bedtools →
2.27.1+dfsg-4 →
armhf → 2019-02-24 05:52:13
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| bedtools 2.27.1+dfsg-4 (armhf) Sun, 24 Feb 2019 05:42:35 +0000 |
+==============================================================================+
Package: bedtools
Version: 2.27.1+dfsg-4
Source Version: 2.27.1+dfsg-4
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-dda3fe28-b43e-4cb4-b9e3-ca8e634cc7ea' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.1 MB]
Fetched 24.4 MB in 9s (2584 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 13.5 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main bedtools 2.27.1+dfsg-4 (dsc) [2244 B]
Get:2 http://172.17.0.1/private buster-staging/main bedtools 2.27.1+dfsg-4 (tar) [13.5 MB]
Get:3 http://172.17.0.1/private buster-staging/main bedtools 2.27.1+dfsg-4 (diff) [12.2 kB]
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Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bedtools-qRi2oG/bedtools-2.27.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bedtools-qRi2oG' 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-LXjLYR/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-LXjLYR/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-LXjLYR/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-LXjLYR/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-LXjLYR/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-LXjLYR/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-LXjLYR/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-LXjLYR/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (11.1 kB/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 packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libgpg-error-l10n libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libnss-systemd libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-LXjLYR/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15799 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 amd64 arm64 armel armhf i386 mips64el mipsel ppc64el all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), python, zlib1g-dev, samtools
Filtered Build-Depends: debhelper (>= 11~), python, zlib1g-dev, samtools
dpkg-deb: building package 'sbuild-build-depends-bedtools-dummy' in '/<<BUILDDIR>>/resolver-LXjLYR/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-LXjLYR/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-LXjLYR/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-LXjLYR/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-LXjLYR/apt_archive ./ Sources [507 B]
Get:5 copy:/<<BUILDDIR>>/resolver-LXjLYR/apt_archive ./ Packages [591 B]
Fetched 2431 B in 0s (12.6 kB/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 packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales
libgpg-error-l10n libnss-systemd libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional 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 libbsd0 libcroco3
libcurl3-gnutls libelf1 libfile-stripnondeterminism-perl libglib2.0-0
libhts2 libicu63 libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5
libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib
librtmp1 libsigsegv2 libssh2-1 libtool libuchardet0 libxml2 m4 man-db
mime-support po-debconf python python-minimal python2 python2-minimal
python2.7 python2.7-minimal samtools zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl python-doc python-tk python2-doc python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs 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 libbsd0 libcroco3
libcurl3-gnutls libelf1 libfile-stripnondeterminism-perl libglib2.0-0
libhts2 libicu63 libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5
libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib
librtmp1 libsigsegv2 libssh2-1 libtool libuchardet0 libxml2 m4 man-db
mime-support po-debconf python python-minimal python2 python2-minimal
python2.7 python2.7-minimal samtools sbuild-build-depends-bedtools-dummy
zlib1g-dev
0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded.
Need to get 23.2 MB of archives.
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Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-2 [782 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.5-2 [1230 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-8 [394 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.15-8 [1089 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python2-minimal armhf 2.7.15-4 [41.4 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15-4 [21.0 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.62 [37.2 kB]
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Get:14 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.15-8 [299 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libpython2-stdlib armhf 2.7.15-4 [20.8 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15-4 [20.8 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf python2 armhf 2.7.15-4 [41.6 kB]
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Get:19 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.35-2 [242 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.35-2 [109 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.35-2 [65.1 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
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Get:33 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.1.1-1 [13.0 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.175-2 [157 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.3-1 [1077 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-6 [7973 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf debhelper all 12.1 [1015 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.36.0-2 [73.6 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.64.0-1 [291 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.9-8 [254 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf samtools armhf 1.9-3 [377 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
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Unpacking sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up libnghttp2-14:armhf (1.36.0-2) ...
Setting up mime-support (3.62) ...
Installing new version of config file /etc/mime.types ...
Setting up libicu63:armhf (63.1-6) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libpsl5:armhf (0.20.2-2) ...
Setting up libelf1:armhf (0.175-2) ...
Setting up libglib2.0-0:armhf (2.58.3-1) ...
No schema files found: removed existing output file.
Setting up gettext-base (0.19.8.1-9) ...
Setting up libpipeline1:armhf (1.5.1-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ...
Setting up m4 (1.4.18-2) ...
Setting up libbsd0:armhf (0.9.1-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libmagic-mgc (1:5.35-2) ...
Setting up libmagic1:armhf (1:5.35-2) ...
Setting up libcroco3:armhf (0.6.12-3) ...
Setting up libssh2-1:armhf (1.8.0-2) ...
Processing triggers for libc-bin (2.28-6+rpi1) ...
Setting up dwz (0.12-3) ...
Setting up autotools-dev (20180224.1) ...
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 libpython2.7-stdlib:armhf (2.7.15-8) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (1.1.1-1) ...
Setting up gettext (0.19.8.1-9) ...
Setting up libcurl3-gnutls:armhf (7.64.0-1) ...
Setting up groff-base (1.22.4-2) ...
Setting up python2.7 (2.7.15-8) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.35-2) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer -> /lib/systemd/system/man-db.timer.
Setting up libpython2-stdlib:armhf (2.7.15-4) ...
Setting up libhts2:armhf (1.9-8) ...
Setting up libtool (2.4.6-9) ...
Setting up po-debconf (1.0.21) ...
Setting up python2 (2.7.15-4) ...
Setting up libpython-stdlib:armhf (2.7.15-4) ...
Setting up samtools (1.9-3) ...
Setting up python (2.7.15-4) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (12.1) ...
Setting up sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (1.1.1-1) ...
Processing triggers for libc-bin (2.28-6+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-11+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-20+rpi1 gcc-8_8.2.0-20+rpi1 libc6-dev_2.28-6+rpi1 libstdc++-8-dev_8.2.0-20+rpi1 libstdc++6_8.2.0-20+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~rc3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.46 bash_5.0-2 binutils_2.31.1-11+rpi1 binutils-arm-linux-gnueabihf_2.31.1-11+rpi1 binutils-common_2.31.1-11+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20190110 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-20+rpi1 dash_0.5.10.2-5 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.70 debhelper_12.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.1-1 diffutils_1:3.6-1 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.155-2 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 e2fsprogs-l10n_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-2 findutils_4.6.0+git+20190105-2 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-20+rpi1 gcc_4:8.2.0-2+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-20+rpi1 gcc-8-base_8.2.0-20+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-agent_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56+nmu1 initramfs-tools_0.133 initramfs-tools-core_0.133 intltool-debian_0.35.0+20060710.5 klibc-utils_2.0.6-1+rpi1 kmod_26-1 krb5-locales_1.17-1 libacl1_2.2.52-3 libapparmor1_2.13.2-7 libapt-pkg5.0_1.8.0~rc3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.2 libasan5_8.2.0-20+rpi1 libassuan0_2.5.2-1 libatomic1_8.2.0-20+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2+b1 libbinutils_2.31.1-11+rpi1 libblkid1_2.33.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-6+rpi1 libc-dev-bin_2.28-6+rpi1 libc6_2.28-6+rpi1 libc6-dev_2.28-6+rpi1 libcap-ng0_0.7.9-2 libcap2_1:2.25-2 libcc1-0_8.2.0-20+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.1.0-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.64.0-1 libdb5.3_5.3.28+dfsg1-0.3 libdbus-1-3_1.12.12-1 libdebconfclient0_0.247 libdevmapper1.02.1_2:1.02.155-2 libdpkg-perl_1.19.2 libdrm-common_2.4.97-1+rpi1 libdrm2_2.4.97-1+rpi1 libelf1_0.175-2 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.1-1 libgcc-8-dev_8.2.0-20+rpi1 libgcc1_1:8.2.0-20+rpi1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libglib2.0-0_2.58.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.6-2 libgomp1_8.2.0-20+rpi1 libgpg-error-l10n_1.35-1 libgpg-error0_1.35-1 libgssapi-krb5-2_1.17-1 libhogweed4_3.4.1-1 libhts2_1.9-8 libicu63_63.1-6 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3 libisl19_0.20-2 libjson-c3_0.12.1+ds-2 libk5crypto3_1.17-1 libkeyutils1_1.6-2 libklibc_2.0.6-1+rpi1 libkmod2_26-1 libkrb5-3_1.17-1 libkrb5support0_1.17-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-3+rpi1 libldap-common_2.4.47+dfsg-3+rpi1 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-2 libmagic1_1:5.35-2 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses5_6.1+20181013-2 libncurses6_6.1+20181013-2 libncursesw5_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libnghttp2-14_1.36.0-2 libnpth0_1.6-1 libnss-systemd_240-5+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-4 libpam-modules-bin_1.1.8-4 libpam-runtime_1.1.8-4 libpam-systemd_240-5+rpi1 libpam0g_1.1.8-4 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.28_5.28.1-4 libpipeline1_1.5.1-2 libplymouth4_0.9.4-1 libpng16-16_1.6.36-5 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libpython-stdlib_2.7.15-4 libpython2-stdlib_2.7.15-4 libpython2.7-minimal_2.7.15-8 libpython2.7-stdlib_2.7.15-8 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.26.0+fossilbc891ac6b-2 libss2_1.44.5-1 libssh2-1_1.8.0-2 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-20+rpi1 libstdc++6_8.2.0-20+rpi1 libsystemd0_240-5+rpi1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-2 libtinfo6_6.1+20181013-2 libtool_2.4.6-9 libubsan1_8.2.0-20+rpi1 libuchardet0_0.0.6-3 libudev1_240-5+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.8+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.5-2 mawk_1.3.3-17 mime-support_3.62 mount_2.33.1-0.1 multiarch-support_2.28-6+rpi1 nano_3.2-1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 netbase_5.6 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-4 perl-base_5.28.1-4 perl-modules-5.24_5.24.1-7 perl-modules-5.28_5.28.1-4 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 python_2.7.15-4 python-minimal_2.7.15-4 python2_2.7.15-4 python2-minimal_2.7.15-4 python2.7_2.7.15-8 python2.7-minimal_2.7.15-8 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 samtools_1.9-3 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 systemd_240-5+rpi1 systemd-sysv_240-5+rpi1 sysvinit-utils_2.93-6 tar_1.30+dfsg-5 tzdata_2018i-1 udev_240-5+rpi1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Feb 14 13:14:15 2019 UTC
gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./bedtools_2.27.1+dfsg-4.dsc
dpkg-source: info: extracting bedtools in /<<BUILDDIR>>/bedtools-2.27.1+dfsg
dpkg-source: info: unpacking bedtools_2.27.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking bedtools_2.27.1+dfsg-4.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 reproducible_build.patch
dpkg-source: info: applying louder
dpkg-source: info: applying flag_no_overwrite
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-dda3fe28-b43e-4cb4-b9e3-ca8e634cc7ea
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package bedtools
dpkg-buildpackage: info: source version 2.27.1+dfsg-4
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from bedtools-2.27.1+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-2.27.1+dfsg'
* Cleaning-up BamTools API
* Cleaning up.
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.27.1+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
dh_auto_build -a
make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.27.1+dfsg'
$CXXFLAGS is [-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11]
Building BEDTools:
=========================================================
* Creating BamTools API
- Building in src/utils/FileRecordTools
- Building in src/utils/FileRecordTools/FileReaders
- Building in src/utils/FileRecordTools/Records
* compiling FileRecordMgr.cpp
* compiling FileReader.cpp
g++ -c -o ../../../obj//FileRecordMgr.o FileRecordMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//fileType/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//GenomeFile/ -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
g++ -c -o ../../../../obj//FileReader.o FileReader.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//BamTools/include/ -I../../../utils//BamTools/src/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//general/ -I../../../utils//gzstream/ -I../../../utils//version/ -I../../../utils//lineFileUtilities/
* compiling Record.cpp
g++ -c -o ../../../../obj//Record.o Record.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
DETECTED_VERSION = v2.27.1
CURRENT_VERSION =
Updating version file.
- Building in src/utils/bedFile
* compiling bedFile.cpp
g++ -c -o ../../../obj//bedFile.o bedFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//gzstream/ -I../../utils//fileType/ -I../../utils//stringUtilities/
* compiling SingleLineDelimTextFileReader.cpp
g++ -c -o ../../../../obj//SingleLineDelimTextFileReader.o SingleLineDelimTextFileReader.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//BamTools/include/ -I../../../utils//BamTools/src/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//general/ -I../../../utils//gzstream/ -I../../../utils//version/ -I../../../utils//lineFileUtilities/
* compiling EmptyRecord.cpp
g++ -c -o ../../../../obj//EmptyRecord.o EmptyRecord.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling FileRecordMergeMgr.cpp
g++ -c -o ../../../obj//FileRecordMergeMgr.o FileRecordMergeMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//fileType/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//GenomeFile/ -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
* compiling Bed3Interval.cpp
g++ -c -o ../../../../obj//Bed3Interval.o Bed3Interval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling BamFileReader.cpp
g++ -c -o ../../../../obj//BamFileReader.o BamFileReader.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//BamTools/include/ -I../../../utils//BamTools/src/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//general/ -I../../../utils//gzstream/ -I../../../utils//version/ -I../../../utils//lineFileUtilities/
* compiling FileRecordMgr.cpp
g++ -c -o ../../../obj//FileRecordMgr.o FileRecordMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//fileType/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//GenomeFile/ -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
In file included from /usr/include/c++/8/vector:69,
from ../../utils//lineFileUtilities/lineFileUtilities.h:4,
from bedFile.h:17,
from bedFile.cpp:12:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
* compiling Bed4Interval.cpp
g++ -c -o ../../../../obj//Bed4Interval.o Bed4Interval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
In file included from /usr/include/c++/8/vector:64,
from ../../utils//lineFileUtilities/lineFileUtilities.h:4,
from bedFile.h:17,
from bedFile.cpp:12:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BedFile::loadBedFileIntoVector()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
* compiling BufferedStreamMgr.cpp
g++ -c -o ../../../../obj//BufferedStreamMgr.o BufferedStreamMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//BamTools/include/ -I../../../utils//BamTools/src/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//general/ -I../../../utils//gzstream/ -I../../../utils//version/ -I../../../utils//lineFileUtilities/
In file included from /usr/include/c++/8/algorithm:62,
from bedFile.h:29,
from bedFile.cpp:12:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
/usr/include/c++/8/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++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
__final_insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling BedGraphInterval.cpp
g++ -c -o ../../../../obj//BedGraphInterval.o BedGraphInterval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling FileRecordMergeMgr.cpp
g++ -c -o ../../../obj//FileRecordMergeMgr.o FileRecordMergeMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//fileType/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//GenomeFile/ -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from bedFile.h:29,
from bedFile.cpp:12:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/8/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++/8/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
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/8/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++/8/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 InputStreamMgr.cpp
g++ -c -o ../../../../obj//InputStreamMgr.o InputStreamMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//BamTools/include/ -I../../../utils//BamTools/src/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//general/ -I../../../utils//gzstream/ -I../../../utils//version/ -I../../../utils//lineFileUtilities/
/usr/include/c++/8/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++/8/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
__pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~
/usr/include/c++/8/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++/8/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++/8/algorithm:62,
from bedFile.h:29,
from bedFile.cpp:12:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from bedFile.h:29,
from bedFile.cpp:12:
/usr/include/c++/8/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
std::__pop_heap(__first, __last, __last, __comp);
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from bedFile.h:29,
from bedFile.cpp:12:
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../../utils//lineFileUtilities/lineFileUtilities.h:4,
from bedFile.h:17,
from bedFile.cpp:12:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BedFile::loadBedFileIntoMapNoBin()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from bedFile.h:29,
from bedFile.cpp:12:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'void BedFile::assignWeightsBasedOnSize()':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling Bed5Interval.cpp
g++ -c -o ../../../../obj//Bed5Interval.o Bed5Interval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
- Building in FileReaders
* compiling InputStreamMgr.cpp
g++ -c -o ../../../../obj//InputStreamMgr.o InputStreamMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//BamTools/include/ -I../../../utils//BamTools/src/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//general/ -I../../../utils//gzstream/ -I../../../utils//version/ -I../../../utils//lineFileUtilities/
- Building in src/utils/BinTree
* compiling BinTree.cpp
g++ -c -o ../../../obj//BinTree.o BinTree.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//Contexts/ -I../../utils//GenomeFile/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
In file included from /usr/include/c++/8/vector:64,
from ../../utils//lineFileUtilities/lineFileUtilities.h:4,
from bedFile.h:17,
from bedFile.cpp:12:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BedFile::addBEDIntoMap(BED)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
* compiling Bed6Interval.cpp
g++ -c -o ../../../../obj//Bed6Interval.o Bed6Interval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BedFile::allHits(std::__cxx11::string, CHRPOS, CHRPOS, std::__cxx11::string, std::vector<BED>&, bool, bool, float, bool)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
- Building in Records
* compiling Bed6Interval.cpp
g++ -c -o ../../../../obj//Bed6Interval.o Bed6Interval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling PlusFields.cpp
g++ -c -o ../../../../obj//PlusFields.o PlusFields.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling BedPlusInterval.cpp
g++ -c -o ../../../../obj//BedPlusInterval.o BedPlusInterval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling Bed12Interval.cpp
g++ -c -o ../../../../obj//Bed12Interval.o Bed12Interval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling PlusFields.cpp
g++ -c -o ../../../../obj//PlusFields.o PlusFields.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
- Building in src/utils/version
* compiling version.cpp
g++ -c -o ../../../obj//version.o version.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2
* compiling BamRecord.cpp
g++ -c -o ../../../../obj//BamRecord.o BamRecord.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling BedPlusInterval.cpp
g++ -c -o ../../../../obj//BedPlusInterval.o BedPlusInterval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling GffRecord.cpp
g++ -c -o ../../../../obj//GffRecord.o GffRecord.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
g++ -c -o ../../../obj//bedGraphFile.o bedGraphFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//gzstream/ -I../../utils//fileType/
* compiling Bed12Interval.cpp
g++ -c -o ../../../../obj//Bed12Interval.o Bed12Interval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling GffRecord.cpp
g++ -c -o ../../../../obj//GffRecord.o GffRecord.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling GffPlusRecord.cpp
g++ -c -o ../../../../obj//GffPlusRecord.o GffPlusRecord.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
g++ -c -o ../../../obj//chromsweep.o chromsweep.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//bedFile/ -I../../utils//gzstream/ -I../../utils//fileType/
* compiling VcfRecord.cpp
g++ -c -o ../../../../obj//VcfRecord.o VcfRecord.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling NoPosPlusRecord.cpp
g++ -c -o ../../../../obj//NoPosPlusRecord.o NoPosPlusRecord.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling GffPlusRecord.cpp
g++ -c -o ../../../../obj//GffPlusRecord.o GffPlusRecord.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
- Building in src/utils/Contexts
* compiling ContextBase.cpp
g++ -c -o ../../../obj//ContextBase.o ContextBase.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
* compiling BlockMgr.cpp
g++ -c -o ../../../../obj//BlockMgr.o BlockMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling VcfRecord.cpp
g++ -c -o ../../../../obj//VcfRecord.o VcfRecord.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
In file included from /usr/include/c++/8/vector:69,
from ../../utils//lineFileUtilities/lineFileUtilities.h:4,
from chromsweep.cpp:12:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../../utils//lineFileUtilities/lineFileUtilities.h:4,
from chromsweep.cpp:12:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void ChromSweep::ScanCache()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
* compiling StrandQueue.cpp
g++ -c -o ../../../../obj//StrandQueue.o StrandQueue.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling BlockMgr.cpp
g++ -c -o ../../../../obj//BlockMgr.o BlockMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
/usr/include/c++/8/bits/stl_vector.h: In member function 'bool ChromSweep::Next(std::pair<BED, std::vector<BED> >&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
* compiling RecordMgr.cpp
g++ -c -o ../../../../obj//RecordMgr.o RecordMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling StrandQueue.cpp
g++ -c -o ../../../../obj//StrandQueue.o StrandQueue.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling RecordList.cpp
g++ -c -o ../../../../obj//RecordList.o RecordList.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling RecordMgr.cpp
g++ -c -o ../../../../obj//RecordMgr.o RecordMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
- Building in src/utils/general
* compiling ParseTools.cpp
g++ -c -o ../../../obj//ParseTools.o ParseTools.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//version/
* compiling ContextIntersect.cpp
g++ -c -o ../../../obj//ContextIntersect.o ContextIntersect.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
* compiling PushBackStreamBuf.cpp
g++ -c -o ../../../obj//PushBackStreamBuf.o PushBackStreamBuf.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//version/
* compiling CompressionTools.cpp
g++ -c -o ../../../obj//CompressionTools.o CompressionTools.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//version/
* compiling Tokenizer.cpp
g++ -c -o ../../../obj//Tokenizer.o Tokenizer.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//version/
* compiling ContextFisher.cpp
g++ -c -o ../../../obj//ContextFisher.o ContextFisher.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
* compiling CommonHelp.cpp
g++ -c -o ../../../obj//CommonHelp.o CommonHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//version/
* compiling RecordKeyList.cpp
g++ -c -o ../../../../obj//RecordKeyList.o RecordKeyList.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling RecordKeyVector.cpp
g++ -c -o ../../../../obj//RecordKeyVector.o RecordKeyVector.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling ContextMap.cpp
g++ -c -o ../../../obj//ContextMap.o ContextMap.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
* compiling ContextSample.cpp
g++ -c -o ../../../obj//ContextSample.o ContextSample.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
* compiling RecordList.cpp
g++ -c -o ../../../../obj//RecordList.o RecordList.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
* compiling RecordKeyVector.cpp
g++ -c -o ../../../../obj//RecordKeyVector.o RecordKeyVector.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/
- Building in src/utils/gzstream
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ../../../obj//gzstream.o gzstream.C -I.
* compiling ContextSpacing.cpp
g++ -c -o ../../../obj//ContextSpacing.o ContextSpacing.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
* compiling ContextMerge.cpp
g++ -c -o ../../../obj//ContextMerge.o ContextMerge.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
* compiling ContextJaccard.cpp
g++ -c -o ../../../obj//ContextJaccard.o ContextJaccard.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
- Building in src/utils/fileType
* compiling fileType.cpp
g++ -c -o ../../../obj//fileType.o fileType.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//BamTools/include/ -I../../utils//general
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
g++ -c -o ../../../obj//bedFilePE.o bedFilePE.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//bedFile/ -I../../utils//gzstream/ -I../../utils//fileType/
* compiling FileRecordTypeChecker.cpp
g++ -c -o ../../../obj//FileRecordTypeChecker.o FileRecordTypeChecker.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//BamTools/include/ -I../../utils//general
- Building in src/utils/KeyListOps
* compiling KeyListOps.cpp
g++ -c -o ../../../obj//KeyListOps.o KeyListOps.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//GenomeFile/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
* compiling ContextClosest.cpp
g++ -c -o ../../../obj//ContextClosest.o ContextClosest.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
FileRecordTypeChecker.cpp: In member function 'bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)':
FileRecordTypeChecker.cpp:365:19: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
for (int j=0; j < len; j++) {
~~^~~~~
In file included from /usr/include/c++/8/vector:69,
from bedFilePE.h:4,
from bedFilePE.cpp:15:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
* compiling ContextSubtract.cpp
g++ -c -o ../../../obj//ContextSubtract.o ContextSubtract.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
In file included from /usr/include/c++/8/vector:64,
from bedFilePE.h:4,
from bedFilePE.cpp:15:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BedFilePE::loadBedPEFileIntoMap()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BedFilePE::FindOverlapsPerBin(int, std::__cxx11::string, CHRPOS, CHRPOS, std::__cxx11::string, std::__cxx11::string, std::vector<MATE>&, float, bool, bool)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
* compiling ContextCoverage.cpp
g++ -c -o ../../../obj//ContextCoverage.o ContextCoverage.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
* compiling ContextComplement.cpp
g++ -c -o ../../../obj//ContextComplement.o ContextComplement.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
- Building in src/utils/NewChromsweep
* compiling NewChromsweep.cpp
g++ -c -o ../../../obj//NewChromsweep.o NewChromsweep.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//Contexts/ -I../../utils//GenomeFile/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
* compiling KeyListOpsMethods.cpp
g++ -c -o ../../../obj//KeyListOpsMethods.o KeyListOpsMethods.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//GenomeFile/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
* compiling ContextGroupBy.cpp
g++ -c -o ../../../obj//ContextGroupBy.o ContextGroupBy.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
g++ -c -o ../../../obj//sequenceUtils.o sequenceUtils.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2
- Building in src/utils/tabFile
* compiling tabFile.cpp
g++ -c -o ../../../obj//tabFile.o tabFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//gzstream/ -I../../utils//fileType/
In file included from /usr/include/c++/8/algorithm:62,
from ../../utils//fileType/FileRecordTypeChecker.h:18,
from ../../utils//FileRecordTools/Records/Record.h:14,
from ../../utils//FileRecordTools/Records/RecordKeyVector.h:12,
from KeyListOpsMethods.h:15,
from KeyListOpsMethods.cpp:8:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
* compiling CloseSweep.cpp
g++ -c -o ../../../obj//CloseSweep.o CloseSweep.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//Contexts/ -I../../utils//GenomeFile/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from ../../utils//fileType/FileRecordTypeChecker.h:18,
from ../../utils//FileRecordTools/Records/Record.h:14,
from ../../utils//FileRecordTools/Records/RecordKeyVector.h:12,
from KeyListOpsMethods.h:15,
from KeyListOpsMethods.cpp:8:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../../utils//fileType/FileRecordTypeChecker.h:18,
from ../../utils//FileRecordTools/Records/Record.h:14,
from ../../utils//FileRecordTools/Records/RecordKeyVector.h:12,
from KeyListOpsMethods.h:15,
from KeyListOpsMethods.cpp:8:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from ../../utils//fileType/FileRecordTypeChecker.h:18,
from ../../utils//FileRecordTools/Records/Record.h:14,
from ../../utils//FileRecordTools/Records/RecordKeyVector.h:12,
from KeyListOpsMethods.h:15,
from KeyListOpsMethods.cpp:8:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
- Building in src/utils/BamTools
In file included from /usr/include/c++/8/algorithm:62,
from ../../utils//fileType/FileRecordTypeChecker.h:18,
from ../../utils//FileRecordTools/Records/Record.h:14,
from ../../utils//FileRecordTools/Records/RecordKeyVector.h:12,
from KeyListOpsMethods.h:15,
from KeyListOpsMethods.cpp:8:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* compiling BamAlignment.cpp
g++ -c src/api/BamAlignment.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/BamAlignment.o
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
g++ -c -o ../../../obj//BamAncillary.o BamAncillary.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I..//BamTools/include -I..//bedFile/ -I..//lineFileUtilities/ -I..//gzstream/ -I..//fileType/ -Lsrc/utils/BamTools//lib
/usr/include/c++/8/bits/stl_algo.h: In member function 'void KeyListOpsMethods::sortArray(bool, bool)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
- Building in src/utils/BlockedIntervals
* compiling BlockedIntervals.cpp
g++ -c -o ../../../obj//BlockedIntervals.o BlockedIntervals.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I..//BamTools/include -I..//bedFile/ -I..//gzstream/ -I..//fileType/ -I..//lineFileUtilities/ -Lsrc/utils/BamTools//lib
In file included from /usr/include/c++/8/vector:69,
from ..//lineFileUtilities/lineFileUtilities.h:4,
from ..//bedFile/bedFile.h:17,
from BamAncillary.h:12,
from BamAncillary.cpp:12:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
* compiling BamMultiReader.cpp
g++ -c src/api/BamMultiReader.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/BamMultiReader.o
* compiling BamAncillary.cpp
g++ -c -o ../../../obj//BamAncillary.h BamAncillary.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I..//BamTools/include -I..//bedFile/ -I..//lineFileUtilities/ -I..//gzstream/ -I..//fileType/ -Lsrc/utils/BamTools//lib
* compiling BamReader.cpp
g++ -c src/api/BamReader.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/BamReader.o
In file included from /usr/include/c++/8/vector:69,
from BlockedIntervals.h:12,
from BlockedIntervals.cpp:12:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
* compiling BamWriter.cpp
g++ -c src/api/BamWriter.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/BamWriter.o
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
* compiling SamHeader.cpp
g++ -c src/api/SamHeader.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/SamHeader.o
In file included from /usr/include/c++/8/vector:64,
from BlockedIntervals.h:12,
from BlockedIntervals.cpp:12:
/usr/include/c++/8/bits/stl_vector.h: In function 'void GetBedBlocks(const BED&, bedVector&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ..//lineFileUtilities/lineFileUtilities.h:4,
from ..//bedFile/bedFile.h:17,
from BamAncillary.h:12,
from BamAncillary.cpp:12:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
- Building in src/utils/Fasta
* compiling Fasta.cpp
g++ -c -o ../../../obj//Fasta.o Fasta.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2
* compiling SamProgram.cpp
g++ -c src/api/SamProgram.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/SamProgram.o
Fasta.cpp: In member function 'std::__cxx11::string FastaReference::getSequence(std::__cxx11::string)':
Fasta.cpp:290:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(seq, sizeof(char), seqlen, file);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Fasta.cpp: In member function 'std::__cxx11::string FastaReference::getSubSequence(std::__cxx11::string, int, int)':
Fasta.cpp:332:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(seq, sizeof(char), (off_t) seqlen, file);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- Building in src/utils/VectorOps
* compiling VectorOps.cpp
g++ -c -o ../../../obj//VectorOps.o VectorOps.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2
* compiling SamProgramChain.cpp
g++ -c src/api/SamProgramChain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/SamProgramChain.o
In file included from /usr/include/c++/8/map:60,
from Fasta.h:12,
from Fasta.cpp:9:
/usr/include/c++/8/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++/8/bits/stl_tree.h:2411:7: 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
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from Fasta.h:12,
from Fasta.cpp:9:
/usr/include/c++/8/bits/stl_map.h: In member function 'std::__cxx11::string FastaReference::sequenceNameStartingWith(std::__cxx11::string)':
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:69,
from Fasta.h:15,
from Fasta.cpp:9:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
* compiling SamReadGroup.cpp
g++ -c src/api/SamReadGroup.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/SamReadGroup.o
* compiling split.cpp
g++ -c -o ../../../obj//split.o split.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2
In file included from /usr/include/c++/8/algorithm:62,
from Fasta.h:18,
from Fasta.cpp:9:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from Fasta.h:18,
from Fasta.cpp:9:
/usr/include/c++/8/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++/8/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
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
* compiling SamReadGroupDictionary.cpp
g++ -c src/api/SamReadGroupDictionary.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/SamReadGroupDictionary.o
In file included from /usr/include/c++/8/algorithm:62,
from Fasta.h:18,
from Fasta.cpp:9:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from Fasta.h:12,
from Fasta.cpp:9:
/usr/include/c++/8/bits/stl_map.h: In function 'std::ostream& operator<<(std::ostream&, FastaIndex&)':
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:64,
from Fasta.h:15,
from Fasta.cpp:9:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from Fasta.h:18,
from Fasta.cpp:9:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from VectorOps.h:21,
from VectorOps.cpp:15:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1840:5: 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++/8/vector:69,
from VectorOps.h:15,
from VectorOps.cpp:15:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: 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++/8/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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
* compiling SamSequence.cpp
g++ -c src/api/SamSequence.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/SamSequence.o
* compiling SamSequenceDictionary.cpp
g++ -c src/api/SamSequenceDictionary.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/SamSequenceDictionary.o
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from VectorOps.h:21,
from VectorOps.cpp:15:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from VectorOps.h:21,
from VectorOps.cpp:15:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'double VectorOps::GetMedian()':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling BamHeader_p.cpp
g++ -c src/api/internal/bam/BamHeader_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/bam/BamHeader_p.o
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from VectorOps.h:21,
from VectorOps.cpp:15:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from VectorOps.h:21,
from VectorOps.cpp:15:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from VectorOps.h:21,
from VectorOps.cpp:15:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from VectorOps.h:21,
from VectorOps.cpp:15:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* compiling BamMultiReader_p.cpp
g++ -c src/api/internal/bam/BamMultiReader_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/bam/BamMultiReader_p.o
/usr/include/c++/8/bits/stl_algo.h: In member function 'std::__cxx11::string VectorOps::GetDistinctSortNum(bool)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling BamRandomAccessController_p.cpp
g++ -c src/api/internal/bam/BamRandomAccessController_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/bam/BamRandomAccessController_p.o
* compiling BamReader_p.cpp
g++ -c src/api/internal/bam/BamReader_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/bam/BamReader_p.o
- Building in src/utils/GenomeFile
* compiling GenomeFile.cpp
g++ -c -o ../../../obj//GenomeFile.o GenomeFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I..//general/ -I..//lineFileUtilities/ -I..//KeyListOps/ -I..//BamTools/include/
GenomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
GenomeFile.cpp:60:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
long c2;
^~
- Building in src/utils/RecordOutputMgr
* compiling RecordOutputMgr.cpp
g++ -c -o ../../../obj//RecordOutputMgr.o RecordOutputMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//Contexts/ -I../../utils//GenomeFile/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
- Building in src/utils/ToolBase
* compiling ToolBase.cpp
g++ -c -o ../../../obj//ToolBase.o ToolBase.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//Contexts/ -I../../utils//GenomeFile/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//RecordOutputMgr/ -I../../utils//KeyListOps/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/
* compiling NewGenomeFile.cpp
g++ -c -o ../../../obj//NewGenomeFile.o NewGenomeFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I..//general/ -I..//lineFileUtilities/ -I..//KeyListOps/ -I..//BamTools/include/
* compiling BamWriter_p.cpp
g++ -c src/api/internal/bam/BamWriter_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/bam/BamWriter_p.o
* compiling BamIndexFactory_p.cpp
g++ -c src/api/internal/index/BamIndexFactory_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/index/BamIndexFactory_p.o
* compiling BamStandardIndex_p.cpp
g++ -c src/api/internal/index/BamStandardIndex_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/index/BamStandardIndex_p.o
- Building in src/utils/driver
* compiling BedtoolsDriver.cpp
g++ -c -o ../../../obj//BedtoolsDriver.o BedtoolsDriver.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//bedFile/ -I../../utils//lineFileUtilities/ -I../../utils//Contexts/ -I../../utils//general/ -I../../utils//fileType/ -I../../utils//gzstream/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src -I../../utils//BlockedIntervals -I../../utils//BamTools-Ancillary -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//RecordOutputMgr/ -I../../utils//NewChromsweep -I../../utils//BinTree -I../../utils//ToolBase -I../../utils//version/ -I../../../src//annotateBed/ -I../../../src//bamToBed/ -I../../../src//bamToFastq/ -I../../../src//bedToBam/ -I../../../src//bedpeToBam/ -I../../../src//bedToIgv/ -I../../../src//bed12ToBed6/ -I../../../src//closestFile/ -I../../../src//clusterBed/ -I../../../src//complementFile/ -I../../../src//coverageFile/ -I../../../src//expand/ -I../../../src//fastaFromBed/ -I../../../src//flankBed/ -I../../../src//genomeCoverageBed/ -I../../../src//getOverlap/ -I../../../src//groupBy/ -I../../../src//intersectFile/ -I../../../src//fisher/ -I../../../src//jaccard/ -I../../../src//linksBed/ -I../../../src//maskFastaFromBed/ -I../../../src//mapFile/ -I../../../src//mergeFile/ -I../../../src//multiBamCov/ -I../../../src//multiIntersectBed/ -I../../../src//nekSandbox1/ -I../../../src//nucBed/ -I../../../src//pairToBed/ -I../../../src//pairToPair/ -I../../../src//randomBed/ -I../../../src//regressTest/ -I../../../src//reldist/ -I../../../src//sampleFile/ -I../../../src//shiftBed/ -I../../../src//shuffleBed/ -I../../../src//slopBed/ -I../../../src//sortBed/ -I../../../src//spacingFile/ -I../../../src//split/ -I../../../src//subtractFile/ -I../../../src//tagBam/ -I../../../src//unionBedGraphs/ -I../../../src//windowBed/ -I../../../src//windowMaker/
- Building in src/annotateBed
* compiling annotateMain.cpp
g++ -c -o ../../obj//annotateMain.o annotateMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//BamTools/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/
* compiling BamToolsIndex_p.cpp
g++ -c src/api/internal/index/BamToolsIndex_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/index/BamToolsIndex_p.o
In file included from /usr/include/c++/8/vector:69,
from src/api/BamAux.h:18,
from src/api/BamAlignment.h:14,
from src/api/internal/index/BamStandardIndex_p.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BaiAlignmentChunk&}; _Tp = BamTools::Internal::BaiAlignmentChunk; _Alloc = std::allocator<BamTools::Internal::BaiAlignmentChunk>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<BamTools::Internal::BaiAlignmentChunk>::iterator' {aka '__gnu_cxx::__normal_iterator<BamTools::Internal::BaiAlignmentChunk*, std::vector<BamTools::Internal::BaiAlignmentChunk> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from src/api/BamAux.h:18,
from src/api/BamAlignment.h:14,
from src/api/internal/index/BamStandardIndex_p.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BamTools::Internal::BamStandardIndex::MergeAlignmentChunks(BamTools::Internal::BaiAlignmentChunkVector&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BaiAlignmentChunk*, std::vector<BamTools::Internal::BaiAlignmentChunk> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BaiAlignmentChunk*, std::vector<BamTools::Internal::BaiAlignmentChunk> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
bool haveTitles = false;
^~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BamTools::Internal::BamStandardIndex::SaveAlignmentChunkToBin(BamTools::Internal::BaiBinMap&, const uint32_t&, const uint64_t&, const uint64_t&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BaiAlignmentChunk*, std::vector<BamTools::Internal::BaiAlignmentChunk> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BaiAlignmentChunk*, std::vector<BamTools::Internal::BaiAlignmentChunk> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from src/api/BamAux.h:18,
from src/api/BamAlignment.h:14,
from src/api/internal/index/BamStandardIndex_p.cpp:10:
/usr/include/c++/8/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 unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from src/api/BamAux.h:18,
from src/api/BamAlignment.h:14,
from src/api/internal/index/BamStandardIndex_p.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BamTools::Internal::BamStandardIndex::SaveLinearOffsetEntry(BamTools::Internal::BaiLinearOffsetVector&, const int&, const int&, const uint64_t&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from src/api/BamAux.h:18,
from src/api/BamAlignment.h:14,
from src/api/internal/index/BamStandardIndex_p.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from src/api/BamAux.h:18,
from src/api/BamAlignment.h:14,
from src/api/internal/index/BamToolsIndex_p.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BtiBlock&}; _Tp = BamTools::Internal::BtiBlock; _Alloc = std::allocator<BamTools::Internal::BtiBlock>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<BamTools::Internal::BtiBlock>::iterator' {aka '__gnu_cxx::__normal_iterator<BamTools::Internal::BtiBlock*, std::vector<BamTools::Internal::BtiBlock> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BamTools::Internal::BtiReferenceSummary}; _Tp = BamTools::Internal::BtiReferenceSummary; _Alloc = std::allocator<BamTools::Internal::BtiReferenceSummary>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<BamTools::Internal::BtiReferenceSummary>::iterator' {aka '__gnu_cxx::__normal_iterator<BamTools::Internal::BtiReferenceSummary*, std::vector<BamTools::Internal::BtiReferenceSummary> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'void BamTools::Internal::BamToolsIndex::InitializeFileSummary(const int&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BtiReferenceSummary*, std::vector<BamTools::Internal::BtiReferenceSummary> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void BamTools::Internal::BamStandardIndex::CalculateCandidateOffsets(const BamTools::Internal::BaiReferenceSummary&, const uint64_t&, std::set<short unsigned int>&, std::vector<long long int>&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from src/api/internal/index/BamStandardIndex_p.cpp:21:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: 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++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from src/api/internal/index/BamStandardIndex_p.cpp:21:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from src/api/internal/index/BamStandardIndex_p.cpp:21:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: 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++/8/bits/stl_algo.h:1940:5: 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++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from src/api/BamAux.h:18,
from src/api/BamAlignment.h:14,
from src/api/internal/index/BamToolsIndex_p.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BamTools::Internal::BamToolsIndex::ReadBlocks(const BamTools::Internal::BtiReferenceSummary&, BamTools::Internal::BtiBlockVector&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BtiBlock*, std::vector<BamTools::Internal::BtiBlock> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'void BamTools::Internal::BamStandardIndex::GetOffset(const BamTools::BamRegion&, int64_t&, bool*)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling annotateBed.cpp
g++ -c -o ../../obj//annotateBed.o annotateBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//BamTools/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from src/api/internal/index/BamStandardIndex_p.cpp:21:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
* compiling BamDeviceFactory_p.cpp
g++ -c src/api/internal/io/BamDeviceFactory_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/BamDeviceFactory_p.o
In file included from /usr/include/c++/8/algorithm:62,
from src/api/internal/index/BamStandardIndex_p.cpp:21:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'void BamTools::Internal::BamStandardIndex::SortLinearOffsets(BamTools::Internal::BaiLinearOffsetVector&)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual bool BamTools::Internal::BamToolsIndex::Create()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BtiBlock*, std::vector<BamTools::Internal::BtiBlock> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BtiBlock*, std::vector<BamTools::Internal::BtiBlock> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BtiBlock*, std::vector<BamTools::Internal::BtiBlock> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
* compiling BamFile_p.cpp
g++ -c src/api/internal/io/BamFile_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/BamFile_p.o
- Building in src/bamToBed
* compiling bamToBed.cpp
g++ -c -o ../../obj//bamToBed.o bamToBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BlockedIntervals -I../utils//version/
- Building in src/bamToFastq
* compiling bamToFastqMain.cpp
g++ -c -o ../../obj//bamToFastqMain.o bamToFastqMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//BamTools/include -I../utils//sequenceUtilities/ -I../utils//version/
* compiling BamFtp_p.cpp
g++ -c src/api/internal/io/BamFtp_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/BamFtp_p.o
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:88:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
bool useAlignmentScore = false;
^~~~~~~~~~~~~~~~~
bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
bool haveFastq2 = false;
^~~~~~~~~~
- Building in src/bedToBam
* compiling bedToBam.cpp
g++ -c -o ../../obj//bedToBam.o bedToBam.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//version/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/
* compiling bamToFastq.cpp
g++ -c -o ../../obj//bamToFastq.o bamToFastq.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//BamTools/include -I../utils//sequenceUtilities/ -I../utils//version/
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
bool haveMapQual = false;
^~~~~~~~~~~
* compiling BamHttp_p.cpp
g++ -c src/api/internal/io/BamHttp_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/BamHttp_p.o
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
g++ -c -o ../../obj//bedpeToBam.o bedpeToBam.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//version/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/
* compiling BamPipe_p.cpp
g++ -c src/api/internal/io/BamPipe_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/BamPipe_p.o
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
bool haveMapQual = false;
^~~~~~~~~~~
- Building in src/bedToIgv
* compiling bedToIgv.cpp
g++ -c -o ../../obj//bedToIgv.o bedToIgv.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
g++ -c -o ../../obj//bed12ToBed6.o bed12ToBed6.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BlockedIntervals -I../utils//version/
* compiling BgzfStream_p.cpp
g++ -c src/api/internal/io/BgzfStream_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/BgzfStream_p.o
- Building in src/closestFile
* compiling closestHelp.cpp
g++ -c -o ../../obj//closestHelp.o closestHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/
* compiling ByteArray_p.cpp
g++ -c src/api/internal/io/ByteArray_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/ByteArray_p.o
* compiling closestFile.cpp
g++ -c -o ../../obj//closestFile.o closestFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/
- Building in src/clusterBed
* compiling clusterMain.cpp
g++ -c -o ../../obj//clusterMain.o clusterMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/
* compiling HostAddress_p.cpp
g++ -c src/api/internal/io/HostAddress_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/HostAddress_p.o
* compiling HostInfo_p.cpp
g++ -c src/api/internal/io/HostInfo_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/HostInfo_p.o
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
bool haveMaxDistance = false;
^~~~~~~~~~~~~~~
src/api/internal/io/HostAddress_p.cpp: In member function 'void BamTools::Internal::HostAddress::Clear()':
src/api/internal/io/HostAddress_p.cpp:283:49: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct BamTools::Internal::IPv6Address'; use assignment or value-initialization instead [-Wclass-memaccess]
memset(&m_ip6Address, 0, sizeof(IPv6Address));
^
In file included from src/api/internal/io/HostAddress_p.cpp:10:
src/api/internal/io/HostAddress_p.h:30:8: note: 'struct BamTools::Internal::IPv6Address' declared here
struct IPv6Address {
^~~~~~~~~~~
src/api/internal/io/HostAddress_p.cpp: In member function 'std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const':
src/api/internal/io/HostAddress_p.cpp:325:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ( i != 0 )
^~
src/api/internal/io/HostAddress_p.cpp:327:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) |
^~
* compiling HttpHeader_p.cpp
g++ -c src/api/internal/io/HttpHeader_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/HttpHeader_p.o
* compiling clusterBed.cpp
g++ -c -o ../../obj//clusterBed.o clusterBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/
- Building in src/complementFile
* compiling complementHelp.cpp
g++ -c -o ../../obj//complementHelp.o complementHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/
* compiling complementFile.cpp
g++ -c -o ../../obj//complementFile.o complementFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/
* compiling ILocalIODevice_p.cpp
g++ -c src/api/internal/io/ILocalIODevice_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/ILocalIODevice_p.o
- Building in src/coverageFile
* compiling coverageHelp.cpp
g++ -c -o ../../obj//coverageHelp.o coverageHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/
* compiling RollingBuffer_p.cpp
g++ -c src/api/internal/io/RollingBuffer_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/RollingBuffer_p.o
* compiling coverageFile.cpp
g++ -c -o ../../obj//coverageFile.o coverageFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/
- Building in src/expand
* compiling expand.cpp
g++ -c -o ../../obj//expand.o expand.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//tabFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//VectorOps/ -I../utils//version/
* compiling TcpSocketEngine_p.cpp
g++ -c src/api/internal/io/TcpSocketEngine_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/TcpSocketEngine_p.o
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
g++ -c -o ../../obj//fastaFromBedMain.o fastaFromBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//BamTools/include -I../utils//sequenceUtilities/ -I../utils//BlockedIntervals -I../utils//fileType/ -I../utils//Fasta/ -I../utils//version/
* compiling TcpSocketEngine_unix_p.cpp
g++ -c src/api/internal/io/TcpSocketEngine_unix_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/TcpSocketEngine_unix_p.o
coverageFile.cpp: In member function 'virtual void CoverageFile::giveFinalReport(RecordOutputMgr*)':
coverageFile.cpp:100:11: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
asprintf(&depthPctString, "%0.7f", depthPct);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
coverageFile.cpp: In member function 'void CoverageFile::doMean(RecordOutputMgr*, RecordKeyVector&)':
coverageFile.cpp:181:10: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
asprintf(&meanString, "%0.7f", mean);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
coverageFile.cpp: In member function 'void CoverageFile::doHist(RecordOutputMgr*, RecordKeyVector&)':
coverageFile.cpp:210:11: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
asprintf(&coveredFractionString, "%0.7f", coveredFraction);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
coverageFile.cpp: In member function 'void CoverageFile::doDefault(RecordOutputMgr*, RecordKeyVector&)':
coverageFile.cpp:230:10: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
asprintf(&coveredFractionString, "%0.7f", coveredFraction);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* compiling TcpSocket_p.cpp
g++ -c src/api/internal/io/TcpSocket_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/TcpSocket_p.o
* compiling fastaFromBed.cpp
g++ -c -o ../../obj//fastaFromBed.o fastaFromBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//BamTools/include -I../utils//sequenceUtilities/ -I../utils//BlockedIntervals -I../utils//fileType/ -I../utils//Fasta/ -I../utils//version/
* compiling SamFormatParser_p.cpp
g++ -c src/api/internal/sam/SamFormatParser_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/sam/SamFormatParser_p.o
- Building in src/flankBed
* compiling flankBedMain.cpp
g++ -c -o ../../obj//flankBedMain.o flankBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
g++ -c -o ../../obj//genomeCoverageMain.o genomeCoverageMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BlockedIntervals -I../utils//version/
* compiling SamFormatPrinter_p.cpp
g++ -c src/api/internal/sam/SamFormatPrinter_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/sam/SamFormatPrinter_p.o
* compiling SamHeaderValidator_p.cpp
g++ -c src/api/internal/sam/SamHeaderValidator_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/sam/SamHeaderValidator_p.o
* compiling flankBed.cpp
g++ -c -o ../../obj//flankBed.o flankBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/
* compiling genomeCoverageBed.cpp
g++ -c -o ../../obj//genomeCoverageBed.o genomeCoverageBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BlockedIntervals -I../utils//version/
- Building in src/getOverlap
* compiling getOverlap.cpp
g++ -c -o ../../obj//getOverlap.o getOverlap.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/
* compiling BamException_p.cpp
g++ -c src/api/internal/utils/BamException_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/utils/BamException_p.o
genomeCoverageBed.cpp: In member function 'void BedGenomeCoverage::CoverageBam(std::__cxx11::string)':
genomeCoverageBed.cpp:322:23: warning: comparison of integer expressions of different signedness: 'CHRPOS' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if(end<_fragmentSize) { //sometimes fragmentSize is bigger :(
~~~^~~~~~~~~~~~~~
- Building in src/groupBy
* compiling groupBy.cpp
g++ -c -o ../../obj//groupBy.o groupBy.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//stringUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/
* linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
bool haveColumns = false;
^~~~~~~~~~~
ranlib lib/libbamtools.a
- Building in src/intersectFile
* compiling intersectHelp.cpp
g++ -c -o ../../obj//intersectHelp.o intersectHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//ToolBase -I../utils//version/
* compiling intersectFile.cpp
g++ -c -o ../../obj//intersectFile.o intersectFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//ToolBase -I../utils//version/
- Building in src/fisher
* compiling fisherHelp.cpp
g++ -c -o ../../obj//fisherHelp.o fisherHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//gzstream/ -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I . -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ -I../../src//jaccard/
* compiling groupByHelp.cpp
g++ -c -o ../../obj//groupByHelp.o groupByHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//stringUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/
intersectFile.cpp: In member function 'virtual void IntersectFile::processHits(RecordOutputMgr*, RecordKeyVector&)':
intersectFile.cpp:70:33: warning: variable 'hitListIter' set but not used [-Wunused-but-set-variable]
RecordKeyVector::iterator_type hitListIter = hits.begin();
^~~~~~~~~~~
* compiling fisher.cpp
g++ -c -o ../../obj//fisher.o fisher.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//gzstream/ -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I . -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ -I../../src//jaccard/
- Building in src/jaccard
* compiling jaccardHelp.cpp
g++ -c -o ../../obj//jaccardHelp.o jaccardHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/
* compiling jaccard.cpp
g++ -c -o ../../obj//jaccard.o jaccard.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/
- Building in src/linksBed
* compiling linksMain.cpp
g++ -c -o ../../obj//linksMain.o linksMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/
* compiling kfunc.cpp
g++ -c -o ../../obj//kfunc.o kfunc.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//gzstream/ -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I . -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ -I../../src//jaccard/
* compiling linksBed.cpp
g++ -c -o ../../obj//linksBed.o linksBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
g++ -c -o ../../obj//maskFastaFromBedMain.o maskFastaFromBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//sequenceUtilities/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//Fasta/ -I../utils//version/
- Building in src/mapFile
* compiling mapHelp.cpp
g++ -c -o ../../obj//mapHelp.o mapHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/
- Building in src/mergeFile
* compiling mergeHelp.cpp
g++ -c -o ../../obj//mergeHelp.o mergeHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/
* compiling mapFile.cpp
g++ -c -o ../../obj//mapFile.o mapFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/
* compiling maskFastaFromBed.cpp
g++ -c -o ../../obj//maskFastaFromBed.o maskFastaFromBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//sequenceUtilities/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//Fasta/ -I../utils//version/
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
g++ -c -o ../../obj//multiBamCovMain.o multiBamCovMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BlockedIntervals -I../utils//version/
* compiling mergeFile.cpp
g++ -c -o ../../obj//mergeFile.o mergeFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/
* compiling multiBamCov.cpp
g++ -c -o ../../obj//multiBamCov.o multiBamCov.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BlockedIntervals -I../utils//version/
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
bool haveBed = false;
^~~~~~~
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
bool haveBams = false;
^~~~~~~~
multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
bool haveFraction = false;
^~~~~~~~~~~~
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
g++ -c -o ../../obj//multiIntersectBedMain.o multiIntersectBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//GenomeFile/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//Point/ -I../utils//BamTools/include -I../utils//version/
- Building in src/nucBed
* compiling nucBedMain.cpp
g++ -c -o ../../obj//nucBedMain.o nucBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//sequenceUtilities/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//Fasta/ -I../utils//version/
* compiling multiIntersectBed.cpp
g++ -c -o ../../obj//multiIntersectBed.o multiIntersectBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//GenomeFile/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//Point/ -I../utils//BamTools/include -I../utils//version/
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
bool haveFiles = false;
^~~~~~~~~
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
bool haveGenome = false;
^~~~~~~~~~
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
bool haveFiller = true;
^~~~~~~~~~
- Building in src/pairToBed
* compiling pairToBedMain.cpp
g++ -c -o ../../obj//pairToBedMain.o pairToBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFilePE/ -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/
- Building in src/pairToPair
* compiling pairToPairMain.cpp
g++ -c -o ../../obj//pairToPairMain.o pairToPairMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFilePE/ -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//version/ -I../utils//fileType/ -I../utils//version/
* compiling nucBed.cpp
g++ -c -o ../../obj//nucBed.o nucBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//sequenceUtilities/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//Fasta/ -I../utils//version/
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
bool haveFraction = false;
^~~~~~~~~~~~
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
bool haveFraction = false;
^~~~~~~~~~~~
* compiling pairToPair.cpp
g++ -c -o ../../obj//pairToPair.o pairToPair.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFilePE/ -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//version/ -I../utils//fileType/ -I../utils//version/
- Building in src/randomBed
* compiling randomBedMain.cpp
g++ -c -o ../../obj//randomBedMain.o randomBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//version/
* compiling pairToBed.cpp
g++ -c -o ../../obj//pairToBed.o pairToBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFilePE/ -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/
- Building in src/regressTest
compiling RegressTest.cpp
g++ -c -o ../../obj//RegressTest.o RegressTest.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//general/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//version/ -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders -I../utils//FileRecordTools/Records -I../utils//KeyListOps/ -I../utils//general
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
bool found1 = false;
^~~~~~
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
bool found2 = false;
^~~~~~
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
CHRPOS spanLength = 0;
^~~~~~~~~~
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
int spanLength = 0;
^~~~~~~~~~
* compiling randomBed.cpp
g++ -c -o ../../obj//randomBed.o randomBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//version/
RegressTest.cpp: In member function 'bool RegressTest::executeAndCompareCorrectness(const fileListType&)':
RegressTest.cpp:431:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(diffCmd.c_str());
~~~~~~^~~~~~~~~~~~~~~~~
RegressTest.cpp: In member function 'bool RegressTest::startMemoryProfile(bool)':
RegressTest.cpp:573:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(sLine, 4192, fp);
~~~~~^~~~~~~~~~~~~~~~~
RegressTest.cpp: In member function 'bool RegressTest::calcMemoryStats()':
RegressTest.cpp:622:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(sLine, 4192, fp);
~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from pairToPair.cpp:12:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from pairToPair.cpp:12:
/usr/include/c++/8/bits/stl_vector.h: In member function 'bool PairToPair::FindHitsOnBothEnds(const BEDPE&, const std::vector<MATE>&, const std::vector<MATE>&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
- Building in src/reldist
* compiling reldistMain.cpp
g++ -c -o ../../obj//reldistMain.o reldistMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//chromsweep -I../utils//version/
/usr/include/c++/8/bits/stl_vector.h: In member function 'void PairToPair::FindHitsOnEitherEnd(const BEDPE&, const std::vector<MATE>&, const std::vector<MATE>&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MATE*, std::vector<MATE> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from pairToBed.cpp:12:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from pairToBed.cpp:12:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BedIntersectPE::FindOverlaps(const BEDPE&, std::vector<BED>&, std::vector<BED>&, const string&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
* compiling reldist.cpp
g++ -c -o ../../obj//reldist.o reldist.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//chromsweep -I../utils//version/
- Building in src/sampleFile
* compiling sampleHelp.cpp
g++ -c -o ../../obj//sampleHelp.o sampleHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//version/ -I../utils//ToolBase/
compiling regressTestMain.cpp
g++ -c -o ../../obj//regressTestMain.o regressTestMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//general/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//version/ -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders -I../utils//FileRecordTools/Records -I../utils//KeyListOps/ -I../utils//general
reldist.cpp: In member function 'void RelativeDistance::ReportDistanceSummary()':
reldist.cpp:69:16: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'unsigned int' [-Wformat=]
printf("%.2f\t%lu\t%lu\t%.3f\n",
^~~~~~~~~~~~~~~~~~~~~~~~
reldist.cpp:71:16:
freqItr->second,
~~~~~~~~~~~~~~~
reldist.cpp:69:16: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
* compiling sampleFile.cpp
g++ -c -o ../../obj//sampleFile.o sampleFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//version/ -I../utils//ToolBase/
- Building in src/shiftBed
* compiling shiftBedMain.cpp
g++ -c -o ../../obj//shiftBedMain.o shiftBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/
* compiling shiftBed.cpp
g++ -c -o ../../obj//shiftBed.o shiftBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
g++ -c -o ../../obj//shuffleBedMain.o shuffleBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/
- Building in src/slopBed
* compiling slopBedMain.cpp
g++ -c -o ../../obj//slopBedMain.o slopBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/
* compiling slopBed.cpp
g++ -c -o ../../obj//slopBed.o slopBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/
- Building in src/sortBed
* compiling sortMain.cpp
g++ -c -o ../../obj//sortMain.o sortMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/
slopBed.cpp: In member function 'void BedSlop::AddSlop(BED&)':
slopBed.cpp:81:53: warning: comparison of integer expressions of different signedness: 'long int' and 'CHRPOS' {aka 'unsigned int'} [-Wsign-compare]
if (((int)bed.start - (long)_rightSlop) >= chromSize && _rightSlop < 0) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
slopBed.cpp:91:47: warning: comparison of integer expressions of different signedness: 'long int' and 'CHRPOS' {aka 'unsigned int'} [-Wsign-compare]
if ( ((int)bed.end + (long)_leftSlop) <= chromSize ) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
slopBed.cpp:108:52: warning: comparison of integer expressions of different signedness: 'long int' and 'CHRPOS' {aka 'unsigned int'} [-Wsign-compare]
if( ((int)bed.start - (long)_leftSlop) >= chromSize && _leftSlop < 0)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
slopBed.cpp:120:48: warning: comparison of integer expressions of different signedness: 'long int' and 'CHRPOS' {aka 'unsigned int'} [-Wsign-compare]
if ( ((int)bed.end + (long)_rightSlop) <= chromSize )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
* compiling sortBed.cpp
g++ -c -o ../../obj//sortBed.o sortBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/
* compiling shuffleBed.cpp
g++ -c -o ../../obj//shuffleBed.o shuffleBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/
- Building in src/spacingFile
* compiling spacingHelp.cpp
g++ -c -o ../../obj//spacingHelp.o spacingHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//version/ -I../utils//ToolBase/
* compiling spacingFile.cpp
g++ -c -o ../../obj//spacingFile.o spacingFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//version/ -I../utils//ToolBase/
- Building in src/split
* compiling splitBed.cpp
g++ -c -o ../../obj//splitBed.o splitBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/
- Building in src/subtractFile
* compiling subtractHelp.cpp
g++ -c -o ../../obj//subtractHelp.o subtractHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/
In file included from /usr/include/c++/8/vector:69,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from sortBed.cpp:13:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
* compiling subtractFile.cpp
g++ -c -o ../../obj//subtractFile.o subtractFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/
In file included from /usr/include/c++/8/algorithm:62,
from ../utils//bedFile/bedFile.h:29,
from sortBed.h:12,
from sortBed.cpp:14:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: 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++/8/vector:69,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from splitBed.cpp:16:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
__final_insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from ../utils//bedFile/bedFile.h:29,
from sortBed.h:12,
from sortBed.cpp:14:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from splitBed.cpp:16:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BedSplit::loadBed()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../utils//bedFile/bedFile.h:29,
from splitBed.h:10,
from splitBed.cpp:18:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/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
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/8/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
- Building in src/tagBam
* compiling tagBamMain.cpp
g++ -c -o ../../obj//tagBamMain.o tagBamMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/
/usr/include/c++/8/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++/8/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
__pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~
/usr/include/c++/8/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++/8/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++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
* compiling splitBedMain.cpp
g++ -c -o ../../obj//splitBedMain.o splitBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from ../utils//bedFile/bedFile.h:29,
from splitBed.h:10,
from splitBed.cpp:18:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../utils//bedFile/bedFile.h:29,
from sortBed.h:12,
from sortBed.cpp:14:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from ../utils//bedFile/bedFile.h:29,
from sortBed.h:12,
from sortBed.cpp:14:
/usr/include/c++/8/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
std::__pop_heap(__first, __last, __last, __comp);
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../utils//bedFile/bedFile.h:29,
from sortBed.h:12,
from sortBed.cpp:14:
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from sortBed.cpp:13:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BedSort::SortBedBySizeAsc()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../utils//bedFile/bedFile.h:29,
from sortBed.h:12,
from sortBed.cpp:14:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/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
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h: In member function 'void BedSort::SortBedByChromThenSizeAsc()':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'void BedSort::SortBedByChromThenSizeDesc()':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/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
__pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~
/usr/include/c++/8/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++/8/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++/8/bits/stl_algo.h: In member function 'void BedSort::SortBedByChromThenScoreAsc()':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling tagBam.cpp
g++ -c -o ../../obj//tagBam.o tagBam.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/
/usr/include/c++/8/bits/stl_algo.h: In member function 'void BedSort::SortBedByChromThenScoreDesc()':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from sortBed.cpp:13:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BedSort::SortBedBySizeDesc()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../utils//bedFile/bedFile.h:29,
from sortBed.h:12,
from sortBed.cpp:14:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../utils//bedFile/bedFile.h:29,
from splitBed.h:10,
from splitBed.cpp:18:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from ../utils//bedFile/bedFile.h:29,
from splitBed.h:10,
from splitBed.cpp:18:
/usr/include/c++/8/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
std::__pop_heap(__first, __last, __last, __comp);
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../utils//bedFile/bedFile.h:29,
from splitBed.h:10,
from splitBed.cpp:18:
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'int BedSplit::doEuristicSplitOnTotalSize()':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BED*, std::vector<BED> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
- Building in src/unionBedGraphs
* compiling unionBedGraphsMain.cpp
g++ -c -o ../../obj//unionBedGraphsMain.o unionBedGraphsMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedGraphFile/ -I../utils//lineFileUtilities/ -I../utils//GenomeFile/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//Point/ -I../utils//BamTools/include -I../utils//version/
- Building in src/windowBed
* compiling windowMain.cpp
g++ -c -o ../../obj//windowMain.o windowMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
bool haveFiles = false;
^~~~~~~~~
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
bool haveGenome = false;
^~~~~~~~~~
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
bool haveFiller = true;
^~~~~~~~~~
- Building in src/windowMaker
* compiling windowMakerMain.cpp
g++ -c -o ../../obj//windowMakerMain.o windowMakerMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//GenomeFile/ -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//BamTools/include -I../utils//version/
* compiling windowBed.cpp
g++ -c -o ../../obj//windowBed.o windowBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/
* compiling unionBedGraphs.cpp
g++ -c -o ../../obj//unionBedGraphs.o unionBedGraphs.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedGraphFile/ -I../utils//lineFileUtilities/ -I../utils//GenomeFile/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//Point/ -I../utils//BamTools/include -I../utils//version/
* compiling windowMaker.cpp
g++ -c -o ../../obj//windowMaker.o windowMaker.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//GenomeFile/ -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//BamTools/include -I../utils//version/
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.27.1+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.27.1+dfsg'
mv test/shuffle debian/
dh_auto_test
make -j4 test
make[2]: Entering directory '/<<BUILDDIR>>/bedtools-2.27.1+dfsg'
$CXXFLAGS is [-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11]
Building BEDTools:
=========================================================
* Creating BamTools API
DETECTED_VERSION = v2.27.1
CURRENT_VERSION = v2.27.1
- Building in src/utils/FileRecordTools
- Building in src/utils/FileRecordTools/FileReaders
- Building in src/utils/FileRecordTools/Records
- Building in src/utils/bedFile
make[3]: Nothing to be done for 'all'.
make[3]: '../../../obj//bedFile.o' is up to date.
make[3]: Nothing to be done for 'all'.
- Building in FileReaders
- Building in src/utils/BinTree
- Building in src/utils/version
- Building in src/utils/bedGraphFile
make[4]: Nothing to be done for 'all'.
- Building in Records
make[3]: '../../../obj//BinTree.o' is up to date.
make[3]: Nothing to be done for 'all'.
make[3]: '../../../obj//bedGraphFile.o' is up to date.
- Building in src/utils/chromsweep
- Building in src/utils/Contexts
make[4]: Nothing to be done for 'all'.
- Building in src/utils/general
- Building in src/utils/gzstream
make[3]: '../../../obj//chromsweep.o' is up to date.
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
- Building in src/utils/fileType
make[3]: '../../../obj//gzstream.o' is up to date.
- Building in src/utils/bedFilePE
- Building in src/utils/KeyListOps
- Building in src/utils/NewChromsweep
make[3]: Nothing to be done for 'all'.
- Building in src/utils/sequenceUtilities
make[3]: '../../../obj//bedFilePE.o' is up to date.
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
- Building in src/utils/tabFile
- Building in src/utils/BamTools
- Building in src/utils/BamTools-Ancillary
make[3]: '../../../obj//sequenceUtils.o' is up to date.
- Building in src/utils/BlockedIntervals
make[3]: '../../../obj//tabFile.o' is up to date.
make[3]: Nothing to be done for 'all'.
- Building in src/utils/Fasta
make[3]: Nothing to be done for 'all'.
- Building in src/utils/VectorOps
make[3]: Nothing to be done for 'all'.
- Building in src/utils/GenomeFile
- Building in src/utils/RecordOutputMgr
make[3]: Nothing to be done for 'all'.
make[3]: '../../../obj//VectorOps.o' is up to date.
- Building in src/utils/ToolBase
make[3]: '../../../obj//NewGenomeFile.o' is up to date.
- Building in src/utils/driver
make[3]: '../../../obj//RecordOutputMgr.o' is up to date.
- Building in src/annotateBed
make[3]: '../../../obj//ToolBase.o' is up to date.
- Building in src/bamToBed
make[3]: Nothing to be done for 'all'.
- Building in src/bamToFastq
make[3]: Nothing to be done for 'all'.
- Building in src/bedToBam
make[3]: Nothing to be done for 'all'.
- Building in src/bedpeToBam
make[3]: Nothing to be done for 'all'.
- Building in src/bedToIgv
make[3]: Nothing to be done for 'all'.
- Building in src/bed12ToBed6
- Building in src/closestFile
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
- Building in src/clusterBed
make[3]: Nothing to be done for 'all'.
- Building in src/complementFile
make[3]: Nothing to be done for 'all'.
- Building in src/coverageFile
- Building in src/expand
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
- Building in src/fastaFromBed
- Building in src/flankBed
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
- Building in src/genomeCoverageBed
- Building in src/getOverlap
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
- Building in src/groupBy
- Building in src/intersectFile
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
- Building in src/fisher
- Building in src/jaccard
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
- Building in src/linksBed
- Building in src/maskFastaFromBed
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
- Building in src/mapFile
- Building in src/mergeFile
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
- Building in src/multiBamCov
- Building in src/multiIntersectBed
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
- Building in src/nucBed
- Building in src/pairToBed
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
- Building in src/pairToPair
- Building in src/randomBed
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
- Building in src/regressTest
- Building in src/reldist
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
- Building in src/sampleFile
- Building in src/shiftBed
make[3]: Nothing to be done for 'all'.
compiling RegressTest.cpp
g++ -c -o ../../obj//RegressTest.o RegressTest.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//general/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//version/ -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders -I../utils//FileRecordTools/Records -I../utils//KeyListOps/ -I../utils//general
- Building in src/shuffleBed
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
- Building in src/slopBed
make[3]: Nothing to be done for 'all'.
- Building in src/sortBed
- Building in src/spacingFile
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
- Building in src/split
make[3]: Nothing to be done for 'all'.
- Building in src/subtractFile
- Building in src/tagBam
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
- Building in src/unionBedGraphs
make[3]: Nothing to be done for 'all'.
- Building in src/windowBed
- Building in src/windowMaker
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
RegressTest.cpp: In member function 'bool RegressTest::executeAndCompareCorrectness(const fileListType&)':
RegressTest.cpp:431:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(diffCmd.c_str());
~~~~~~^~~~~~~~~~~~~~~~~
RegressTest.cpp: In member function 'bool RegressTest::startMemoryProfile(bool)':
RegressTest.cpp:573:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(sLine, 4192, fp);
~~~~~^~~~~~~~~~~~~~~~~
RegressTest.cpp: In member function 'bool RegressTest::calcMemoryStats()':
RegressTest.cpp:622:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(sLine, 4192, fp);
~~~~~^~~~~~~~~~~~~~~~~
compiling regressTestMain.cpp
g++ -c -o ../../obj//regressTestMain.o regressTestMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//general/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//version/ -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders -I../utils//FileRecordTools/Records -I../utils//KeyListOps/ -I../utils//general
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
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
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 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...ok
kclosest.t12...ok
kclosest.t13...ok
kclosest.t14...ok
kclosest.t15...ok
kclosest.t16...ok
kclosest.t17...ok
kclosest.t18...ok
kclosest.t19...ok
kclosest.t20...ok
kclosest.t21...ok
kclosest.t22...ok
kclosest.t23...ok
kclosest.t24...ok
kclosest.t25...ok
kclosest.t26...ok
kclosest.t27...ok
kclosest.t28...ok
kclosest.t29...ok
kclosest.t30...ok
kclosest.t31...ok
kclosest.t32...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
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
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
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.t12...ok
getfasta.t13...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.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...ok
intersect.new.t10...ok
intersect.new.t11...ok
intersect.new.t12...ok
intersect.new.t13...ok
intersect.new.t14...ok
intersect.new.t15...ok
intersect.new.t16...ok
intersect.new.t17...ok
intersect.new.t18...ok
intersect.new.t19...ok
intersect.new.t20...ok
intersect.new.t20.b...ok
intersect.new.t20.c...ok
intersect.new.t21...ok
intersect.new.t22...ok
intersect.new.t23...ok
intersect.new.t24...ok
intersect.new.t25...ok
intersect.new.t26...ok
intersect.new.t27...ok
intersect.new.t28...ok
intersect.new.t29...ok
intersect.new.t30...ok
intersect.new.t31...ok
intersect.new.t32...ok
intersect.new.t33...ok
intersect.new.t34...ok
intersect.new.t35...ok
intersect.new.t36...ok
intersect.new.t37...ok
intersect.new.t38...ok
intersect.new.t39...ok
intersect.new.t40...ok
intersect.new.t41...ok
intersect.new.t42...ok
intersect.new.t43...ok
intersect.new.t44...ok
intersect.new.t45...ok
intersect.new.t46...ok
intersect.new.t47...ok
intersect.new.t48...ok
intersect.new.t49...ok
intersect.new.t50...ok
intersect.new.t51...ok
intersect.new.t52...ok
intersect.new.t53...ok
intersect.new.t54...ok
intersect.new.t55...ok
intersect.new.t56...ok
intersect.new.t57...ok
intersect.new.t58...ok
intersect.new.t59...ok
intersect.new.t60...ok
intersect.new.t61...ok
intersect.new.t62...ok
intersect.new.t63...ok
intersect.new.t64...ok
intersect.new.t65...ok
intersect.new.t66...ok
intersect.new.t67a...ok
intersect.new.t67b...ok
intersect.new.t68a...ok
intersect.new.t68b...ok
intersect.new.t69...ok
intersect.new.t70...ok
intersect.new.t71...ok
intersect.new.t72...ok
###########################################################
#
# 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.t13...ok
intersect.t14...ok
intersect.t15...ok
intersect.t16...ok
intersect.t17...ok
intersect.t18...ok
intersect.t19...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
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
Testing bedtools negativecontrol:
Testing bedtools reldist:
reldist.t01...ok
reldist.t02...ok
reldist.t03...ok
Testing bedtools sample:
sample.t01...ok
sample.new.t02...ok
sample.new.t03...ok
sample.new.t04...ok
sample.new.t05...ok
sample.new.t06...ok
sample.new.t07...ok
sample.new.t08...ok
sample.new.t09...ok
Testing bedtools shift:
shift.t1...ok
shift.t2...ok
shift.t3...ok
shift.t3...ok
shift.t4...ok
shift.t5...ok
shift.t6...ok
shift.t7...ok
shift.t8...ok
shift.t9...ok
shift.t10...ok
Testing bedtools slop:
slop.t1...ok
slop.t2...ok
slop.t3...ok
slop.t4...ok
slop.t5...ok
slop.t6...ok
slop.t7...ok
slop.t8...ok
slop.t9...ok
slop.t10...ok
slop.t11...ok
slop.t12...ok
slop.t13...ok
slop.t14...ok
slop.t15...ok
slop.t16...ok
slop.t17...ok
slop.t18...ok
slop.t19...ok
slop.t20...ok
slop.t21...ok
slop.t22...ok
Testing bedtools sort:
sort.t01...ok
sort.t02...ok
sort.t03...ok
sort.t04...ok
sort.t05...ok
sort.t06...ok
sort.t07...ok
sort.t08...ok
sort.t09...ok
sort.t10...ok
Testing bedtools spacing:
spacing.t01...ok
Testing bedtools split:
split.01.size...ok
split.02.simple...ok
spliit.03.simple...ok
Testing bedtools subtract:
subtract.t1...ok
subtract.t2...ok
subtract.t3...ok
subtract.t4...ok
subtract.t5...ok
subtract.t6...ok
subtract.t7...ok
subtract.t8...ok
subtract.t9...ok
subtract.t10...ok
subtract.t11...ok
subtract.t12...ok
subtract.t13...ok
subtract.t14...ok
subtract.t15...ok
subtract.t16...ok
subtract.t17...ok
subtract.t18...ok
subtract.t19...ok
subtract.t20...ok
subtract.t21...ok
--------------------------
Test Results
--------------------------
Tools passing: bamtobed bamtofastq bed12tobed6 closest cluster complement coverage expand fisher flank general genomecov getfasta groupby intersect jaccard makewindows map merge multicov reldist sample shift slop sort spacing split subtract
Tools failing: negativecontrol
NB: the 'negativecontrol' test is supposed to fail. If it wasn't caught,
something went wrong with this test script.
make[2]: Leaving directory '/<<BUILDDIR>>/bedtools-2.27.1+dfsg'
mv debian/shuffle test/
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.27.1+dfsg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
rm -f -- debian/bedtools.substvars
rm -fr -- debian/.debhelper/generated/bedtools/ debian/bedtools/ debian/tmp/
dh_auto_install -a
install -d /<<BUILDDIR>>/bedtools-2.27.1\+dfsg/debian/tmp
make -j4 install DESTDIR=/<<BUILDDIR>>/bedtools-2.27.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.27.1+dfsg'
$CXXFLAGS is [-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11]
Building BEDTools:
=========================================================
* Creating BamTools API
DETECTED_VERSION = v2.27.1
CURRENT_VERSION = v2.27.1
- Building in src/utils/FileRecordTools
- Building in src/utils/FileRecordTools/FileReaders
- Building in src/utils/FileRecordTools/Records
- Building in src/utils/bedFile
make[2]: '../../../obj//bedFile.o' is up to date.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in FileReaders
- Building in Records
- Building in src/utils/BinTree
- Building in src/utils/version
make[2]: '../../../obj//BinTree.o' is up to date.
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/utils/bedGraphFile
- Building in src/utils/chromsweep
- Building in src/utils/Contexts
- Building in src/utils/general
make[2]: '../../../obj//bedGraphFile.o' is up to date.
make[2]: '../../../obj//chromsweep.o' is up to date.
- Building in src/utils/gzstream
make[2]: Nothing to be done for 'all'.
- Building in src/utils/fileType
make[2]: Nothing to be done for 'all'.
- Building in src/utils/bedFilePE
- Building in src/utils/KeyListOps
make[2]: '../../../obj//gzstream.o' is up to date.
make[2]: Nothing to be done for 'all'.
- Building in src/utils/NewChromsweep
- Building in src/utils/sequenceUtilities
make[2]: '../../../obj//bedFilePE.o' is up to date.
make[2]: Nothing to be done for 'all'.
- Building in src/utils/tabFile
- Building in src/utils/BamTools
make[2]: Nothing to be done for 'all'.
make[2]: '../../../obj//sequenceUtils.o' is up to date.
- Building in src/utils/BamTools-Ancillary
make[2]: '../../../obj//tabFile.o' is up to date.
- Building in src/utils/BlockedIntervals
- Building in src/utils/Fasta
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/utils/VectorOps
- Building in src/utils/GenomeFile
make[2]: Nothing to be done for 'all'.
- Building in src/utils/RecordOutputMgr
- Building in src/utils/ToolBase
make[2]: '../../../obj//VectorOps.o' is up to date.
make[2]: '../../../obj//NewGenomeFile.o' is up to date.
make[2]: '../../../obj//RecordOutputMgr.o' is up to date.
- Building in src/utils/driver
- Building in src/annotateBed
make[2]: '../../../obj//ToolBase.o' is up to date.
- Building in src/bamToBed
- Building in src/bamToFastq
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/bedToBam
make[2]: Nothing to be done for 'all'.
- Building in src/bedpeToBam
- Building in src/bedToIgv
- Building in src/bed12ToBed6
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/closestFile
make[2]: Nothing to be done for 'all'.
- Building in src/clusterBed
- Building in src/complementFile
- Building in src/coverageFile
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/expand
make[2]: Nothing to be done for 'all'.
- Building in src/fastaFromBed
- Building in src/flankBed
- Building in src/genomeCoverageBed
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/getOverlap
- Building in src/groupBy
make[2]: Nothing to be done for 'all'.
- Building in src/intersectFile
- Building in src/fisher
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/jaccard
- Building in src/linksBed
make[2]: Nothing to be done for 'all'.
- Building in src/maskFastaFromBed
- Building in src/mapFile
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/mergeFile
- Building in src/multiBamCov
make[2]: Nothing to be done for 'all'.
- Building in src/multiIntersectBed
- Building in src/nucBed
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/pairToBed
- Building in src/pairToPair
make[2]: Nothing to be done for 'all'.
- Building in src/randomBed
- Building in src/regressTest
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/reldist
- Building in src/sampleFile
- Building in src/shiftBed
compiling RegressTest.cpp
g++ -c -o ../../obj//RegressTest.o RegressTest.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//general/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//version/ -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders -I../utils//FileRecordTools/Records -I../utils//KeyListOps/ -I../utils//general
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/shuffleBed
- Building in src/slopBed
- Building in src/sortBed
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/spacingFile
- Building in src/split
- Building in src/subtractFile
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/tagBam
make[2]: Nothing to be done for 'all'.
- Building in src/unionBedGraphs
- Building in src/windowBed
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/windowMaker
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
RegressTest.cpp: In member function 'bool RegressTest::executeAndCompareCorrectness(const fileListType&)':
RegressTest.cpp:431:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(diffCmd.c_str());
~~~~~~^~~~~~~~~~~~~~~~~
RegressTest.cpp: In member function 'bool RegressTest::startMemoryProfile(bool)':
RegressTest.cpp:573:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(sLine, 4192, fp);
~~~~~^~~~~~~~~~~~~~~~~
RegressTest.cpp: In member function 'bool RegressTest::calcMemoryStats()':
RegressTest.cpp:622:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(sLine, 4192, fp);
~~~~~^~~~~~~~~~~~~~~~~
compiling regressTestMain.cpp
g++ -c -o ../../obj//regressTestMain.o regressTestMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//general/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//version/ -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders -I../utils//FileRecordTools/Records -I../utils//KeyListOps/ -I../utils//general
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
mkdir -p /<<BUILDDIR>>/bedtools-2.27.1+dfsg/debian/tmp/usr/local/bin
for file in bin/* ; do \
cp -f $file /<<BUILDDIR>>/bedtools-2.27.1+dfsg/debian/tmp/usr/local/bin; \
done
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.27.1+dfsg'
rm -f debian/bedtools.debhelper.log
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.27.1+dfsg'
dh_install
install -d debian/bedtools//usr/share/bash-completion/completions
cp --reflink=auto -a ./debian/bash_completion/bedtools debian/bedtools//usr/share/bash-completion/completions/
install -d debian/bedtools/usr/bin
cp --reflink=auto -a ./bin/annotateBed ./bin/bamToBed ./bin/bamToFastq ./bin/bed12ToBed6 ./bin/bedToBam ./bin/bedToIgv ./bin/bedpeToBam ./bin/bedtools ./bin/closestBed ./bin/clusterBed ./bin/complementBed ./bin/coverageBed ./bin/expandCols ./bin/fastaFromBed ./bin/flankBed ./bin/genomeCoverageBed ./bin/getOverlap ./bin/groupBy ./bin/intersectBed ./bin/linksBed ./bin/mapBed ./bin/maskFastaFromBed ./bin/mergeBed ./bin/multiBamCov ./bin/multiIntersectBed ./bin/nucBed ./bin/pairToBed ./bin/pairToPair ./bin/randomBed ./bin/shiftBed ./bin/shuffleBed ./bin/slopBed ./bin/sortBed ./bin/subtractBed ./bin/tagBam ./bin/unionBedGraphs ./bin/windowBed ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp --reflink=auto -a ./genomes debian/bedtools/usr/share/bedtools/
install -d debian/.debhelper/generated/bedtools
install -d debian/.debhelper/generated/bedtools-test
# make sure all *.sh files are featuring a '#!/bin/bash' as first line
# since there are at least two files (test/intersect/{new_test-intersect.sh,performanceTest.sh}
# requiring bash this is taken for all scripts instead of checking first via /bin/sh -n
for sh in `find /<<BUILDDIR>>/bedtools-2.27.1+dfsg/debian -name "*.sh"` ; do \
if ! head -n1 ${sh} | grep -q '^#! */bin/[ba]*sh' ; then \
sed -i '1 i #!/bin/bash' ${sh} ; \
fi ; \
done
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.27.1+dfsg'
dh_installdocs -a
install -d debian/bedtools/usr/share/doc/bedtools
cp --reflink=auto -a ./README.md debian/bedtools/usr/share/doc/bedtools
cp --reflink=auto -a ./debian/README.test debian/bedtools/usr/share/doc/bedtools
cp --reflink=auto -a ./debian/tests/run-unit-test debian/bedtools/usr/share/doc/bedtools
chown -R 0:0 debian/bedtools/usr/share/doc
chmod -R u\+rw,go=rX debian/bedtools/usr/share/doc
install -p -m0644 debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
rm -f debian/bedtools.debhelper.log
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.27.1+dfsg'
dh_installchangelogs RELEASE_HISTORY
install -p -m0644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
install -p -m0644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.27.1+dfsg'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
cd debian/bedtools
chmod a-x usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
gzip -9nf usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
cd '/<<BUILDDIR>>/bedtools-2.27.1+dfsg'
rm -f debian/bedtools.debhelper.log
debian/rules override_dh_fixperms-arch
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.27.1+dfsg'
dh_fixperms
find debian/bedtools -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/bedtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/bedtools/usr/share/doc -type f -a -true -a ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/bedtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/bedtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/bedtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
chmod -x /<<BUILDDIR>>/bedtools-2.27.1+dfsg/debian/bedtools/usr/share/bedtools/genomes/*.genome
find /<<BUILDDIR>>/bedtools-2.27.1+dfsg/debian -name "*.bed" -executable -exec chmod -x \{\} \;
find /<<BUILDDIR>>/bedtools-2.27.1+dfsg/debian -name "*.sh" -not -executable -exec chmod +x \{\} \;
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.27.1+dfsg'
dh_missing -a
dh_strip -a
install -d debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/59
objcopy --only-keep-debug --compress-debug-sections debian/bedtools/usr/bin/bedtools debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/59/9909befd736b657a98837c0f9b785e6df858e6.debug
chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/59/9909befd736b657a98837c0f9b785e6df858e6.debug
chown 0:0 -- debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/59/9909befd736b657a98837c0f9b785e6df858e6.debug
strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
objcopy --add-gnu-debuglink debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/59/9909befd736b657a98837c0f9b785e6df858e6.debug debian/bedtools/usr/bin/bedtools
install -d debian/.debhelper/bedtools/dbgsym-root/usr/share/doc
ln -s bedtools debian/.debhelper/bedtools/dbgsym-root/usr/share/doc/bedtools-dbgsym
dh_makeshlibs -a
rm -f debian/bedtools/DEBIAN/shlibs
dh_shlibdeps -a
install -d debian/bedtools/DEBIAN
dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bedtools contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb -a
dh_gencontrol -a
echo misc:Depends= >> debian/bedtools.substvars
echo misc:Pre-Depends= >> debian/bedtools.substvars
install -d debian/.debhelper/bedtools/dbgsym-root/DEBIAN
dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/.debhelper/bedtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=bedtools-dbgsym "-DDepends=bedtools (= \${binary:Version})" "-DDescription=debug symbols for bedtools" -DBuild-Ids=599909befd736b657a98837c0f9b785e6df858e6 -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/control
chown 0:0 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/control
dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools -UMulti-Arch
chmod 0644 -- debian/bedtools/DEBIAN/control
chown 0:0 -- debian/bedtools/DEBIAN/control
dh_md5sums -a
cd debian/bedtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/bedtools/DEBIAN/md5sums
chown 0:0 -- debian/bedtools/DEBIAN/md5sums
cd debian/.debhelper/bedtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/md5sums
chown 0:0 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --build debian/bedtools ..
dpkg-deb --build debian/.debhelper/bedtools/dbgsym-root ..
dpkg-deb: building package 'bedtools' in '../bedtools_2.27.1+dfsg-4_armhf.deb'.
dpkg-deb: building package 'bedtools-dbgsym' in '../bedtools-dbgsym_2.27.1+dfsg-4_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../bedtools_2.27.1+dfsg-4_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-source: info: using options from bedtools-2.27.1+dfsg/debian/source/options: --single-debian-patch
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-02-24T05:52:09Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
bedtools_2.27.1+dfsg-4_armhf.changes:
-------------------------------------
Format: 1.8
Date: Thu, 14 Feb 2019 22:11:21 +0900
Source: bedtools
Binary: bedtools bedtools-test
Architecture: armhf
Version: 2.27.1+dfsg-4
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Charles Plessy <plessy@debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
bedtools-test - test data for the bedtools package
Closes: 890117
Changes:
bedtools (2.27.1+dfsg-4) unstable; urgency=medium
.
* Disable the shuffle test on other 32-bit architectures.
* Restrict build to little-endian release architectures. Closes: #890117
* QA-build with Salsa.
Checksums-Sha1:
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1b36b54ca12b0539f9403d4491bb467d91874caf 5688 bedtools_2.27.1+dfsg-4_armhf.buildinfo
79fa4e77b381fb988c3bdc15831f4ca07731e513 478716 bedtools_2.27.1+dfsg-4_armhf.deb
Checksums-Sha256:
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062d1fcdbd810ed09ab7e7ace862c1a0b8278874aa321c8ec9db6e6080c80a93 5688 bedtools_2.27.1+dfsg-4_armhf.buildinfo
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Files:
67e6e4a8077cb86cf8ab5bde138db18a 15128808 debug optional bedtools-dbgsym_2.27.1+dfsg-4_armhf.deb
f15c513134a98b133d79894aafe8449c 5688 science optional bedtools_2.27.1+dfsg-4_armhf.buildinfo
826703e74daf60cb2790e3ccad6a0c4b 478716 science optional bedtools_2.27.1+dfsg-4_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
bedtools-dbgsym_2.27.1+dfsg-4_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 15128808 bytes: control archive=540 bytes.
388 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: bedtools-dbgsym
Source: bedtools
Version: 2.27.1+dfsg-4
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 15191
Depends: bedtools (= 2.27.1+dfsg-4)
Section: debug
Priority: optional
Description: debug symbols for bedtools
Build-Ids: 599909befd736b657a98837c0f9b785e6df858e6
drwxr-xr-x root/root 0 2019-02-14 13:11 ./
drwxr-xr-x root/root 0 2019-02-14 13:11 ./usr/
drwxr-xr-x root/root 0 2019-02-14 13:11 ./usr/lib/
drwxr-xr-x root/root 0 2019-02-14 13:11 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-02-14 13:11 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-02-14 13:11 ./usr/lib/debug/.build-id/59/
-rw-r--r-- root/root 15544700 2019-02-14 13:11 ./usr/lib/debug/.build-id/59/9909befd736b657a98837c0f9b785e6df858e6.debug
drwxr-xr-x root/root 0 2019-02-14 13:11 ./usr/share/
drwxr-xr-x root/root 0 2019-02-14 13:11 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-02-14 13:11 ./usr/share/doc/bedtools-dbgsym -> bedtools
bedtools_2.27.1+dfsg-4_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 478716 bytes: control archive=2176 bytes.
871 bytes, 20 lines control
2985 bytes, 51 lines md5sums
Package: bedtools
Version: 2.27.1+dfsg-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1602
Depends: libc6 (>= 2.23), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3)
Conflicts: filo
Replaces: filo
Provides: filo
Section: science
Priority: optional
Homepage: https://github.com/arq5x/bedtools2
Description: suite of utilities for comparing genomic features
The BEDTools utilities allow one to address common genomics tasks such as
finding feature overlaps and computing coverage. The utilities are largely
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
BEDTools, one can develop sophisticated pipelines that answer complicated
research questions by streaming several BEDTools together.
.
The groupBy utility is distributed in the filo package.
drwxr-xr-x root/root 0 2019-02-14 13:11 ./
drwxr-xr-x root/root 0 2019-02-14 13:11 ./usr/
drwxr-xr-x root/root 0 2019-02-14 13:11 ./usr/bin/
-rwxr-xr-x root/root 41 2019-02-14 13:11 ./usr/bin/annotateBed
-rwxr-xr-x root/root 41 2019-02-14 13:11 ./usr/bin/bamToBed
-rwxr-xr-x root/root 43 2019-02-14 13:11 ./usr/bin/bamToFastq
-rwxr-xr-x root/root 44 2019-02-14 13:11 ./usr/bin/bed12ToBed6
-rwxr-xr-x root/root 41 2019-02-14 13:11 ./usr/bin/bedToBam
-rwxr-xr-x root/root 36 2019-02-14 13:11 ./usr/bin/bedToIgv
-rwxr-xr-x root/root 43 2019-02-14 13:11 ./usr/bin/bedpeToBam
-rwxr-xr-x root/root 1537676 2019-02-14 13:11 ./usr/bin/bedtools
-rwxr-xr-x root/root 40 2019-02-14 13:11 ./usr/bin/closestBed
-rwxr-xr-x root/root 40 2019-02-14 13:11 ./usr/bin/clusterBed
-rwxr-xr-x root/root 43 2019-02-14 13:11 ./usr/bin/complementBed
-rwxr-xr-x root/root 41 2019-02-14 13:11 ./usr/bin/coverageBed
-rwxr-xr-x root/root 39 2019-02-14 13:11 ./usr/bin/expandCols
-rwxr-xr-x root/root 41 2019-02-14 13:11 ./usr/bin/fastaFromBed
-rwxr-xr-x root/root 38 2019-02-14 13:11 ./usr/bin/flankBed
-rwxr-xr-x root/root 42 2019-02-14 13:11 ./usr/bin/genomeCoverageBed
-rwxr-xr-x root/root 40 2019-02-14 13:11 ./usr/bin/getOverlap
-rwxr-xr-x root/root 40 2019-02-14 13:11 ./usr/bin/groupBy
-rwxr-xr-x root/root 42 2019-02-14 13:11 ./usr/bin/intersectBed
-rwxr-xr-x root/root 38 2019-02-14 13:11 ./usr/bin/linksBed
-rwxr-xr-x root/root 36 2019-02-14 13:11 ./usr/bin/mapBed
-rwxr-xr-x root/root 42 2019-02-14 13:11 ./usr/bin/maskFastaFromBed
-rwxr-xr-x root/root 38 2019-02-14 13:11 ./usr/bin/mergeBed
-rwxr-xr-x root/root 41 2019-02-14 13:11 ./usr/bin/multiBamCov
-rwxr-xr-x root/root 43 2019-02-14 13:11 ./usr/bin/multiIntersectBed
-rwxr-xr-x root/root 36 2019-02-14 13:11 ./usr/bin/nucBed
-rwxr-xr-x root/root 42 2019-02-14 13:11 ./usr/bin/pairToBed
-rwxr-xr-x root/root 43 2019-02-14 13:11 ./usr/bin/pairToPair
-rwxr-xr-x root/root 39 2019-02-14 13:11 ./usr/bin/randomBed
-rwxr-xr-x root/root 38 2019-02-14 13:11 ./usr/bin/shiftBed
-rwxr-xr-x root/root 40 2019-02-14 13:11 ./usr/bin/shuffleBed
-rwxr-xr-x root/root 37 2019-02-14 13:11 ./usr/bin/slopBed
-rwxr-xr-x root/root 37 2019-02-14 13:11 ./usr/bin/sortBed
-rwxr-xr-x root/root 41 2019-02-14 13:11 ./usr/bin/subtractBed
-rwxr-xr-x root/root 36 2019-02-14 13:11 ./usr/bin/tagBam
-rwxr-xr-x root/root 42 2019-02-14 13:11 ./usr/bin/unionBedGraphs
-rwxr-xr-x root/root 39 2019-02-14 13:11 ./usr/bin/windowBed
-rwxr-xr-x root/root 44 2019-02-14 13:11 ./usr/bin/windowMaker
drwxr-xr-x root/root 0 2019-02-14 13:11 ./usr/share/
drwxr-xr-x root/root 0 2019-02-14 13:11 ./usr/share/bash-completion/
drwxr-xr-x root/root 0 2019-02-14 13:11 ./usr/share/bash-completion/completions/
-rw-r--r-- root/root 638 2019-02-13 12:25 ./usr/share/bash-completion/completions/bedtools
drwxr-xr-x root/root 0 2019-02-14 13:11 ./usr/share/bedtools/
drwxr-xr-x root/root 0 2017-12-14 17:15 ./usr/share/bedtools/genomes/
-rw-r--r-- root/root 868 2017-12-14 17:15 ./usr/share/bedtools/genomes/human.hg18.genome
-rw-r--r-- root/root 1984 2017-12-14 17:15 ./usr/share/bedtools/genomes/human.hg19.genome
-rw-r--r-- root/root 11684 2017-12-14 17:15 ./usr/share/bedtools/genomes/human.hg38.genome
-rw-r--r-- root/root 1417 2017-12-14 17:15 ./usr/share/bedtools/genomes/mouse.mm10.genome
-rw-r--r-- root/root 577 2017-12-14 17:15 ./usr/share/bedtools/genomes/mouse.mm8.genome
-rw-r--r-- root/root 596 2017-12-14 17:15 ./usr/share/bedtools/genomes/mouse.mm9.genome
drwxr-xr-x root/root 0 2019-02-14 13:11 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-02-14 13:11 ./usr/share/doc/bedtools/
-rw-r--r-- root/root 3244 2017-12-14 17:15 ./usr/share/doc/bedtools/README.md
-rw-r--r-- root/root 278 2019-02-13 12:25 ./usr/share/doc/bedtools/README.test
-rw-r--r-- root/root 3518 2019-02-14 13:11 ./usr/share/doc/bedtools/changelog.Debian.gz
-rw-r--r-- root/root 15699 2017-12-14 17:15 ./usr/share/doc/bedtools/changelog.gz
-rw-r--r-- root/root 5341 2019-02-13 12:25 ./usr/share/doc/bedtools/copyright
-rw-r--r-- root/root 398 2019-02-13 12:25 ./usr/share/doc/bedtools/run-unit-test
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 297744
Build-Time: 248
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 303
Job: bedtools_2.27.1+dfsg-4
Machine Architecture: armhf
Package: bedtools
Package-Time: 574
Source-Version: 2.27.1+dfsg-4
Space: 297744
Status: successful
Version: 2.27.1+dfsg-4
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Finished at 2019-02-24T05:52:09Z
Build needed 00:09:34, 297744k disk space