bedtools →
2.29.2+dfsg-3 →
armhf → 2020-06-12 17:18:02
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| bedtools 2.29.2+dfsg-3 (armhf) Fri, 12 Jun 2020 16:57:37 +0000 |
+==============================================================================+
Package: bedtools
Version: 2.29.2+dfsg-3
Source Version: 2.29.2+dfsg-3
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-e2f3427e-9c8a-4915-a658-3e7dc0c180e7' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.5 MB in 26s (957 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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 14.0 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main bedtools 2.29.2+dfsg-3 (dsc) [2187 B]
Get:2 http://172.17.0.1/private bullseye-staging/main bedtools 2.29.2+dfsg-3 (tar) [14.0 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main bedtools 2.29.2+dfsg-3 (diff) [12.7 kB]
Fetched 14.0 MB in 1s (10.3 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bedtools-oxa41g/bedtools-2.29.2+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bedtools-oxa41g' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-GEoL8q/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-GEoL8q/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-GEoL8q/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-GEoL8q/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-GEoL8q/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-GEoL8q/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-GEoL8q/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-GEoL8q/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2828 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 39 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-GEoL8q/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (23.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12234 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), python3, zlib1g-dev, libbz2-dev, liblzma-dev, samtools (>= 1.10)
Filtered Build-Depends: debhelper-compat (= 12), python3, zlib1g-dev, libbz2-dev, liblzma-dev, samtools (>= 1.10)
dpkg-deb: building package 'sbuild-build-depends-bedtools-dummy' in '/<<BUILDDIR>>/resolver-GEoL8q/apt_archive/sbuild-build-depends-bedtools-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-bedtools-dummy sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-GEoL8q/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-GEoL8q/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-GEoL8q/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-GEoL8q/apt_archive ./ Sources [530 B]
Get:5 copy:/<<BUILDDIR>>/resolver-GEoL8q/apt_archive ./ Packages [611 B]
Fetched 2474 B in 1s (3200 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install bedtools build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils bzip2 debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libbz2-1.0
libbz2-dev libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1
libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2
libhts3 libicu67 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
liblzma-dev libmagic-mgc libmagic1 libmpdec2 libncurses6 libnghttp2-14
libpipeline1 libpsl5 libpython3-stdlib libpython3.8-minimal
libpython3.8-stdlib librtmp1 libsigsegv2 libssh2-1 libssl1.1
libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4 man-db
mime-support po-debconf python3 python3-minimal python3.8 python3.8-minimal
samtools sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation bzip2-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev
groff krb5-doc krb5-user liblzma-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv python3.8-venv
python3.8-doc binfmt-support
Recommended packages:
curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl
libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2
publicsuffix libltdl-dev libmail-sendmail-perl cwltool
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libbz2-dev
libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libexpat1
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts3
libicu67 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev
libmagic-mgc libmagic1 libmpdec2 libncurses6 libnghttp2-14 libpipeline1
libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib librtmp1
libsigsegv2 libssh2-1 libssl1.1 libsub-override-perl libtinfo5 libtool
libuchardet0 libxml2 m4 man-db mime-support po-debconf python3
python3-minimal python3.8 python3.8-minimal samtools
sbuild-build-depends-bedtools-dummy sensible-utils zlib1g-dev
The following packages will be upgraded:
bzip2 libbz2-1.0
2 upgraded, 65 newly installed, 0 to remove and 37 not upgraded.
Need to get 27.9 MB of archives.
After this operation, 98.1 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-GEoL8q/apt_archive ./ sbuild-build-depends-bedtools-dummy 0.invalid.0 [900 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.2-1 [318 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.2-1 [1269 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1g-1 [1272 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-minimal armhf 3.8.3-1 [751 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf python3.8-minimal armhf 3.8.3-1 [1629 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.8.2-3 [37.6 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf bzip2 armhf 1.0.8-3 [46.9 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libbz2-1.0 armhf 1.0.8-3 [44.0 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-3 [68.1 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-stdlib armhf 3.8.3-1 [1600 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf python3.8 armhf 3.8.3-1 [416 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.8.2-3 [20.8 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.8.2-3 [63.7 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-1 [775 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.1 [187 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.8.1-1 [25.2 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.8.1-1 [14.9 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.3-1 [1159 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-2 [8286 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5+b1 [593 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.1 [1012 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6.1 [255 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-3 [28.0 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-7+rpi1+b1 [61.8 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-7+rpi1+b1 [112 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-7+rpi1+b1 [318 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-7+rpi1+b1 [136 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.41.0-2 [61.2 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.68.0-1 [284 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.6-1 [47.4 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.10.2-3 [319 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2-1 [79.5 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf samtools armhf 1.10-3 [477 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libpipeline1:armhf (1.5.2-2) ...
Setting up libkeyutils1:armhf (1.6.1-2) ...
Setting up libpsl5:armhf (0.21.0-1.1) ...
Setting up mime-support (3.64) ...
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Setting up libglib2.0-0:armhf (2.64.3-1) ...
No schema files found: doing nothing.
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Setting up libnghttp2-14:armhf (1.41.0-2) ...
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Setting up libdeflate0:armhf (1.6-1) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-5) ...
Setting up bzip2 (1.0.8-3) ...
Setting up libkrb5support0:armhf (1.17-7+rpi1+b1) ...
Setting up autotools-dev (20180224.1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Setting up libncurses6:armhf (6.2-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libk5crypto3:armhf (1.17-7+rpi1+b1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-7+rpi1+b1) ...
Setting up libmpdec2:armhf (2.4.2-3) ...
Setting up libpython3.8-stdlib:armhf (3.8.3-1) ...
Setting up python3.8 (3.8.3-1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.2-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.10+dfsg-5+b1) ...
Setting up libpython3-stdlib:armhf (3.8.2-3) ...
Setting up libbz2-dev:armhf (1.0.8-3) ...
Setting up libfile-stripnondeterminism-perl (1.8.1-1) ...
Setting up libtool (2.4.6-14) ...
Setting up m4 (1.4.18-4) ...
Setting up python3 (3.8.2-3) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-7+rpi1+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.8.1-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-5) ...
Setting up automake (1:1.16.2-1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up libcurl3-gnutls:armhf (7.68.0-1) ...
Setting up man-db (2.9.2-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libhts3:armhf (1.10.2-3) ...
Setting up po-debconf (1.0.21) ...
Setting up samtools (1.10-3) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.1) ...
Setting up sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.30-8+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.34-8+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-12+rpi1 gcc-9_9.3.0-12+rpi1 libc6-dev_2.30-8+rpi1 libstdc++-9-dev_9.3.0-12+rpi1 libstdc++6_10.1.0-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.1.4 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8+rpi1 binutils-arm-linux-gnueabihf_2.34-8+rpi1 binutils-common_2.34-8+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.35.1-5 build-essential_12.8 bzip2_1.0.8-3 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-12+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.8.1-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.1-5 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-12+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-1+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1 gcc-8-base_8.4.0-3+rpi1 gcc-9_9.3.0-12+rpi1 gcc-9-base_9.3.0-12+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg6.0_2.1.4 libarchive-zip-perl_1.68-1 libasan5_9.3.0-12+rpi1 libassuan0_2.5.3-7 libatomic1_10.1.0-1+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-8+rpi1 libblkid1_2.35.1-5 libbrotli1_1.0.7-6.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-3 libbz2-dev_1.0.8-3 libc-bin_2.30-8+rpi1 libc-dev-bin_2.30-8+rpi1 libc6_2.30-8+rpi1 libc6-dev_2.30-8+rpi1 libcap-ng0_0.7.9-2.1+b1 libcc1-0_10.1.0-1+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-8+rpi1 libctf0_2.34-8+rpi1 libcurl3-gnutls_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.252 libdebhelper-perl_13.1 libdeflate0_1.6-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.35.1-5 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.1-1 libgcc-9-dev_9.3.0-12+rpi1 libgcc-s1_10.1.0-1+rpi1 libgcc1_1:10.1.0-1+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.3-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10.1.0-1+rpi1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-7+rpi1+b1 libhogweed5_3.5.1+really3.5.1-2 libhts3_1.10.2-3 libicu67_67.1-2 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libk5crypto3_1.17-7+rpi1+b1 libkeyutils1_1.6.1-2 libkrb5-3_1.17-7+rpi1+b1 libkrb5support0_1.17-7+rpi1+b1 libksba8_1.3.5-2 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.1-5 libmpc3_1.1.0-1 libmpdec2_2.4.2-3 libmpfr6_4.0.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.41.0-2 libnpth0_1.6-1 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-10 libpipeline1_1.5.2-2 libpsl5_0.21.0-1.1 libpython3-stdlib_3.8.2-3 libpython3.8-minimal_3.8.3-1 libpython3.8-stdlib_3.8.3-1 libreadline8_8.0-4 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.1-5 libsqlite3-0_3.31.1-5 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-12+rpi1 libstdc++6_10.1.0-1+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.5-3+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo5_6.2-1 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-1+rpi1 libuchardet0_0.0.7-1 libudev1_245.5-3+rpi1 libunistring2_0.9.10-2 libuuid1_2.35.1-5 libxml2_2.9.10+dfsg-5+b1 libzstd1_1.4.4+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.2-1 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.35.1-5 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-10 perl-base_5.30.0-10 perl-modules-5.30_5.30.0-10 pinentry-curses_1.1.0-4 po-debconf_1.0.21 python3_3.8.2-3 python3-minimal_3.8.2-3 python3.8_3.8.3-1 python3.8-minimal_3.8.3-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 samtools_1.10-3 sbuild-build-depends-bedtools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.35.1-5 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri Feb 14 15:03:13 2020 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./bedtools_2.29.2+dfsg-3.dsc
dpkg-source: info: extracting bedtools in /<<BUILDDIR>>/bedtools-2.29.2+dfsg
dpkg-source: info: unpacking bedtools_2.29.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking bedtools_2.29.2+dfsg-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying gzstream.h.patch
dpkg-source: info: applying fix_test_script.patch
dpkg-source: info: applying remove_barski_binding_site.png.patch
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying fix_intersect_test.patch
dpkg-source: info: applying spelling
dpkg-source: info: applying hardening
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-e2f3427e-9c8a-4915-a658-3e7dc0c180e7
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package bedtools
dpkg-buildpackage: info: source version 2.29.2+dfsg-3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from bedtools-2.29.2+dfsg/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.29.2+dfsg'
* Cleaning up.
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.29.2+dfsg'
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 build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.29.2+dfsg'
dh_auto_build -- VERBOSE=1
make -j4 "INSTALL=install --strip-program=true" VERBOSE=1
make[2]: Entering directory '/<<BUILDDIR>>/bedtools-2.29.2+dfsg'
Building BEDTools:
cd src/utils/htslib && make config.h
=========================================================
make[3]: Entering directory '/<<BUILDDIR>>/bedtools-2.29.2+dfsg/src/utils/htslib'
DETECTED_VERSION = v2.29.2
CURRENT_VERSION =
Updating version file.
CXXFLAGS is [-g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security]
* compiling src/bedtools.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/annotateBed/annotateMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/annotateBed/annotateBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
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 '/<<BUILDDIR>>/bedtools-2.29.2+dfsg/src/utils/htslib'
* compiling src/bamToBed/bamToBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
src/annotateBed/annotateMain.cpp: In function 'int annotate_main(int, char**)':
src/annotateBed/annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
39 | bool haveTitles = false;
| ^~~~~~~~~~
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;
| ^~~~~~~~~~~~~~~~~
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:32:16: 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/bamToFastq/bamToFastqMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/bamToFastq/bamToFastq.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/bedToBam/bedToBam.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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:32:16: 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;
| ^~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/utils/BamTools/include/SamHeader.hpp:6,
from src/utils/BamTools/include/api/BamReader.h:1,
from src/bamToFastq/bamToFastq.h:15,
from src/bamToFastq/bamToFastq.cpp:15:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::BamAlignment&}; _Tp = BamTools::BamAlignment; _Alloc = std::allocator<BamTools::BamAlignment>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BamTools::BamAlignment>::iterator' {aka '__gnu_cxx::__normal_iterator<BamTools::BamAlignment*, std::vector<BamTools::BamAlignment> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
* compiling src/bedToIgv/bedToIgv.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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++/9/vector:67,
from src/utils/BamTools/include/SamHeader.hpp:6,
from src/utils/BamTools/include/api/BamReader.h:1,
from src/bamToFastq/bamToFastq.h:15,
from src/bamToFastq/bamToFastq.cpp:15:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void BamToFastq::PairedFastq()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::BamAlignment*, std::vector<BamTools::BamAlignment> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::BamAlignment*, std::vector<BamTools::BamAlignment> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
* compiling src/bed12ToBed6/bed12ToBed6.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/complementFile/complementHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
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/complementFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/expand/expand.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/fastaFromBed/fastaFromBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
src/coverageFile/coverageFile.cpp: In member function 'virtual void CoverageFile::giveFinalReport(RecordOutputMgr*)':
src/coverageFile/coverageFile.cpp:100:11: 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:181:10: 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:210:11: 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:230:10: 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/fastaFromBed/fastaFromBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/flankBed/flankBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
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/groupByHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
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:32:16: 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/groupBy/groupBy.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/intersectFile/intersectFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/fisher/fisher.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/fisher/kfunc.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/jaccard/jaccardHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/jaccard/jaccard.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/linksBed/linksMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/maskFastaFromBed/maskFastaFromBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/multiBamCov/multiBamCovMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/multiBamCov/multiBamCov.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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:32:16: 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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/pairToBed/pairToBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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++/9/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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Point&}; _Tp = Point; _Alloc = std::allocator<Point>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Point, std::allocator<Point> >::iterator' {aka '__gnu_cxx::__normal_iterator<Point*, std::vector<Point, std::allocator<Point> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/multiIntersectBed/multiIntersectBed.cpp:17:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Point*, std::vector<Point, std::allocator<Point> > >; _Distance = int; _Tp = Point; _Compare = __gnu_cxx::__ops::_Iter_comp_val<std::less<Point> >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Point*, std::vector<Point, std::allocator<Point> > >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/general/BedtoolsTypes.h:26,
from src/utils/bedFile/bedFile.h:16,
from src/multiIntersectBed/multiIntersectBed.cpp:19:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void MultiIntersectBed::AddInterval(int)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Point*, std::vector<Point, std::allocator<Point> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Point*, std::vector<Point, std::allocator<Point> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/multiIntersectBed/multiIntersectBed.cpp:17:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Point*, std::vector<Point, std::allocator<Point> > >; _Distance = int; _Tp = Point; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<Point> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Point*, std::vector<Point, std::allocator<Point> > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
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;
| ^~~~~~~~~~~~
* compiling src/pairToBed/pairToBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/randomBed/randomBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
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 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 string&)':
src/pairToBed/pairToBed.cpp:310:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
310 | CHRPOS spanLength = 0;
| ^~~~~~~~~~
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:32:16: 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/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;
| ^~~~~~
* compiling src/randomBed/randomBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/regressTest/regressTestMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
In file included from /usr/include/c++/9/vector:72,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/pairToPair/pairToPair.cpp:12:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MATE&}; _Tp = MATE; _Alloc = std::allocator<MATE>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MATE>::iterator' {aka '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/pairToPair/pairToPair.cpp:12:
/usr/include/c++/9/bits/stl_vector.h: In member function 'bool PairToPair::FindHitsOnBothEnds(const BEDPE&, const std::vector<MATE>&, const std::vector<MATE>&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
* compiling src/regressTest/RegressTest.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
/usr/include/c++/9/bits/stl_vector.h: In member function 'void PairToPair::FindHitsOnEitherEnd(const BEDPE&, const std::vector<MATE>&, const std::vector<MATE>&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/pairToBed/pairToBed.cpp:12:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator<BED>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BED>::iterator' {aka '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
src/regressTest/RegressTest.cpp: In member function 'bool RegressTest::executeAndCompareCorrectness(const fileListType&)':
src/regressTest/RegressTest.cpp:431:8: 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:573:7: 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:622:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
622 | fgets(sLine, 4192, fp);
| ~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/pairToBed/pairToBed.cpp:12:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void BedIntersectPE::FindOverlaps(const BEDPE&, std::vector<BED>&, std::vector<BED>&, const string&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
* compiling src/reldist/reldist.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/sampleFile/sampleHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/sampleFile/sampleFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
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}
In file included from /usr/include/c++/9/vector:72,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/reldist/reldist.cpp:12:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/reldist/reldist.h:15,
from src/reldist/reldist.cpp:13:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/reldist/reldist.h:15,
from src/reldist/reldist.cpp:13:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/reldist/reldist.h:15,
from src/reldist/reldist.cpp:13:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/reldist/reldist.cpp:12:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void RelativeDistance::LoadMidpoints()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/reldist/reldist.h:15,
from src/reldist/reldist.cpp:13:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/shiftBed/shiftBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/shiftBed/shiftBed.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/shuffleBed/shuffleBedMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/subtractFile/subtractHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/subtractFile/subtractFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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++/9/vector:72,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/sortBed/sortBed.cpp:13:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator<BED>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BED>::iterator' {aka '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
* compiling src/summaryFile/summaryHelp.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/sortBed/sortBed.h:12,
from src/sortBed/sortBed.cpp:14:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
* compiling src/summaryFile/summaryFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1879 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/sortBed/sortBed.h:12,
from src/sortBed/sortBed.cpp:14:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Distance = int; _Tp = BED; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/split/splitBed.cpp:15:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator<BED>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BED>::iterator' {aka '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/split/splitBed.cpp:15:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void BedSplit::loadBed()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
* compiling src/tagBam/tagBamMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h:243:5: 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++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/split/splitBed.h:10,
from src/split/splitBed.cpp:17:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/vector:72,
from src/utils/general/FreeList.h:13,
from src/utils/FileRecordTools/Records/Record.h:12,
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:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Interval&}; _Tp = Interval; _Alloc = std::allocator<Interval>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Interval>::iterator' {aka '__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/sortBed/sortBed.h:12,
from src/sortBed/sortBed.cpp:14:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/sortBed/sortBed.h:12,
from src/sortBed/sortBed.cpp:14:
/usr/include/c++/9/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
408 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/sortBed/sortBed.h:12,
from src/sortBed/sortBed.cpp:14:
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/split/splitBed.h:10,
from src/split/splitBed.cpp:17:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Distance = int; _Tp = BED; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/fileType/FileRecordTypeChecker.h:18,
from src/utils/FileRecordTools/Records/Record.h:14,
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:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const Interval&, const Interval&)>]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const Interval&, const Interval&)>]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/utils/fileType/FileRecordTypeChecker.h:18,
from src/utils/FileRecordTools/Records/Record.h:14,
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:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >; _Distance = int; _Tp = Interval; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const Interval&, const Interval&)>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/fileType/FileRecordTypeChecker.h:18,
from src/utils/FileRecordTools/Records/Record.h:14,
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:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const Interval&, const Interval&)>]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/general/FreeList.h:13,
from src/utils/FileRecordTools/Records/Record.h:12,
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:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual bool SummaryFile::findNext(RecordKeyVector&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/fileType/FileRecordTypeChecker.h:18,
from src/utils/FileRecordTools/Records/Record.h:14,
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:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval*, std::vector<Interval> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
* compiling src/tagBam/tagBam.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h:243:5: 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++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/split/splitBed.h:10,
from src/split/splitBed.cpp:17:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/split/splitBed.h:10,
from src/split/splitBed.cpp:17:
/usr/include/c++/9/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
408 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/split/splitBed.h:10,
from src/split/splitBed.cpp:17:
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/unionBedGraphs/unionBedGraphsMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 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:32:16: 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);
| ~~~~~~~~~~~~~^~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/sortBed/sortBed.cpp:13:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void BedSort::SortBedBySizeAsc()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/sortBed/sortBed.h:12,
from src/sortBed/sortBed.cpp:14:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'void BedSort::SortBedByChromThenSizeAsc()':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'void BedSort::SortBedByChromThenSizeDesc()':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'void BedSort::SortBedByChromThenScoreAsc()':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'void BedSort::SortBedByChromThenScoreDesc()':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/sortBed/sortBed.cpp:13:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void BedSort::SortBedBySizeDesc()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/sortBed/sortBed.h:12,
from src/sortBed/sortBed.cpp:14:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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;
| ^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'int BedSplit::doEuristicSplitOnTotalSize()':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/unionBedGraphs/unionBedGraphs.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/windowBed/windowMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/windowMaker/windowMakerMain.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/unionBedGraphs/unionBedGraphs.cpp:17:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PointWithDepth*, std::vector<PointWithDepth, std::allocator<PointWithDepth> > >; _Distance = int; _Tp = PointWithDepth; _Compare = __gnu_cxx::__ops::_Iter_comp_val<std::less<PointWithDepth> >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PointWithDepth*, std::vector<PointWithDepth, std::allocator<PointWithDepth> > >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
* compiling src/windowMaker/windowMaker.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
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:32:16: 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);
| ~~~~~~~~~~~~~^~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PointWithDepth&}; _Tp = PointWithDepth; _Alloc = std::allocator<PointWithDepth>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<PointWithDepth, std::allocator<PointWithDepth> >::iterator' {aka '__gnu_cxx::__normal_iterator<PointWithDepth*, std::vector<PointWithDepth, std::allocator<PointWithDepth> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/utils/bedGraphFile/bedGraphFile.h:16,
from src/unionBedGraphs/unionBedGraphs.cpp:19:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void UnionBedGraphs::AddInterval(int)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PointWithDepth*, std::vector<PointWithDepth, std::allocator<PointWithDepth> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PointWithDepth*, std::vector<PointWithDepth, std::allocator<PointWithDepth> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/unionBedGraphs/unionBedGraphs.cpp:17:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PointWithDepth*, std::vector<PointWithDepth, std::allocator<PointWithDepth> > >; _Distance = int; _Tp = PointWithDepth; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<PointWithDepth> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PointWithDepth*, std::vector<PointWithDepth, std::allocator<PointWithDepth> > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
* compiling src/utils/FileRecordTools/FileRecordMgr.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/FileRecordTools/FileRecordMergeMgr.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp: In member function 'bool BufferedStreamMgr::readFileChunk()':
src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:147:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
147 | if (_mainBufCurrLen < _useBufSize) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'CHRPOS SingleLineDelimTextFileReader::getVcfSVlen()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
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:32:16: 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/Record.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/FileRecordTools/Records/EmptyRecord.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/FileRecordTools/Records/Bed4Interval.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/FileRecordTools/Records/PlusFields.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/FileRecordTools/Records/BedPlusInterval.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/FileRecordTools/Records/VcfRecord.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/FileRecordTools/Records/BlockMgr.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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++/9/vector:72,
from src/utils/general/FreeList.h:13,
from src/utils/FileRecordTools/Records/Record.h:12,
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:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void Tokenize(const string&, std::vector<long long int>&, char)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/BlockMgr.cpp: In member function 'int BlockMgr::getNonRedundantOverlap()':
src/utils/FileRecordTools/Records/BlockMgr.cpp:194:21: 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/StrandQueue.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
In file included from /usr/include/c++/9/vector:72,
from src/utils/FileRecordTools/Records/BlockMgr.h:11,
from src/utils/FileRecordTools/Records/BlockMgr.cpp:8:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/fileType/FileRecordTypeChecker.h:18,
from src/utils/FileRecordTools/Records/BlockMgr.h:16,
from src/utils/FileRecordTools/Records/BlockMgr.cpp:8:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1879 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1879:5: 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++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/utils/fileType/FileRecordTypeChecker.h:18,
from src/utils/FileRecordTools/Records/BlockMgr.h:16,
from src/utils/FileRecordTools/Records/BlockMgr.cpp:8:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/fileType/FileRecordTypeChecker.h:18,
from src/utils/FileRecordTools/Records/BlockMgr.h:16,
from src/utils/FileRecordTools/Records/BlockMgr.cpp:8:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'int BlockMgr::getNonRedundantOverlap()':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/FileRecordTools/Records/BlockMgr.h:11,
from src/utils/FileRecordTools/Records/BlockMgr.cpp:8:
/usr/include/c++/9/bits/stl_vector.h: In member function 'int BlockMgr::findBlockedOverlaps(RecordKeyVector&, RecordKeyVector&, RecordKeyVector&, RecordKeyVector*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
* compiling src/utils/FileRecordTools/Records/RecordList.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/FileRecordTools/Records/RecordKeyList.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/chromsweep/chromsweep.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/Contexts/ContextBase.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 /usr/include/c++/9/vector:72,
from src/utils/general/BedtoolsTypes.h:26,
from src/utils/bedFile/bedFile.h:16,
from src/utils/bedFile/bedFile.cpp:12:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator<BED>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BED>::iterator' {aka '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
* compiling src/utils/Contexts/ContextIntersect.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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++/9/set:60,
from src/utils/general/BedtoolsTypes.h:27,
from src/utils/bedFile/bedFile.h:16,
from src/utils/bedFile/bedFile.cpp:12:
/usr/include/c++/9/bits/stl_tree.h: In member 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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/9/bits/stl_tree.h:2187:5: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, DEPTH> >'} changed in GCC 7.1
2187 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, DEPTH> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/utils/chromsweep/chromsweep.cpp:12:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator<BED>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BED>::iterator' {aka '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/utils/chromsweep/chromsweep.cpp:12:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void ChromSweep::ScanCache()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/general/BedtoolsTypes.h:26,
from src/utils/bedFile/bedFile.h:16,
from src/utils/bedFile/bedFile.cpp:12:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void BedFile::loadBedFileIntoVector()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/utils/bedFile/bedFile.cpp:12:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1879 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'bool ChromSweep::Next(std::pair<BED, std::vector<BED> >&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/utils/general/BedtoolsTypes.h:26,
from src/utils/bedFile/bedFile.h:16,
from src/utils/bedFile/bedFile.cpp:12:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BEDCOV&}; _Tp = BEDCOV; _Alloc = std::allocator<BEDCOV>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BEDCOV>::iterator' {aka '__gnu_cxx::__normal_iterator<BEDCOV*, std::vector<BEDCOV> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/utils/bedFile/bedFile.cpp:12:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Distance = int; _Tp = BED; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
* compiling src/utils/Contexts/ContextFisher.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h:243:5: 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++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/utils/bedFile/bedFile.cpp:12:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<BED*, std::vector<BED> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const BED&, const BED&)>]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/utils/bedFile/bedFile.cpp:12:
/usr/include/c++/9/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
408 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/utils/bedFile/bedFile.cpp:12:
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/utils/Contexts/ContextMap.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/Contexts/ContextSample.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
/usr/include/c++/9/bits/stl_algo.h: In member function 'void BedFile::assignWeightsBasedOnSize()':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/general/BedtoolsTypes.h:26,
from src/utils/bedFile/bedFile.h:16,
from src/utils/bedFile/bedFile.cpp:12:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void BedFile::loadBedFileIntoMapNoBin()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/bedFile/bedFile.h:30,
from src/utils/bedFile/bedFile.cpp:12:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/general/BedtoolsTypes.h:26,
from src/utils/bedFile/bedFile.h:16,
from src/utils/bedFile/bedFile.cpp:12:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void BedFile::loadBedCovFileIntoMap()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BEDCOV*, std::vector<BEDCOV> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
* compiling src/utils/Contexts/ContextSpacing.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
In file included from /usr/include/c++/9/map:61,
from src/utils/general/BedtoolsTypes.h:28,
from src/utils/bedFile/bedFile.h:16,
from src/utils/bedFile/bedFile.cpp:12:
/usr/include/c++/9/bits/stl_map.h: In member function 'void BedFile::countListHits(const BED&, int, bool, bool)':
/usr/include/c++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, DEPTH> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, DEPTH> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, DEPTH> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:67,
from src/utils/general/BedtoolsTypes.h:26,
from src/utils/bedFile/bedFile.h:16,
from src/utils/bedFile/bedFile.cpp:12:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void BedFile::addBEDIntoMap(BED)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
* compiling src/utils/Contexts/ContextJaccard.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
/usr/include/c++/9/bits/stl_vector.h: In member function 'void BedFile::allHits(std::string, CHRPOS, CHRPOS, std::string, std::vector<BED>&, bool, bool, float, bool)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
* compiling src/utils/Contexts/ContextClosest.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 /usr/include/c++/9/vector:72,
from src/utils/general/BedtoolsTypes.h:26,
from src/utils/bedFile/bedFile.h:16,
from src/utils/bedFile/bedFile.cpp:12:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BEDCOVLIST&}; _Tp = BEDCOVLIST; _Alloc = std::allocator<BEDCOVLIST>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BEDCOVLIST>::iterator' {aka '__gnu_cxx::__normal_iterator<BEDCOVLIST*, std::vector<BEDCOVLIST> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/general/BedtoolsTypes.h:26,
from src/utils/bedFile/bedFile.h:16,
from src/utils/bedFile/bedFile.cpp:12:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void BedFile::loadBedCovListFileIntoMap()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BEDCOVLIST*, std::vector<BEDCOVLIST> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
* compiling src/utils/Contexts/ContextSubtract.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/Contexts/ContextCoverage.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/Contexts/ContextComplement.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/Contexts/ContextGroupBy.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/general/ParseTools.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/general/PushBackStreamBuf.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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:366:19: 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 /usr/include/c++/9/algorithm:62,
from src/utils/fileType/FileRecordTypeChecker.h:18,
from src/utils/FileRecordTools/Records/Record.h:14,
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++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<double> >]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::greater<double> >]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/vector:72,
from src/utils/bedFilePE/bedFilePE.h:4,
from src/utils/bedFilePE/bedFilePE.cpp:15:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MATE&}; _Tp = MATE; _Alloc = std::allocator<MATE>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MATE>::iterator' {aka '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/utils/fileType/FileRecordTypeChecker.h:18,
from src/utils/FileRecordTools/Records/Record.h:14,
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++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<double> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/fileType/FileRecordTypeChecker.h:18,
from src/utils/FileRecordTools/Records/Record.h:14,
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++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<double> >]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/utils/fileType/FileRecordTypeChecker.h:18,
from src/utils/FileRecordTools/Records/Record.h:14,
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++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::greater<double> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/fileType/FileRecordTypeChecker.h:18,
from src/utils/FileRecordTools/Records/Record.h:14,
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++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::greater<double> >]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/utils/NewChromsweep/NewChromsweep.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 file included from /usr/include/c++/9/vector:67,
from src/utils/bedFilePE/bedFilePE.h:4,
from src/utils/bedFilePE/bedFilePE.cpp:15:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void BedFilePE::FindOverlapsPerBin(int, std::string, CHRPOS, CHRPOS, std::string, std::string, std::vector<MATE>&, float, bool, bool)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'void KeyListOpsMethods::sortArray(bool, bool)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/utils/NewChromsweep/CloseSweep.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
/usr/include/c++/9/bits/stl_vector.h: In member function 'void BedFilePE::loadBedPEFileIntoMap()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
* compiling src/utils/sequenceUtilities/sequenceUtils.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/BamTools-Ancillary/BamAncillary.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
* compiling src/utils/BlockedIntervals/BlockedIntervals.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
In file included from /usr/include/c++/9/vector:72,
from src/utils/general/FreeList.h:13,
from src/utils/general/BTlist.h:28,
from src/utils/NewChromsweep/NewChromsweep.h:16,
from src/utils/NewChromsweep/CloseSweep.h:11,
from src/utils/NewChromsweep/CloseSweep.cpp:8:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
* compiling src/utils/Fasta/Fasta.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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++/9/vector:67,
from src/utils/general/FreeList.h:13,
from src/utils/general/BTlist.h:28,
from src/utils/NewChromsweep/NewChromsweep.h:16,
from src/utils/NewChromsweep/CloseSweep.h:11,
from src/utils/NewChromsweep/CloseSweep.cpp:8:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void CloseSweep::addSingleRec(Record*, CHRPOS, int&, RecordKeyVector&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'int CloseSweep::addRecsToRetList(RecDistList::elemsType*, CHRPOS, RecordKeyVector&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/utils/general/FreeList.h:13,
from src/utils/general/BTlist.h:28,
from src/utils/NewChromsweep/NewChromsweep.h:16,
from src/utils/NewChromsweep/CloseSweep.h:11,
from src/utils/NewChromsweep/CloseSweep.cpp:8:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/general/FreeList.h:13,
from src/utils/general/BTlist.h:28,
from src/utils/NewChromsweep/NewChromsweep.h:16,
from src/utils/NewChromsweep/CloseSweep.h:11,
from src/utils/NewChromsweep/CloseSweep.cpp:8:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'CloseSweep::CloseSweep(ContextClosest*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator<BED>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BED>::iterator' {aka '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:60,
from src/utils/fileType/FileRecordTypeChecker.h:17,
from src/utils/FileRecordTools/Records/Record.h:14,
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:
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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, long long int>; _KeyOfValue = std::_Select1st<std::pair<const long long int, long long int> >; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, long long int> >]':
/usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from src/utils/fileType/FileRecordTypeChecker.h:17,
from src/utils/FileRecordTools/Records/Record.h:14,
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:
/usr/include/c++/9/bits/stl_map.h: In member function 'void CloseSweep::checkMultiDbs(RecordKeyVector&)':
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:67,
from src/utils/general/FreeList.h:13,
from src/utils/general/BTlist.h:28,
from src/utils/NewChromsweep/NewChromsweep.h:16,
from src/utils/NewChromsweep/CloseSweep.h:11,
from src/utils/NewChromsweep/CloseSweep.cpp:8:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
src/utils/Fasta/Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
src/utils/Fasta/Fasta.cpp:292:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
292 | fread(seq, sizeof(char), seqlen, file);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/utils/Fasta/Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, CHRPOS, CHRPOS)':
src/utils/Fasta/Fasta.cpp:334:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
334 | fread(seq, sizeof(char), (off_t) seqlen, file);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/utils/Fasta/split.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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++/9/vector:72,
from src/utils/BlockedIntervals/BlockedIntervals.h:12,
from src/utils/BlockedIntervals/BlockedIntervals.cpp:12:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator<BED>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BED>::iterator' {aka '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >'} changed in GCC 7.1
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void Tokenize(const string&, std::vector<long long int>&, char)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:60,
from src/utils/Fasta/Fasta.h:12,
from src/utils/Fasta/Fasta.cpp:9:
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> >]':
/usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from src/utils/Fasta/Fasta.h:12,
from src/utils/Fasta/Fasta.cpp:9:
/usr/include/c++/9/bits/stl_map.h: In member function 'std::string FastaReference::sequenceNameStartingWith(std::string)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
* compiling src/utils/VectorOps/VectorOps.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator<BED>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BED>::iterator' {aka '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/utils/Fasta/Fasta.h:15,
from src/utils/Fasta/Fasta.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const FastaIndexEntry&}; _Tp = FastaIndexEntry; _Alloc = std::allocator<FastaIndexEntry>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<FastaIndexEntry>::iterator' {aka '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<FastaIndexEntry>::iterator' {aka '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >'} changed in GCC 7.1
* compiling src/utils/GenomeFile/NewGenomeFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/Fasta/Fasta.h:18,
from src/utils/Fasta/Fasta.cpp:9:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(FastaIndexEntry, FastaIndexEntry)>]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FastaIndexEntry, FastaIndexEntry)>]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/utils/Fasta/Fasta.h:18,
from src/utils/Fasta/Fasta.cpp:9:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >; _Distance = int; _Tp = FastaIndexEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_val<bool (*)(FastaIndexEntry, FastaIndexEntry)>]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/BlockedIntervals/BlockedIntervals.h:12,
from src/utils/BlockedIntervals/BlockedIntervals.cpp:12:
/usr/include/c++/9/bits/stl_vector.h: In function 'void GetBedBlocks(const BED&, bedVector&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >; _Distance = int; _Tp = FastaIndexEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FastaIndexEntry, FastaIndexEntry)>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FastaIndexEntry, FastaIndexEntry)>]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/Fasta/Fasta.h:18,
from src/utils/Fasta/Fasta.cpp:9:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FastaIndexEntry, FastaIndexEntry)>]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from src/utils/Fasta/Fasta.h:12,
from src/utils/Fasta/Fasta.cpp:9:
/usr/include/c++/9/bits/stl_map.h: In function 'std::ostream& operator<<(std::ostream&, FastaIndex&)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:67,
from src/utils/Fasta/Fasta.h:15,
from src/utils/Fasta/Fasta.cpp:9:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/Fasta/Fasta.h:18,
from src/utils/Fasta/Fasta.cpp:9:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/utils/GenomeFile/GenomeFile.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/VectorOps/VectorOps.h:21,
from src/utils/VectorOps/VectorOps.cpp:15:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<double> >]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::greater<double> >]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/utils/VectorOps/VectorOps.h:15,
from src/utils/VectorOps/VectorOps.cpp:15:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function '_OIter std::transform(_IIter, _IIter, _OIter, _UnaryOperation) [with _IIter = __gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char>*, std::vector<std::__cxx11::basic_string<char> > >; _OIter = std::back_insert_iterator<std::vector<double> >; _UnaryOperation = double (*)(const std::__cxx11::basic_string<char>&)]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
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++/9/vector:67,
from src/utils/general/BedtoolsTypes.h:26,
from src/utils/GenomeFile/NewGenomeFile.h:18,
from src/utils/GenomeFile/NewGenomeFile.cpp:12:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void NewGenomeFile::loadGenomeFileIntoMap()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/utils/VectorOps/VectorOps.h:21,
from src/utils/VectorOps/VectorOps.cpp:15:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/VectorOps/VectorOps.h:21,
from src/utils/VectorOps/VectorOps.cpp:15:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'double VectorOps::GetMedian()':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/utils/GenomeFile/GenomeFile.cpp:12:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
426 | 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:170:42: 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:455:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
455 | for (size_t i = 1; i < _context->getNumInputFiles(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/utils/ToolBase/ToolBase.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/utils/VectorOps/VectorOps.h:21,
from src/utils/VectorOps/VectorOps.cpp:15:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<double> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/VectorOps/VectorOps.h:21,
from src/utils/VectorOps/VectorOps.cpp:15:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<double> >]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/utils/VectorOps/VectorOps.h:21,
from src/utils/VectorOps/VectorOps.cpp:15:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::greater<double> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/utils/lineFileUtilities/lineFileUtilities.h:4,
from src/utils/GenomeFile/GenomeFile.cpp:12:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/VectorOps/VectorOps.h:21,
from src/utils/VectorOps/VectorOps.cpp:15:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::greater<double> >]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'std::string VectorOps::GetDistinctSortNum(bool)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling src/utils/driver/BedtoolsDriver.cpp
g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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/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
cd src/utils/htslib && make lib-static
make[3]: Entering directory '/<<BUILDDIR>>/bedtools-2.29.2+dfsg/src/utils/htslib'
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c
- Creating executables for old CLI.
done.
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_samtools.o cram/cram_samtools.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/files.o cram/files.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -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 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/rANS_static.o cram/rANS_static.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/sam_header.o cram/sam_header.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.29.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c
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 '/<<BUILDDIR>>/bedtools-2.29.2+dfsg/src/utils/htslib'
- Building main bedtools binary.
g++ -Wl,-z,relro -Wl,-z,now -o bin/bedtools obj/bedtools.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/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 '/<<BUILDDIR>>/bedtools-2.29.2+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.29.2+dfsg'
rm -f debian/bedtools.debhelper.log
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.29.2+dfsg'
mv test/shuffle debian/
dh_auto_test
make -j4 test
make[2]: Entering directory '/<<BUILDDIR>>/bedtools-2.29.2+dfsg'
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
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
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...index file test.iupac.fa.fai not found, generating...
ok
getfasta.t09...index file test.iupac.fa.fai not found, generating...
ok
getfasta.t10...index file test.fa.fai not found, generating...
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
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.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...[E::sam_parse1] missing SAM header
[W::sam_read1] Parse error at line 1
ok
intersect.new.t10...[E::sam_parse1] missing SAM header
[W::sam_read1] Parse error at line 1
ok
intersect.new.t11...[E::sam_parse1] missing SAM header
[W::sam_read1] Parse error at line 1
ok
intersect.new.t12...[E::sam_parse1] missing SAM header
[W::sam_read1] Parse error at line 1
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...[W::sam_read1] Parse error at line 1
ok
intersect.new.t33...[W::sam_read1] Parse error at line 1
ok
intersect.new.t34...[W::sam_read1] Parse error at line 1
ok
intersect.new.t35...[W::sam_read1] Parse error at line 1
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...[W::sam_read1] Parse error at line 1
ok
intersect.new.t45...[W::sam_read1] Parse error at line 1
ok
intersect.new.t46...[W::sam_read1] Parse error at line 1
ok
intersect.new.t47...[W::sam_read1] Parse error at line 1
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
###########################################################
#
# 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
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:
test-sample.sh: line 29: 5332 Segmentation fault (core dumped) $BT random -l 1000 -n 1000 -g human.hg19.genome >> mainFile.bed
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
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...1,2c1,2
< chr1 0 1 a1 1 +
< chr1 0 1 a2 2 -
---
> chr1 0 1000 a1 1 +
> chr1 0 1000 a2 2 -
fail
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 shift sort spacing split subtract
Tools failing: negativecontrol sample slop
NB: the 'negativecontrol' test is supposed to fail. If it wasn't caught,
something went wrong with this test script.
make[2]: *** [Makefile:220: test] Error 1
make[2]: Leaving directory '/<<BUILDDIR>>/bedtools-2.29.2+dfsg'
dh_auto_test: error: make -j4 test returned exit code 2
make[1]: *** [debian/rules:52: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.29.2+dfsg'
make: *** [debian/rules:13: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2020-06-12T17:17:57Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 0
Build-Time: 852
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 308
Job: bedtools_2.29.2+dfsg-3
Machine Architecture: armhf
Package: bedtools
Package-Time: 1220
Source-Version: 2.29.2+dfsg-3
Space: 0
Status: failed
Version: 2.29.2+dfsg-3
--------------------------------------------------------------------------------
Finished at 2020-06-12T17:17:57Z
Build needed 00:00:00, 0k disc space