclosest.t3...ok
kclosest.t4...ok
kclosest.t5...ok
kclosest.t6...ok
kclosest.t7...ok
kclosest.t8...ok
kclosest.t9...ok
kclosest.t10...ok
kclosest.t11...Warning: Fewer hits (5) found on chr1 than requested (7). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t12...Warning: Fewer hits (5) found on chr1 than requested (7). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t13...Warning: Fewer hits (3) found on chr1 than requested (7). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t14...Warning: Fewer hits (1) found on chr1 than requested (7). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t15...Warning: Fewer hits (11) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t16...ok
kclosest.t17...Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t18...Warning: Fewer hits (11) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t19...Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t20...Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t21...Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t22...Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t23...Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t24...Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t25...Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t26...Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t27...Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t28...Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t29...Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t30...ok
kclosest.t31...Warning: Fewer hits (9) found on chr1 than requested (10). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t32...Warning: Fewer hits (9) found on chr1 than requested (10). It is likely that there are fewer total records on that chromosome than requested.
ok
kclosest.t33...ok
kclosest.t34...ok
kclosest.t35...ok
kclosest.t36...ok
kclosest.t37...ok
kclosest.t38...ok
kclosest.t39...ok
kclosest.t40...ok
kclosest.t41...ok
kclosest.t42...ok
kclosest.t43...ok
kclosest.t44...ok
kclosest.t45...ok
Testing bedtools cluster:
cluster.t1...ok
cluster.t2...ok
Testing bedtools complement:
complement.t1...ok
complement.t2...ok
complement.t3...ok
complement.t4...ok
complement.t5...ok
complement.t6...ok
complement.t7...ok
complement.t8...ok
complement.t9...ok
complement.t9...ok
complement.t10...ok
Testing bedtools coverage:
coverage.t1...ok
coverage.t1b...ok
coverage.t2...ok
coverage.t2b...ok
coverage.t3...ok
coverage.t3b...ok
coverage.t4...ok
coverage.t4b...ok
coverage.t5...ok
coverage.t5b...ok
coverage.t6...ok
coverage.t6b...ok
coverage.t7...ok
coverage.t7b...ok
coverage.t8...ok
coverage.t8b...ok
coverage.t9...ok
coverage.t9b...ok
coverage.t10...ok
coverage.t10b...ok
coverage.t11...ok
coverage.t11b...ok
coverage.t12...ok
coverage.t12b...ok
coverage.t13...ok
coverage.t13b...ok
coverage.t14...ok
coverage.t14b...ok
coverage.t15...ok
coverage.t15b...ok
coverage.t16...ok
coverage.t16b...ok
coverage.t17...ok
coverage.t17b...ok
coverage.t18...ok
coverage.t18b...ok
coverage.t19...ok
coverage.t19b...ok
coverage.t20...ok
Testing bedtools expand:
expand.t1...ok
expand.t2...ok
expand.t3...ok
Testing bedtools fisher:
fisher.t1...ok
fisher.t2...ok
fisher.t3...ok
fisher.t4...ok
fisher.t5...ok
fisher.t6...ok
Testing bedtools flank:
flank.t1...ok
flank.t2...ok
flank.t3...ok
flank.t4...ok
flank.t5...ok
flank.t6...ok
flank.t7...ok
flank.t8...ok
flank.t9...ok
flank.t10...ok
flank.t11...ok
Testing bedtools general:
general.t01...ok
general.t02...ok
general.t03...ok
general.t05...ok
general.t06...ok
general.t07...ok
general.t08...ok
general.t09...ok
general.t10...ok
general.t11...ok
general.t12...ok
general.t13...ok
general.t14...ok
general.15...ok
general.t16...ok
general.t17...ok
general.t18...ok
general.t19...ok
general.t20...ok
general.t21...ok
general.22...ok
general.t23...ok
general.t24...ok
general.t25...ok
general.t26...ok
general.t27...ok
general.t28...ok
general.29...ok
general.t30...ok
general.t31...ok
general.t32...ok
general.t33...ok
general.t34...ok
general.t35...ok
general.36...ok
general.t37...ok
general.t38...ok
general.t39...ok
general.t40...ok
general.t41...ok
general.t42...ok
general.t43...ok
general.t44...ok
general.t45...ok
general.t46...ok
Testing bedtools genomecov:
genomecov.t1...ok
genomecov.t2...ok
genomecov.t3...ok
genomecov.t4...ok
genomecov.t5...ok
genomecov.t6...ok
genomecov.t7...ok
genomecov.t8...ok
genomecov.t9...ok
genomecov.t10...ok
genomecov.t11...ok
genomecov.t12...ok
genomecov.t13...ok
genomecov.t14...ok
genomecov.t15...ok
genomecov.t16...ok
genomecov.t17...ok
genomecov.t18...ok
Testing bedtools getfasta:
getfasta.t01...ok
getfasta.t02...ok
getfasta.t03...ok
getfasta.t04...ok
getfasta.t05...ok
getfasta.t06...ok
getfasta.t07...ok
getfasta.t08...ok
getfasta.t09...ok
getfasta.t10...ok
getfasta.t11...ok
getfasta.t12a...ok
getfasta.t12a...ok
getfasta.t12b...ok
getfasta.t13a...ok
getfasta.t13b...ok
getfasta.t13c...ok
getfasta.t14...ok
getfasta.t15...ok
getfasta.t134..ok
getfasta.t16..ok
getfasta.t17..ok
getfasta.t18...ok
Testing bedtools groupby:
groupby.t1...ok
groupby.t2...ok
groupby.t3...ok
groupby.t4...ok
groupby.t5...ok
groupby.t6...ok
groupby.t7...ok
groupby.t8...ok
groupby.t9...ok
groupby.t10...ok
groupby.t11...ok
groupby.t12...ok
groupby.t13...ok
groupby.t14...ok
groupby.t16...ok
groupby.t17...ok
groupby.t18...ok
groupby.t19...\c
ok
groupby.t20...\c
ok
Testing bedtools intersect:
intersect.t01...ok
intersect.t02...ok
intersect.t03...ok
intersect.t04...ok
intersect.t05...ok
intersect.t06...ok
intersect.t07...ok
intersect.t08...ok
intersect.t09...ok
intersect.t10...ok
intersect.t11...ok
intersect.t12...ok
intersect.t13...ok
intersect.t14...ok
intersect.t15...ok
intersect.t16...ok
intersect.t17...ok
intersect.t18...ok
intersect.t19...ok
intersect.t20...ok
intersect.t21...ok
intersect.t22...ok
intersect.t22.a...ok
intersect.t22.b...ok
intersect.t22.c...ok
intersect.t22.d...ok
intersect.t22.e...ok
intersect.t22.f...ok
intersect.t22.g...ok
intersect.t22.h...ok
intersect.t22.i...ok
intersect.t22.j...ok
intersect.t22.j...ok
intersect.t22.k...ok
intersect.t22.l...ok
intersect.t22.m...ok
intersect.t22.n...ok
intersect.t22.o...ok
intersect.t22.p...ok
intersect.t22.q...ok
intersect.t22.r...ok
intersect.t22.s...ok
intersect.t22.t...ok
intersect.t22.u...ok
intersect.t22.v...ok
intersect.t22.w...ok
intersect.t23...ok
intersect.t24...ok
intersect.t25...ok
intersect.t26...ok
intersect.t27...ok
intersect.t28...ok
intersect.t29...ok
intersect.t30...ok
intersect.t31...ok
intersect.t32...ok
intersect.t33...ok
intersect.t34...ok
intersect.t35...ok
intersect.t36...ok
intersect.t37...ok
intersect.t38...ok
intersect.t39...ok
intersect.t40...ok
intersect.t41...ok
intersect.t42...ok
intersect.t43...ok
intersect.t44...ok
intersect.t45...ok
intersect.t46...ok
intersect.t47...ok
intersect.t48...ok
intersect.t49...ok
intersect.t50...ok
intersect.t51...ok
intersect.t52...ok
intersect.t53...ok
intersect.t54...ok
intersect.t55...ok
intersect.t56...ok
intersect.t57...ok
intersect.t58...ok
intersect.t59...ok
intersect.t60...ok
intersect.t61...ok
intersect.t62...ok
intersect.t63...ok
intersect.t64...ok
intersect.t65...ok
intersect.t66...ok
intersect.t67...ok
intersect.t68...ok
intersect.t69...ok
intersect.t70...ok
intersect.t71...ok
intersect.t72...ok
intersect.t73...ok
intersect.t74...ok
intersect.t75...ok
intersect.t76...ok
intersect.t77...ok
intersect.t78...ok
intersect.t79...ok
intersect.t80...ok
intersect.t81...ok
intersect.t82...ok
intersect.t83...ok
intersect.new.t01...ok
intersect.new.t02...ok
intersect.new.t03...ok
intersect.new.t04...ok
intersect.new.t05...ok
intersect.new.t06...ok
intersect.new.t07...ok
intersect.new.t08...ok
intersect.new.t09...ok
intersect.new.t10...ok
intersect.new.t11...ok
intersect.new.t12...ok
intersect.new.t13...ok
intersect.new.t14...ok
intersect.new.t15...ok
intersect.new.t16...ok
intersect.new.t17...ok
intersect.new.t18...ok
intersect.new.t19...ok
intersect.new.t20...ok
intersect.new.t20.b...ok
intersect.new.t20.c...ok
intersect.new.t21...ok
intersect.new.t22...ok
intersect.new.t23...ok
intersect.new.t24...ok
intersect.new.t25...ok
intersect.new.t26...ok
intersect.new.t27...ok
intersect.new.t28...ok
intersect.new.t29...ok
intersect.new.t30...ok
intersect.new.t31...ok
intersect.new.t32...ok
intersect.new.t33...ok
intersect.new.t34...ok
intersect.new.t35...ok
intersect.new.t36...ok
intersect.new.t37...ok
intersect.new.t38...ok
intersect.new.t39...ok
intersect.new.t40...ok
intersect.new.t41...ok
intersect.new.t42...ok
intersect.new.t43...ok
intersect.new.t44...ok
intersect.new.t45...ok
intersect.new.t46...ok
intersect.new.t47...ok
intersect.new.t48...ok
intersect.new.t49...ok
intersect.new.t50...ok
intersect.new.t51...ok
intersect.new.t52...ok
intersect.new.t53...ok
intersect.new.t54...ok
intersect.new.t55...ok
intersect.new.t56...ok
intersect.new.t57...ok
intersect.new.t58...ok
intersect.new.t59...ok
intersect.new.t60...ok
intersect.new.t61...ok
intersect.new.t62...ok
intersect.new.t63...ok
intersect.new.t64...ok
intersect.new.t65...ok
intersect.new.t66...ok
intersect.new.t67a...ok
intersect.new.t67b...ok
intersect.new.t68a...ok
intersect.new.t68b...ok
intersect.new.t69...ok
intersect.new.t70...ok
intersect.new.t71...ok
intersect.new.t72...ok
intersect.new.t73...ok
intersect.new.t74...ok
intersect.new.t75...ok
intersect.new.t76...ok
intersect.new.t77...ok
intersect.new.t78...ok
intersect.new.t79...ok
intersect.new.t80...ok
intersect.new.t81...ok
###########################################################
#
# MULTIPLE DATABASE INTERSECTION
#
###########################################################
intersect.t01...ok
intersect.t02...ok
intersect.t03...ok
intersect.t04...ok
intersect.t05...ok
intersect.t06...ok
intersect.t07...ok
intersect.t08...ok
intersect.t09...ok
intersect.t10...ok
intersect.t11...ok
intersect.t12...ok
intersect.t13...ok
intersect.t14...ok
intersect.t15...ok
intersect.t16...ok
intersect.t17...ok
intersect.t18...ok
intersect.t13...ok
intersect.t19...ok
intersect.t20...ok
intersect.t21...ok
intersect.t22...ok
intersect.t23...ok
intersect.t24...ok
###########################################################
#
# CHROMOSOME SORT ORDER AND NAMING CONVENTIONS
#
###########################################################
intersect.t01...ok
intersect.t02...ok
intersect.t03...ok
intersect.t04...ok
intersect.t05...ok
intersect.t06...ok
intersect.t07...ok
intersect.t08...ok
intersect.t09...ok
intersect.t10...ok
intersect.t11...ok
intersect.t12...ok
intersect.t13...ok
intersect.t14...ok
intersect.t15...ok
intersect.t16...ok
intersect.t17...ok
intersect.t18...ok
intersect.t19...ok
intersect.20...ok
intersect.21...ok
intersect.22...ok
intersect.23...ok
Testing bedtools jaccard:
jaccard.t01...ok
jaccard.t02...ok
jaccard.t03...ok
jaccard.t05...ok
jaccard.t06...ok
jaccard.t07...ok
jaccard.t08...ok
jaccard.t09...ok
jaccard.t10...ok
jaccard.t11...ok
jaccard.t12...ok
jaccard.t13...ok
jaccard.t14...ok
jaccard.t15...ok
jaccard.t16...ok
Testing bedtools makewindows:
makewindows.t01...ok
makewindows.t02...ok
makewindows.t03...ok
makewindows.t04...ok
makewindows.t05...ok
makewindows.t06...ok
makewindows.t07...ok
makewindows.t08...ok
makewindows.t09...ok
Testing bedtools map:
map.t01...ok
map.t02...ok
map.t03...ok
map.t04...ok
map.t05...ok
map.t06...ok
map.t07...ok
map.t08...ok
map.t09...ok
map.t10...ok
map.t11...ok
map.t12...ok
map.t13...ok
map.t14...ok
map.t15...ok
map.t16...ok
map.t17...ok
map.t18...ok
map.t19...ok
map.t20...ok
map.t21...ok
map.t22..ok
map.t23..ok
map.t24..ok
map.t25..ok
map.t26..ok
map.t27..ok
map.t28..ok
map.t29..ok
map.t30..ok
map.t31..ok
map.t32..ok
map.t33..ok
map.t33..ok
map.t33..ok
map.t34..ok
map.t35..ok
map.t36..ok
map.t37..ok
map.t38..ok
map.t39..ok
map.t40..ok
map.t41..ok
map.t42..ok
map.t43..ok
map.t44...ok
map.t45...ok
map.t46...ok
map.t47...ok
map.t48...ok
map.t49...ok
map.t50...ok
map.t51...ok
map.t52...ok
map.t53...ok
map.t54...ok
map.t55...ok
Testing bedtools merge:
merge.t1...ok
merge.t2...ok
merge.t3...ok
merge.t4...ok
merge.t5...ok
merge.t6...ok
merge.t7...ok
merge.t8...ok
merge.t9a...ok
merge.t9b...ok
merge.t10...ok
merge.t11...ok
merge.t12...ok
merge.t13...ok
merge.t14...ok
merge.t15...ok
merge.t16...ok
merge.t17...ok
merge.t18...ok
merge.t19...ok
merge.t20...ok
merge.t21...ok
merge.t22...ok
merge.t23a...ok
merge.t23b...ok
merge.t24...ok
merge.t25...ok
merge.t26...ok
merge.t27...ok
merge.t28...ok
merge.t29...ok
merge.t30...ok
merge.t31...ok
merge.t32...ok
merge.t33...ok
merge.t34...ok
merge.t35...ok
merge.t36...ok
merge.t37...ok
merge.t38...ok
merge.t39...ok
merge.t40...ok
merge.t41...ok
merge.t42...ok
merge.t43...ok
merge.t44a...ok
merge.t44b...skipped - could not find vcfSVtest.2.vcf
merge.t45...ok
merge.t46...ok
merge.t47...ok
merge.t48...ok
merge.t49...ok
merge.t50...ok
Testing bedtools multicov:
multicov.t1...ok
multicov.t2...ok
multicov.t3...ok
multicov.t4...ok
multicov.t5...ok
multicov.t6...ok
multicov.t7...ok
multicov.t8...ok
multicov.t9...ok
multicov.t10...ok
Testing bedtools negativecontrol:
Testing bedtools reldist:
reldist.t01...ok
reldist.t02...ok
reldist.t03...ok
reldist.t02...ok
Testing bedtools sample:
sample.t01...ok
sample.new.t02...ok
sample.new.t03...ok
sample.new.t04...ok
sample.new.t05...ok
sample.new.t06...ok
sample.new.t07...ok
sample.new.t08...ok
sample.new.t09...ok
Testing bedtools shift:
shift.t1...ok
shift.t2...ok
shift.t3...ok
shift.t3...ok
shift.t4...ok
shift.t5...ok
shift.t6...ok
shift.t7...ok
shift.t8...ok
shift.t9...ok
shift.t10...ok
shift.t11...ok
Testing bedtools slop:
slop.t1...ok
slop.t2...ok
slop.t3...ok
slop.t4...ok
slop.t5...ok
slop.t6...ok
slop.t7...ok
slop.t8...ok
slop.t9...ok
slop.t10...ok
slop.t11...ok
slop.t12...ok
slop.t13...ok
slop.t14...ok
slop.t15...ok
slop.t16...ok
slop.t17...ok
slop.t18...ok
slop.t19...ok
slop.t20...ok
slop.t21...ok
slop.t22...ok
Testing bedtools sort:
sort.t01...ok
sort.t02...ok
sort.t03...ok
sort.t04...ok
sort.t05...ok
sort.t06...ok
sort.t07...ok
sort.t08...ok
sort.t09...ok
sort.t10...ok
Testing bedtools spacing:
spacing.t01...ok
Testing bedtools split:
split.01.size...ok
split.02.simple...ok
spliit.03.simple...ok
Testing bedtools subtract:
subtract.t1...ok
subtract.t2...ok
subtract.t3...ok
subtract.t4...ok
subtract.t5...ok
subtract.t6...ok
subtract.t7...ok
subtract.t8...ok
subtract.t9...ok
subtract.t10...ok
subtract.t11...ok
subtract.t12...ok
subtract.t13...ok
subtract.t14...ok
subtract.t15...ok
subtract.t16...ok
subtract.t17...ok
subtract.t18...ok
subtract.t19...ok
subtract.t20...ok
subtract.t21...ok
--------------------------
Test Results
--------------------------
Tools passing: bamtobed bamtofastq bed12tobed6 bedtobam bigchroms closest cluster complement coverage expand fisher flank general genomecov getfasta groupby intersect jaccard makewindows map merge multicov reldist sample shift slop sort spacing split subtract
Tools failing: negativecontrol
NB: the 'negativecontrol' test is supposed to fail. If it wasn't caught,
something went wrong with this test script.
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -fr -- /tmp/dh-xdg-rundir-zWh6SMe8
mv debian/shuffle test/
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep -a
rm -f -- debian/bedtools.substvars
rm -fr -- debian/.debhelper/generated/bedtools/ debian/bedtools/ debian/tmp/
rm -f debian/bedtools.debhelper.log
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install -- VERBOSE=1
install -m0755 -d /<<BUILDDIR>>/bedtools-2.31.0\+dfsg/debian/tmp
make -j4 install DESTDIR=/<<BUILDDIR>>/bedtools-2.31.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" VERBOSE=1
make[2]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p /<<PKGBUILDDIR>>/debian/tmp/usr/local/bin
for file in bin/* ; do \
cp -f $file /<<PKGBUILDDIR>>/debian/tmp/usr/local/bin; \
done
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f debian/bedtools.debhelper.log
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
install -m0755 -d debian/bedtools/usr/bin
cp --reflink=auto -a debian/tmp/usr/local/bin/annotateBed debian/tmp/usr/local/bin/bamToBed debian/tmp/usr/local/bin/bamToFastq debian/tmp/usr/local/bin/bed12ToBed6 debian/tmp/usr/local/bin/bedToBam debian/tmp/usr/local/bin/bedToIgv debian/tmp/usr/local/bin/bedpeToBam debian/tmp/usr/local/bin/bedtools debian/tmp/usr/local/bin/closestBed debian/tmp/usr/local/bin/clusterBed debian/tmp/usr/local/bin/complementBed debian/tmp/usr/local/bin/coverageBed debian/tmp/usr/local/bin/expandCols debian/tmp/usr/local/bin/fastaFromBed debian/tmp/usr/local/bin/flankBed debian/tmp/usr/local/bin/genomeCoverageBed debian/tmp/usr/local/bin/getOverlap debian/tmp/usr/local/bin/groupBy debian/tmp/usr/local/bin/intersectBed debian/tmp/usr/local/bin/linksBed debian/tmp/usr/local/bin/mapBed debian/tmp/usr/local/bin/maskFastaFromBed debian/tmp/usr/local/bin/mergeBed debian/tmp/usr/local/bin/multiBamCov debian/tmp/usr/local/bin/multiIntersectBed debian/tmp/usr/local/bin/nucBed debian/tmp/usr/local/bin/pairToBed debian/tmp/usr/local/bin/pairToPair debian/tmp/usr/local/bin/randomBed debian/tmp/usr/local/bin/shiftBed debian/tmp/usr/local/bin/shuffleBed debian/tmp/usr/local/bin/slopBed debian/tmp/usr/local/bin/sortBed debian/tmp/usr/local/bin/subtractBed debian/tmp/usr/local/bin/tagBam debian/tmp/usr/local/bin/unionBedGraphs debian/tmp/usr/local/bin/windowBed debian/tmp/usr/local/bin/windowMaker debian/bedtools/usr/bin/
install -m0755 -d debian/bedtools/usr/share/bash-completion/completions
cp --reflink=auto -a ./debian/bash_completion/bedtools debian/bedtools/usr/share/bash-completion/completions/
install -m0755 -d debian/bedtools/usr/share/bedtools
cp --reflink=auto -a ./genomes debian/bedtools/usr/share/bedtools/
# make sure all *.sh files are featuring a '#!/bin/bash' as first line
# since there are at least two files (test/intersect/{new_test-intersect.sh,performanceTest.sh}
# requiring bash this is taken for all scripts instead of checking first via /bin/sh -n
for sh in `find /<<PKGBUILDDIR>>/debian -name "*.sh"` ; do \
if ! head -n1 ${sh} | grep -q '^#! */bin/[ba]*sh' ; then \
sed -i '1 i #!/bin/bash' ${sh} ; \
fi ; \
done
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
install -m0755 -d debian/bedtools/usr/share/doc/bedtools
install -m0755 -d debian/bedtools/usr/share/doc/bedtools
cp --reflink=auto -a ./README.md debian/bedtools/usr/share/doc/bedtools
cp --reflink=auto -a ./debian/README.test debian/bedtools/usr/share/doc/bedtools
cp --reflink=auto -a ./debian/tests/run-unit-test debian/bedtools/usr/share/doc/bedtools
chmod -R u\+rw,go=rX debian/bedtools/usr/share/doc
install -p -m0644 debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installchangelogs -a
install -m0755 -d debian/bedtools/usr/share/doc/bedtools
install -p -m0644 debian/.debhelper/generated/bedtools/dh_installchangelogs.dch.trimmed debian/bedtools/usr/share/doc/bedtools/changelog.Debian
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
cd debian/bedtools
chmod a-x usr/share/doc/bedtools/changelog.Debian
gzip -9nf usr/share/doc/bedtools/changelog.Debian
cd '/<<PKGBUILDDIR>>'
rm -f debian/bedtools.debhelper.log
debian/rules override_dh_fixperms-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_fixperms
find debian/bedtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/bedtools/usr/share/doc -type f -a -true -a ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/bedtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/bedtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/bedtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
chmod -x /<<PKGBUILDDIR>>/debian/bedtools/usr/share/bedtools/genomes/*.genome
find /<<PKGBUILDDIR>>/debian -name "*.bed" -executable -exec chmod -x \{\} \;
find /<<PKGBUILDDIR>>/debian -name "*.sam" -executable -exec chmod -x \{\} \;
find /<<PKGBUILDDIR>>/debian -name "*.sh" -not -executable -exec chmod +x \{\} \;
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_missing -a
dh_dwz -a
dwz -- debian/bedtools/usr/bin/bedtools
dh_strip -a
install -m0755 -d debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/d6
objcopy --only-keep-debug --compress-debug-sections debian/bedtools/usr/bin/bedtools debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/d6/0f17c5a75a1b3ea88efe5c58be37d1daceef88.debug
chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/d6/0f17c5a75a1b3ea88efe5c58be37d1daceef88.debug
strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
objcopy --add-gnu-debuglink debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/d6/0f17c5a75a1b3ea88efe5c58be37d1daceef88.debug debian/bedtools/usr/bin/bedtools
install -m0755 -d debian/.debhelper/bedtools/dbgsym-root/usr/share/doc
ln -s bedtools debian/.debhelper/bedtools/dbgsym-root/usr/share/doc/bedtools-dbgsym
install -m0755 -d debian/.debhelper/bedtools
dh_makeshlibs -a
rm -f debian/bedtools/DEBIAN/shlibs
dh_shlibdeps -a
install -m0755 -d debian/bedtools/DEBIAN
dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bedtools contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/bedtools/usr/bin/bedtools was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
install -m0755 -d debian/bedtools/DEBIAN
dh_gencontrol -a
install -m0755 -d debian/bedtools/DEBIAN
echo misc:Depends= >> debian/bedtools.substvars
echo misc:Pre-Depends= >> debian/bedtools.substvars
install -m0755 -d debian/.debhelper/bedtools/dbgsym-root/DEBIAN
dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/.debhelper/bedtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=bedtools-dbgsym "-DDepends=bedtools (= \${binary:Version})" "-DDescription=debug symbols for bedtools" -DBuild-Ids=d60f17c5a75a1b3ea88efe5c58be37d1daceef88 -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/control
dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
chmod 0644 -- debian/bedtools/DEBIAN/control
dh_md5sums -a
install -m0755 -d debian/bedtools/DEBIAN
cd debian/bedtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/bedtools/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/bedtools/dbgsym-root/DEBIAN
cd debian/.debhelper/bedtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --root-owner-group --build debian/bedtools ..
dpkg-deb --root-owner-group --build debian/.debhelper/bedtools/dbgsym-root ..
dpkg-deb: building package 'bedtools-dbgsym' in '../bedtools-dbgsym_2.31.0+dfsg-2_armhf.deb'.
dpkg-deb: building package 'bedtools' in '../bedtools_2.31.0+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=any -O../bedtools_2.31.0+dfsg-2_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi5 test autobuilder <root@raspbian.org> -O../bedtools_2.31.0+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-source: info: using options from bedtools-2.31.0+dfsg/debian/source/options: --single-debian-patch
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2023-11-21T05:44:42Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
bedtools_2.31.0+dfsg-2_armhf.changes:
-------------------------------------
Format: 1.8
Date: Sat, 18 Nov 2023 16:34:59 +0100
Source: bedtools
Binary: bedtools bedtools-dbgsym
Architecture: armhf
Version: 2.31.0+dfsg-2
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian pi5 test autobuilder <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Closes: 1055414
Changes:
bedtools (2.31.0+dfsg-2) unstable; urgency=medium
.
* gcc-13.patch: fixed upstream by different change.
The Applied-Upstream field is set accordingly to point to PR 1067.
* d/rules: use sse for floating point calculations.
This fixes bedtools "intersect" test failures during build time.
This change is brought for consistency with htslib's own settings.
While this is an architecture baseline violation, the alternative
is no htslib support at all for the i386 distribution, since it
fails its own test suite with anything else than sse for floating
point calculations. (Closes: #1055414)
* d/control: depend on python3:any per M-A hint.
Checksums-Sha1:
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Checksums-Sha256:
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Files:
26b7fccaab0065a65bfe23740b250c3f 11182156 debug optional bedtools-dbgsym_2.31.0+dfsg-2_armhf.deb
e92f56fa94304edf0c9f8c1c6dfd4b94 5639 science optional bedtools_2.31.0+dfsg-2_armhf.buildinfo
a2b934c15ec50c6aba64469db1fec4c7 518176 science optional bedtools_2.31.0+dfsg-2_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: bedtools
Binary: bedtools bedtools-dbgsym
Architecture: armhf
Version: 2.31.0+dfsg-2
Checksums-Md5:
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Checksums-Sha1:
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Checksums-Sha256:
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Tue, 21 Nov 2023 05:44:42 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.71-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-13),
autotools-dev (= 20220109.1),
base-files (= 13+rpi1),
base-passwd (= 3.6.2),
bash (= 5.2.15-2),
binutils (= 2.41-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.41-6+rpi1),
binutils-common (= 2.41-6+rpi1),
bsdextrautils (= 2.39.2-6),
bsdutils (= 1:2.39.2-6),
build-essential (= 12.9),
bzip2 (= 1.0.8-5+b2),
coreutils (= 9.1-1),
cpp (= 4:13.2.0-1+rpi1),
cpp-12 (= 12.3.0-10+rpi1),
cpp-13 (= 13.2.0-5+rpi1),
dash (= 0.5.12-6),
debconf (= 1.5.82),
debhelper (= 13.11.8),
debianutils (= 5.14),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.1-1),
diffutils (= 1:3.10-1),
dpkg (= 1.22.1+rpi1),
dpkg-dev (= 1.22.1+rpi1),
dwz (= 0.15-1),
file (= 1:5.45-2),
findutils (= 4.9.0-5),
g++ (= 4:13.2.0-1+rpi1),
g++-13 (= 13.2.0-5+rpi1),
gcc (= 4:13.2.0-1+rpi1),
gcc-12 (= 12.3.0-10+rpi1),
gcc-12-base (= 12.3.0-10+rpi1),
gcc-13 (= 13.2.0-5+rpi1),
gcc-13-base (= 13.2.0-5+rpi1),
gettext (= 0.21-13),
gettext-base (= 0.21-13),
grep (= 3.11-3),
groff-base (= 1.23.0-3),
gzip (= 1.12-1),
hostname (= 3.23+nmu1),
init-system-helpers (= 1.65.2),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-3),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 13.2.0-5+rpi1),
libatomic1 (= 13.2.0-5+rpi1),
libattr1 (= 1:2.5.1-4),
libaudit-common (= 1:3.1.1-1),
libaudit1 (= 1:3.1.1-1),
libbinutils (= 2.41-6+rpi1),
libblkid1 (= 2.39.2-6),
libbz2-1.0 (= 1.0.8-5+b2),
libbz2-dev (= 1.0.8-5+b2),
libc-bin (= 2.37-12+rpi2),
libc-dev-bin (= 2.37-12+rpi2),
libc6 (= 2.37-12+rpi2),
libc6-dev (= 2.37-12+rpi2),
libcap-ng0 (= 0.8.3-1+b1),
libcap2 (= 1:2.66-4),
libcc1-0 (= 13.2.0-5+rpi1),
libcom-err2 (= 1.47.0-2),
libcrypt-dev (= 1:4.4.36-2),
libcrypt1 (= 1:4.4.36-2),
libctf-nobfd0 (= 2.41-6+rpi1),
libctf0 (= 2.41-6+rpi1),
libdb5.3 (= 5.3.28+dfsg2-2),
libdebconfclient0 (= 0.271),
libdebhelper-perl (= 13.11.8),
libdpkg-perl (= 1.22.1+rpi1),
libelf1 (= 0.188-2.1+rpi1),
libexpat1 (= 2.5.0-2),
libffi8 (= 3.4.4-1),
libfile-stripnondeterminism-perl (= 1.13.1-1),
libgcc-12-dev (= 12.3.0-10+rpi1),
libgcc-13-dev (= 13.2.0-5+rpi1),
libgcc-s1 (= 13.2.0-5+rpi1),
libgcrypt20 (= 1.10.2-3),
libgdbm-compat4 (= 1.23-3),
libgdbm6 (= 1.23-3),
libgmp10 (= 2:6.3.0+dfsg-2),
libgomp1 (= 13.2.0-5+rpi1),
libgpg-error0 (= 1.47-2),
libgssapi-krb5-2 (= 1.20.1-4),
libicu72 (= 72.1-4),
libisl23 (= 0.26-3),
libjansson4 (= 2.14-2),
libk5crypto3 (= 1.20.1-4),
libkeyutils1 (= 1.6.3-2),
libkrb5-3 (= 1.20.1-4),
libkrb5support0 (= 1.20.1-4),
liblz4-1 (= 1.9.4-1+rpi1+b1),
liblzma-dev (= 5.4.4-0.1),
liblzma5 (= 5.4.4-0.1),
libmagic-mgc (= 1:5.45-2),
libmagic1 (= 1:5.45-2),
libmd0 (= 1.1.0-1),
libmount1 (= 2.39.2-6),
libmpc3 (= 1.3.1-1),
libmpfr6 (= 4.2.1-1),
libncursesw6 (= 6.4+20231016-1),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libpam-modules (= 1.5.2-9.1),
libpam-modules-bin (= 1.5.2-9.1),
libpam-runtime (= 1.5.2-9.1),
libpam0g (= 1.5.2-9.1),
libpcre2-8-0 (= 10.42-4),
libperl5.36 (= 5.36.0-9),
libpipeline1 (= 1.5.7-1),
libpython3-stdlib (= 3.11.4-5),
libpython3.11-minimal (= 3.11.6-3),
libpython3.11-stdlib (= 3.11.6-3),
libreadline8 (= 8.2-1.3),
libseccomp2 (= 2.5.4-1+rpi1+b1),
libselinux1 (= 3.5-1),
libsframe1 (= 2.41-6+rpi1),
libsmartcols1 (= 2.39.2-6),
libsqlite3-0 (= 3.43.2-1),
libssl3 (= 3.0.11-1),
libstdc++-13-dev (= 13.2.0-5+rpi1),
libstdc++6 (= 13.2.0-5+rpi1),
libsub-override-perl (= 0.09-4),
libsystemd0 (= 254.5-1+rpi1),
libtinfo6 (= 6.4+20231016-1),
libtirpc-common (= 1.3.3+ds-1),
libtirpc-dev (= 1.3.3+ds-1),
libtirpc3 (= 1.3.3+ds-1),
libtool (= 2.4.7-7),
libubsan1 (= 13.2.0-5+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 254.5-1+rpi1),
libunistring5 (= 1.1-2),
libuuid1 (= 2.39.2-6),
libxml2 (= 2.9.14+dfsg-1.3),
libzstd1 (= 1.5.5+dfsg2-2),
linux-libc-dev (= 6.5.6-1+rpi1),
login (= 1:4.13+dfsg1-3),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.12.0-1),
mawk (= 1.3.4.20230808-1),
media-types (= 10.1.0),
ncurses-base (= 6.4+20231016-1),
ncurses-bin (= 6.4+20231016-1),
patch (= 2.7.6-7),
perl (= 5.36.0-9),
perl-base (= 5.36.0-9),
perl-modules-5.36 (= 5.36.0-9),
po-debconf (= 1.0.21+nmu1),
python3 (= 3.11.4-5),
python3-minimal (= 3.11.4-5),
python3.11 (= 3.11.6-3),
python3.11-minimal (= 3.11.6-3),
readline-common (= 8.2-1.3),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-1),
sensible-utils (= 0.0.20),
sysvinit-utils (= 3.08-3),
tar (= 1.34+dfsg-1.2),
tzdata (= 2023c-10),
usr-is-merged (= 37),
util-linux (= 2.39.2-6),
xz-utils (= 5.4.4-0.1),
zlib1g (= 1:1.2.13.dfsg-3),
zlib1g-dev (= 1:1.2.13.dfsg-3)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
LC_COLLATE="C.UTF-8"
SOURCE_DATE_EPOCH="1700321699"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
bedtools-dbgsym_2.31.0+dfsg-2_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 11182156 bytes: control archive=544 bytes.
388 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: bedtools-dbgsym
Source: bedtools
Version: 2.31.0+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 11206
Depends: bedtools (= 2.31.0+dfsg-2)
Section: debug
Priority: optional
Description: debug symbols for bedtools
Build-Ids: d60f17c5a75a1b3ea88efe5c58be37d1daceef88
drwxr-xr-x root/root 0 2023-11-18 15:34 ./
drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/
drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/lib/
drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/lib/debug/
drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/lib/debug/.build-id/d6/
-rw-r--r-- root/root 11463688 2023-11-18 15:34 ./usr/lib/debug/.build-id/d6/0f17c5a75a1b3ea88efe5c58be37d1daceef88.debug
drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/share/
drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/share/doc/
lrwxrwxrwx root/root 0 2023-11-18 15:34 ./usr/share/doc/bedtools-dbgsym -> bedtools
bedtools_2.31.0+dfsg-2_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 518176 bytes: control archive=2184 bytes.
917 bytes, 20 lines control
2915 bytes, 50 lines md5sums
Package: bedtools
Version: 2.31.0+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1657
Depends: libbz2-1.0, libc6 (>= 2.34), libgcc-s1 (>= 3.5), liblzma5 (>= 5.1.1alpha+20120614), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4)
Conflicts: filo
Replaces: filo
Provides: filo
Section: science
Priority: optional
Homepage: https://github.com/arq5x/bedtools2
Description: suite of utilities for comparing genomic features
The BEDTools utilities allow one to address common genomics tasks such as
finding feature overlaps and computing coverage. The utilities are largely
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
BEDTools, one can develop sophisticated pipelines that answer complicated
research questions by streaming several BEDTools together.
.
The groupBy utility is distributed in the filo package.
drwxr-xr-x root/root 0 2023-11-18 15:34 ./
drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/
drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/bin/
-rwxr-xr-x root/root 41 2023-11-18 15:34 ./usr/bin/annotateBed
-rwxr-xr-x root/root 41 2023-11-18 15:34 ./usr/bin/bamToBed
-rwxr-xr-x root/root 43 2023-11-18 15:34 ./usr/bin/bamToFastq
-rwxr-xr-x root/root 44 2023-11-18 15:34 ./usr/bin/bed12ToBed6
-rwxr-xr-x root/root 41 2023-11-18 15:34 ./usr/bin/bedToBam
-rwxr-xr-x root/root 36 2023-11-18 15:34 ./usr/bin/bedToIgv
-rwxr-xr-x root/root 43 2023-11-18 15:34 ./usr/bin/bedpeToBam
-rwxr-xr-x root/root 1611408 2023-11-18 15:34 ./usr/bin/bedtools
-rwxr-xr-x root/root 40 2023-11-18 15:34 ./usr/bin/closestBed
-rwxr-xr-x root/root 40 2023-11-18 15:34 ./usr/bin/clusterBed
-rwxr-xr-x root/root 43 2023-11-18 15:34 ./usr/bin/complementBed
-rwxr-xr-x root/root 41 2023-11-18 15:34 ./usr/bin/coverageBed
-rwxr-xr-x root/root 39 2023-11-18 15:34 ./usr/bin/expandCols
-rwxr-xr-x root/root 41 2023-11-18 15:34 ./usr/bin/fastaFromBed
-rwxr-xr-x root/root 38 2023-11-18 15:34 ./usr/bin/flankBed
-rwxr-xr-x root/root 42 2023-11-18 15:34 ./usr/bin/genomeCoverageBed
-rwxr-xr-x root/root 40 2023-11-18 15:34 ./usr/bin/getOverlap
-rwxr-xr-x root/root 40 2023-11-18 15:34 ./usr/bin/groupBy
-rwxr-xr-x root/root 42 2023-11-18 15:34 ./usr/bin/intersectBed
-rwxr-xr-x root/root 38 2023-11-18 15:34 ./usr/bin/linksBed
-rwxr-xr-x root/root 36 2023-11-18 15:34 ./usr/bin/mapBed
-rwxr-xr-x root/root 42 2023-11-18 15:34 ./usr/bin/maskFastaFromBed
-rwxr-xr-x root/root 38 2023-11-18 15:34 ./usr/bin/mergeBed
-rwxr-xr-x root/root 41 2023-11-18 15:34 ./usr/bin/multiBamCov
-rwxr-xr-x root/root 43 2023-11-18 15:34 ./usr/bin/multiIntersectBed
-rwxr-xr-x root/root 36 2023-11-18 15:34 ./usr/bin/nucBed
-rwxr-xr-x root/root 42 2023-11-18 15:34 ./usr/bin/pairToBed
-rwxr-xr-x root/root 43 2023-11-18 15:34 ./usr/bin/pairToPair
-rwxr-xr-x root/root 39 2023-11-18 15:34 ./usr/bin/randomBed
-rwxr-xr-x root/root 38 2023-11-18 15:34 ./usr/bin/shiftBed
-rwxr-xr-x root/root 40 2023-11-18 15:34 ./usr/bin/shuffleBed
-rwxr-xr-x root/root 37 2023-11-18 15:34 ./usr/bin/slopBed
-rwxr-xr-x root/root 37 2023-11-18 15:34 ./usr/bin/sortBed
-rwxr-xr-x root/root 41 2023-11-18 15:34 ./usr/bin/subtractBed
-rwxr-xr-x root/root 36 2023-11-18 15:34 ./usr/bin/tagBam
-rwxr-xr-x root/root 42 2023-11-18 15:34 ./usr/bin/unionBedGraphs
-rwxr-xr-x root/root 39 2023-11-18 15:34 ./usr/bin/windowBed
-rwxr-xr-x root/root 44 2023-11-18 15:34 ./usr/bin/windowMaker
drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/share/
drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/share/bash-completion/
drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/share/bash-completion/completions/
-rw-r--r-- root/root 638 2023-06-23 19:59 ./usr/share/bash-completion/completions/bedtools
drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/share/bedtools/
drwxr-xr-x root/root 0 2023-04-28 12:08 ./usr/share/bedtools/genomes/
-rw-r--r-- root/root 868 2023-04-28 12:08 ./usr/share/bedtools/genomes/human.hg18.genome
-rw-r--r-- root/root 1984 2023-04-28 12:08 ./usr/share/bedtools/genomes/human.hg19.genome
-rw-r--r-- root/root 11684 2023-04-28 12:08 ./usr/share/bedtools/genomes/human.hg38.genome
-rw-r--r-- root/root 1417 2023-04-28 12:08 ./usr/share/bedtools/genomes/mouse.mm10.genome
-rw-r--r-- root/root 577 2023-04-28 12:08 ./usr/share/bedtools/genomes/mouse.mm8.genome
-rw-r--r-- root/root 596 2023-04-28 12:08 ./usr/share/bedtools/genomes/mouse.mm9.genome
drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/share/doc/
drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/share/doc/bedtools/
-rw-r--r-- root/root 3355 2023-04-28 12:08 ./usr/share/doc/bedtools/README.md
-rw-r--r-- root/root 278 2023-06-23 19:59 ./usr/share/doc/bedtools/README.test
-rw-r--r-- root/root 2525 2023-11-18 15:34 ./usr/share/doc/bedtools/changelog.Debian.gz
-rw-r--r-- root/root 5451 2023-06-23 20:13 ./usr/share/doc/bedtools/copyright
-rw-r--r-- root/root 628 2023-06-23 19:59 ./usr/share/doc/bedtools/run-unit-test
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 238452
Build-Time: 130
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 24
Job: bedtools_2.31.0+dfsg-2
Machine Architecture: arm64
Package: bedtools
Package-Time: 164
Source-Version: 2.31.0+dfsg-2
Space: 238452
Status: successful
Version: 2.31.0+dfsg-2
--------------------------------------------------------------------------------
Finished at 2023-11-21T05:44:42Z
Build needed 00:02:44, 238452k disk space