bedtools →
2.26.0+dfsg-5 →
armhf → 2017-10-02 07:10:28
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| bedtools 2.26.0+dfsg-5 (armhf) Mon, 02 Oct 2017 07:04:08 +0000 |
+==============================================================================+
Package: bedtools
Version: 2.26.0+dfsg-5
Source Version: 2.26.0+dfsg-5
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-aeeffc8d-031f-420c-9fc4-ce00e39a8b67' 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 [10.2 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.1 MB]
Fetched 22.4 MB in 7s (2870 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://anonscm.debian.org/git/debian-med/bedtools.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/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 2.26.0+dfsg-5 (dsc) [2166 B]
Get:2 http://172.17.0.1/private buster-staging/main bedtools 2.26.0+dfsg-5 (tar) [13.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main bedtools 2.26.0+dfsg-5 (diff) [52.4 kB]
Fetched 13.5 MB in 1s (9695 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bedtools-RdHgL8/bedtools-2.26.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bedtools-RdHgL8' 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-KHFnjK/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-KHFnjK/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-KHFnjK/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-KHFnjK/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-KHFnjK/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-KHFnjK/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-KHFnjK/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-KHFnjK/apt_archive ./ Packages [434 B]
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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 libreadline5 libsasl2-modules libssl1.1 openssl
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 15 not upgraded.
Need to get 772 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-KHFnjK/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 15082 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
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Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10), python, zlib1g-dev, samtools
Filtered Build-Depends: debhelper (>= 10), python, zlib1g-dev, samtools
dpkg-deb: building package 'sbuild-build-depends-bedtools-dummy' in '/<<BUILDDIR>>/resolver-KHFnjK/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-KHFnjK/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-KHFnjK/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-KHFnjK/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-KHFnjK/apt_archive ./ Sources [507 B]
Get:5 copy:/<<BUILDDIR>>/resolver-KHFnjK/apt_archive ./ Packages [587 B]
Fetched 2427 B in 0s (9052 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install bedtools build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates libreadline5 libsasl2-modules openssl
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 file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libcroco3 libcurl3-gnutls
libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2
libhts2 libicu57 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib librtmp1 libsigsegv2 libssh2-1
libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python
python-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 krb5-doc
krb5-user libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales publicsuffix libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libcroco3 libcurl3-gnutls
libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2
libhts2 libicu57 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib librtmp1 libsigsegv2 libssh2-1
libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python
python-minimal python2.7 python2.7-minimal samtools
sbuild-build-depends-bedtools-dummy zlib1g-dev
0 upgraded, 52 newly installed, 0 to remove and 15 not upgraded.
Need to get 24.4 MB of archives.
After this operation, 84.0 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-KHFnjK/apt_archive ./ sbuild-build-depends-bedtools-dummy 0.invalid.0 [796 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-2 [95.8 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.13-2 [389 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.13-2 [1178 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.13-2 [40.5 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libexpat1 armhf 2.2.3-1 [67.1 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.13-2 [1827 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.13-2 [285 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.13-2 [20.0 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.13-2 [154 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-1 [225 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.32-1 [105 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-1 [63.7 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.15.1-2 [58.4 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.15.1-2 [115 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.15.1-2 [265 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.15.1-2 [132 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-4 [609 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.038-1 [11.1 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.0-1 [2650 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.8 [973 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.26.0-1 [72.2 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.18.0-4 [42.4 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-1 [126 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.55.1-1 [262 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.4.1-5 [247 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf samtools armhf 1.4.1-1 [218 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
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Unpacking sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
Setting up libexpat1:armhf (2.2.3-1) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up libnghttp2-14:armhf (1.26.0-1) ...
Setting up mime-support (3.60) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.11-1) ...
Setting up libpsl5:armhf (0.18.0-4) ...
Setting up groff-base (1.22.3-9) ...
Setting up libglib2.0-0:armhf (2.54.0-1) ...
No schema files found: doing nothing.
Setting up gettext-base (0.19.8.1-4) ...
Setting up libpipeline1:armhf (1.4.2-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-6) ...
Setting up libbsd0:armhf (0.8.6-2) ...
Setting up libxml2:armhf (2.9.4+dfsg1-4) ...
Setting up libmagic-mgc (1:5.32-1) ...
Setting up libmagic1:armhf (1:5.32-1) ...
Setting up libcroco3:armhf (0.6.12-1) ...
Setting up libssh2-1:armhf (1.8.0-1) ...
Processing triggers for libc-bin (2.24-14) ...
Setting up autotools-dev (20161112.1) ...
Setting up libkeyutils1:armhf (1.5.9-9) ...
Setting up bsdmainutils (9.0.12+nmu1) ...
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 (2.7.13-2) ...
Setting up autopoint (0.19.8.1-4) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (0.038-1) ...
Setting up gettext (0.19.8.1-4) ...
Setting up python2.7 (2.7.13-2) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.32-1) ...
Setting up libkrb5support0:armhf (1.15.1-2) ...
Setting up libpython-stdlib:armhf (2.7.13-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15.1-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up python (2.7.13-2) ...
Setting up libtool (2.4.6-2) ...
Setting up libk5crypto3:armhf (1.15.1-2) ...
Setting up po-debconf (1.0.20) ...
Setting up libkrb5-3:armhf (1.15.1-2) ...
Setting up libgssapi-krb5-2:armhf (1.15.1-2) ...
Setting up libcurl3-gnutls:armhf (7.55.1-1) ...
Setting up libhts2:armhf (1.4.1-5) ...
Setting up samtools (1.4.1-1) ...
Setting up dh-autoreconf (14) ...
Setting up debhelper (10.8) ...
Setting up sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.038-1) ...
Processing triggers for libc-bin (2.24-14) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.29.1-3+rpi1 dpkg-dev_1.18.24 g++-7_7.2.0-5 gcc-7_7.2.0-5 libc6-dev_2.24-14 libstdc++-7-dev_7.2.0-5 libstdc++6_7.2.0-5 linux-libc-dev_4.9.30-2+deb9u2+rpi1+stretch
Package versions: adduser_3.116 apt_1.5 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1 base-files_10+rpi1 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-3+rpi1 binutils-arm-linux-gnueabihf_2.29.1-3+rpi1 binutils-common_2.29.1-3+rpi1 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-5 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-5 dash_0.5.8-2.5 debconf_1.5.63 debhelper_10.8 debianutils_4.8.2 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.6-1 dirmngr_2.2.1-1 dmsetup_2:1.02.142-1 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.6-1 e2fsprogs_1.43.6-1 fakeroot_1.22-1 fdisk_2.29.2-5 file_1:5.32-1 findutils_4.6.0+git+20170729-2 g++_4:7.2.0-1d1 g++-7_7.2.0-5 gcc_4:7.2.0-1d1 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_4.9.3-14 gcc-5-base_5.4.1-4 gcc-7_7.2.0-5 gcc-7-base_7.2.0-5 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.1-1 gnupg-agent_2.2.1-1 gnupg-l10n_2.2.1-1 gnupg-utils_2.2.1-1 gpg_2.2.1-1 gpg-agent_2.2.1-1 gpg-wks-client_2.2.1-1 gpg-wks-server_2.2.1-1 gpgconf_2.2.1-1 gpgsm_2.2.1-1 gpgv_2.2.1-1 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init-system-helpers_1.49 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.0-11 libapt-pkg5.0_1.5 libarchive-zip-perl_1.59-1 libasan4_7.2.0-5 libassuan0_2.4.3-3 libatomic1_7.2.0-5 libattr1_1:2.4.47-2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b1 libbinutils_2.29.1-3+rpi1 libblkid1_2.29.2-5 libbsd0_0.8.6-2 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-14 libc-dev-bin_2.24-14 libc6_2.24-14 libc6-dev_2.24-14 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.2.0-5 libcilkrts5_7.2.0-5 libcomerr2_1.43.6-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.55.1-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.11.16+really1.10.22-1 libdebconfclient0_0.230 libdevmapper1.02.1_2:1.02.142-1 libdpkg-perl_1.18.24 libdrm-common_2.4.82-1+rpi1 libdrm2_2.4.82-1+rpi1 libexpat1_2.2.3-1 libfakeroot_1.22-1 libfdisk1_2.29.2-5 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-7-dev_7.2.0-5 libgcc1_1:7.2.0-5 libgcrypt20_1.7.9-1 libgdbm3_1.8.3-14 libglib2.0-0_2.54.0-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.15-2 libgomp1_7.2.0-5 libgpg-error0_1.27-3 libgssapi-krb5-2_1.15.1-2 libhogweed4_3.3-2 libhts2_1.4.1-5 libicu57_57.1-6 libidn11_1.33-2 libidn2-0_2.0.2-5 libip4tc0_1.6.1-2 libisl15_0.18-1 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.29.2-5 libmpc3_1.0.3-2 libmpfr4_3.1.6-1 libncurses5_6.0+20170902-1 libncursesw5_6.0+20170902-1 libnettle6_3.3-2 libnghttp2-14_1.26.0-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-4 libperl5.24_5.24.1-7 libperl5.26_5.26.0-8 libpipeline1_1.4.2-1 libplymouth4_0.9.3-1 libpng16-16_1.6.32-3 libprocps6_2:3.3.12-3 libpsl5_0.18.0-4 libpython-stdlib_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libreadline5_5.2+dfsg-3 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libsmartcols1_2.29.2-5 libsqlite3-0_3.20.1-1 libss2_1.43.6-1 libssh2-1_1.8.0-1 libssl1.1_1.1.0f-5 libstdc++-7-dev_7.2.0-5 libstdc++6_7.2.0-5 libsystemd0_234-3 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170902-1 libtool_2.4.6-2 libubsan0_7.2.0-5 libudev1_234-3 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-5 libxml2_2.9.4+dfsg1-4 linux-base_4.5 linux-libc-dev_4.9.30-2+deb9u2+rpi1+stretch login_1:4.4-4.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mime-support_3.60 mount_2.29.2-5 mountall_2.54 multiarch-support_2.24-14 ncurses-base_6.0+20170902-1 ncurses-bin_6.0+20170902-1 openssl_1.1.0f-5 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.26.0-8 perl-base_5.26.0-8 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.0-8 pinentry-curses_1.0.0-2 plymouth_0.9.3-1 po-debconf_1.0.20 procps_2:3.3.12-3 python_2.7.13-2 python-minimal_2.7.13-2 python2.7_2.7.13-2 python2.7-minimal_2.7.13-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 samtools_1.4.1-1 sbuild-build-depends-bedtools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_234-3 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2017b-2 udev_234-3 util-linux_2.29.2-5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Sep 26 13:52:43 2017 UTC
gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./bedtools_2.26.0+dfsg-5.dsc
dpkg-source: info: extracting bedtools in /<<BUILDDIR>>/bedtools-2.26.0+dfsg
dpkg-source: info: unpacking bedtools_2.26.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking bedtools_2.26.0+dfsg-5.debian.tar.xz
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 v2.26.0-19-g6bf23c4.patch
dpkg-source: info: applying do_not_let_random_failure_tests_fail.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
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-aeeffc8d-031f-420c-9fc4-ce00e39a8b67
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package bedtools
dpkg-buildpackage: info: source version 2.26.0+dfsg-5
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build bedtools-2.26.0+dfsg
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from bedtools-2.26.0+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-2.26.0+dfsg'
* Cleaning-up BamTools API
* Cleaning up.
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
dh_autoreconf_clean
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 . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -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
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
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
* compiling Record.cpp
DETECTED_VERSION = v2.26.0
CURRENT_VERSION =
Updating version file.
* compiling EmptyRecord.cpp
* compiling SingleLineDelimTextFileReader.cpp
* compiling Bed3Interval.cpp
* compiling Bed4Interval.cpp
* compiling FileRecordMergeMgr.cpp
* compiling BedGraphInterval.cpp
* compiling BamFileReader.cpp
* compiling Bed5Interval.cpp
* compiling FileRecordMgr.cpp
- Building in src/utils/bedFile
* compiling bedFile.cpp
* compiling Bed6Interval.cpp
* compiling BufferedStreamMgr.cpp
* compiling FileRecordMergeMgr.cpp
* compiling InputStreamMgr.cpp
* compiling PlusFields.cpp
- Building in FileReaders
* compiling InputStreamMgr.cpp
* compiling BedPlusInterval.cpp
- Building in src/utils/BinTree
* compiling BinTree.cpp
In file included from /usr/include/c++/7/vector:69:0,
from ../../utils//lineFileUtilities/lineFileUtilities.h:4,
from bedFile.h:17,
from bedFile.cpp:12:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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>::
^~~~~~~~~~~~~~~~~~~
- Building in Records
* compiling BedPlusInterval.cpp
* compiling Bed12Interval.cpp
In file included from /usr/include/c++/7/vector:64:0,
from ../../utils//lineFileUtilities/lineFileUtilities.h:4,
from bedFile.h:17,
from bedFile.cpp:12:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void BedFile::loadBedFileIntoVector()':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++/7/algorithm:62:0,
from bedFile.h:29,
from bedFile.cpp:12:
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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/utils/version
* compiling version.cpp
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from bedFile.h:29,
from bedFile.cpp:12:
/usr/include/c++/7/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++/7/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,
^~~~~~~~~~~~~
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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
* compiling Bed12Interval.cpp
In file included from /usr/include/c++/7/algorithm:62:0,
from bedFile.h:29,
from bedFile.cpp:12:
/usr/include/c++/7/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++/7/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++/7/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++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from bedFile.h:29,
from bedFile.cpp:12:
/usr/include/c++/7/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++/7/algorithm:62:0,
from bedFile.h:29,
from bedFile.cpp:12:
/usr/include/c++/7/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++/7/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++/7/bits/stl_algo.h: In member function 'void BedFile::assignWeightsBasedOnSize()':
/usr/include/c++/7/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++/7/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++/7/vector:64:0,
from ../../utils//lineFileUtilities/lineFileUtilities.h:4,
from bedFile.h:17,
from bedFile.cpp:12:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void BedFile::loadBedFileIntoMapNoBin()':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++/7/algorithm:62:0,
from bedFile.h:29,
from bedFile.cpp:12:
/usr/include/c++/7/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++/7/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 BamRecord.cpp
* compiling BamRecord.cpp
In file included from /usr/include/c++/7/vector:64:0,
from ../../utils//lineFileUtilities/lineFileUtilities.h:4,
from bedFile.h:17,
from bedFile.cpp:12:
/usr/include/c++/7/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++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h: In member function 'void BedFile::addBEDIntoMap(BED)':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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 GffRecord.cpp
* compiling GffPlusRecord.cpp
* compiling GffRecord.cpp
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
* compiling GffPlusRecord.cpp
* compiling VcfRecord.cpp
* compiling NoPosPlusRecord.cpp
* compiling VcfRecord.cpp
* compiling NoPosPlusRecord.cpp
In file included from /usr/include/c++/7/vector:69:0,
from ../../utils//lineFileUtilities/lineFileUtilities.h:4,
from chromsweep.cpp:12:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/vector:64:0,
from ../../utils//lineFileUtilities/lineFileUtilities.h:4,
from chromsweep.cpp:12:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void ChromSweep::ScanCache()':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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 BlockMgr.cpp
* compiling StrandQueue.cpp
* compiling BlockMgr.cpp
/usr/include/c++/7/bits/stl_vector.h: In member function 'bool ChromSweep::Next(std::pair<BED, std::vector<BED> >&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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
* compiling RecordList.cpp
* compiling StrandQueue.cpp
- Building in src/utils/Contexts
* compiling ContextBase.cpp
* compiling ContextIntersect.cpp
ContextBase.cpp: In constructor 'ContextBase::ContextBase()':
ContextBase.cpp:71:38: warning: passing NULL to non-pointer argument 1 of 'std::vector<_Tp, _Alloc>::vector(std::vector<_Tp, _Alloc>::size_type, const allocator_type&) [with _Tp = FileRecordMgr*; _Alloc = std::allocator<FileRecordMgr*>; std::vector<_Tp, _Alloc>::size_type = unsigned int; std::vector<_Tp, _Alloc>::allocator_type = std::allocator<FileRecordMgr*>]' [-Wconversion-null]
_nameConventionWarningTripped(false)
^
* compiling RecordMgr.cpp
- Building in src/utils/general
* compiling ParseTools.cpp
* compiling PushBackStreamBuf.cpp
* compiling RecordKeyList.cpp
* compiling ContextFisher.cpp
* compiling CompressionTools.cpp
* compiling RecordKeyVector.cpp
* compiling Tokenizer.cpp
* compiling ContextMap.cpp
* compiling RecordKeyList.cpp
* compiling ContextSample.cpp
* compiling CommonHelp.cpp
* compiling ContextSpacing.cpp
* compiling RecordKeyVector.cpp
- Building in src/utils/gzstream
g++ -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ../../../obj//gzstream.o gzstream.C -I.
* compiling ContextMerge.cpp
* compiling ContextJaccard.cpp
* compiling ContextClosest.cpp
* compiling ContextSubtract.cpp
* compiling ContextCoverage.cpp
* compiling ContextComplement.cpp
* compiling ContextGroupBy.cpp
- Building in src/utils/fileType
* compiling fileType.cpp
* compiling FileRecordTypeChecker.cpp
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
- Building in src/utils/KeyListOps
* compiling KeyListOps.cpp
- Building in src/utils/NewChromsweep
* compiling NewChromsweep.cpp
FileRecordTypeChecker.cpp: In member function 'bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)':
FileRecordTypeChecker.cpp:355:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0; j < len; j++) {
~~^~~~~
* compiling CloseSweep.cpp
In file included from /usr/include/c++/7/vector:69:0,
from bedFilePE.h:4,
from bedFilePE.cpp:15:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/vector:64:0,
from bedFilePE.h:4,
from bedFilePE.cpp:15:
/usr/include/c++/7/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++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h: In member function 'void BedFilePE::loadBedPEFileIntoMap()':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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 KeyListOpsMethods.cpp
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
- Building in src/utils/tabFile
* compiling tabFile.cpp
- Building in src/utils/BamTools
* compiling BamAlignment.cpp
* compiling BamMultiReader.cpp
* compiling BamReader.cpp
* compiling BamWriter.cpp
In file included from /usr/include/c++/7/algorithm:62:0,
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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/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++/7/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++/7/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++/7/algorithm:62:0,
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++/7/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++/7/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++/7/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++/7/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++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/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++/7/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++/7/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++/7/algorithm:62:0,
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++/7/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++/7/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++/7/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++/7/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 SamHeader.cpp
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
/usr/include/c++/7/bits/stl_algo.h: In member function 'void KeyListOpsMethods::sortArray(bool, bool)':
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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 SamProgram.cpp
* compiling SamProgramChain.cpp
* compiling SamReadGroup.cpp
- Building in src/utils/BlockedIntervals
* compiling BlockedIntervals.cpp
* compiling BamAncillary.cpp
* compiling SamReadGroupDictionary.cpp
In file included from /usr/include/c++/7/vector:69:0,
from ..//lineFileUtilities/lineFileUtilities.h:4,
from ..//bedFile/bedFile.h:17,
from BamAncillary.h:12,
from BamAncillary.cpp:12:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/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++/7/bits/vector.tcc:105:21: 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 SamSequence.cpp
In file included from /usr/include/c++/7/vector:69:0,
from BlockedIntervals.h:12,
from BlockedIntervals.cpp:12:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/vector:64:0,
from BlockedIntervals.h:12,
from BlockedIntervals.cpp:12:
/usr/include/c++/7/bits/stl_vector.h: In function 'void GetBedBlocks(const BED&, bedVector&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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 SamSequenceDictionary.cpp
In file included from /usr/include/c++/7/vector:69:0,
from ..//lineFileUtilities/lineFileUtilities.h:4,
from ..//bedFile/bedFile.h:17,
from BamAncillary.h:12,
from BamAncillary.cpp:12:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/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++/7/bits/vector.tcc:105:21: 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)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from BlockedIntervals.h:12,
from BlockedIntervals.cpp:12:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/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++/7/bits/vector.tcc:105:21: 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
* compiling BamHeader_p.cpp
- Building in src/utils/VectorOps
* compiling VectorOps.cpp
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);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* compiling BamMultiReader_p.cpp
* compiling BamRandomAccessController_p.cpp
In file included from /usr/include/c++/7/vector:69:0,
from Fasta.h:15,
from Fasta.cpp:9:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:60:0,
from Fasta.h:12,
from Fasta.cpp:9:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(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++/7/bits/stl_tree.h:2395:7: 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++/7/map:61:0,
from Fasta.h:12,
from Fasta.cpp:9:
/usr/include/c++/7/bits/stl_map.h: In member function 'std::__cxx11::string FastaReference::sequenceNameStartingWith(std::__cxx11::string)':
/usr/include/c++/7/bits/stl_map.h:493:4: 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++/7/algorithm:62:0,
from Fasta.h:18,
from Fasta.cpp:9:
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/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++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from Fasta.h:18,
from Fasta.cpp:9:
/usr/include/c++/7/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++/7/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++/7/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++/7/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,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from Fasta.h:18,
from Fasta.cpp:9:
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/map:61:0,
from Fasta.h:12,
from Fasta.cpp:9:
/usr/include/c++/7/bits/stl_map.h: In function 'std::ostream& operator<<(std::ostream&, FastaIndex&)':
/usr/include/c++/7/bits/stl_map.h:493:4: 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++/7/vector:64:0,
from Fasta.h:15,
from Fasta.cpp:9:
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++/7/algorithm:62:0,
from Fasta.h:18,
from Fasta.cpp:9:
/usr/include/c++/7/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++/7/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++/7/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);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling split.cpp
* compiling BamReader_p.cpp
In file included from /usr/include/c++/7/algorithm:62:0,
from VectorOps.h:21,
from VectorOps.cpp:15:
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/vector:69:0,
from VectorOps.h:15,
from VectorOps.cpp:15:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/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++/7/bits/vector.tcc:105:21: 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)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from VectorOps.h:21,
from VectorOps.cpp:15:
/usr/include/c++/7/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++/7/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++/7/algorithm:62:0,
from VectorOps.h:21,
from VectorOps.cpp:15:
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/bits/stl_algo.h: In member function 'double VectorOps::GetMedian()':
/usr/include/c++/7/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++/7/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++/7/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);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from VectorOps.h:21,
from VectorOps.cpp:15:
/usr/include/c++/7/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++/7/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++/7/algorithm:62:0,
from VectorOps.h:21,
from VectorOps.cpp:15:
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from VectorOps.h:21,
from VectorOps.cpp:15:
/usr/include/c++/7/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++/7/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++/7/algorithm:62:0,
from VectorOps.h:21,
from VectorOps.cpp:15:
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/bits/stl_algo.h: In member function 'std::__cxx11::string VectorOps::GetDistinctSortNum(bool)':
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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 BamWriter_p.cpp
* compiling BamIndexFactory_p.cpp
- Building in src/utils/GenomeFile
* compiling GenomeFile.cpp
* compiling BamStandardIndex_p.cpp
* compiling BamToolsIndex_p.cpp
- Building in src/utils/RecordOutputMgr
* compiling RecordOutputMgr.cpp
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;
^~
In file included from /usr/include/c++/7/vector:69:0,
from src/api/BamAux.h:18,
from src/api/BamAlignment.h:14,
from src/api/internal/index/BamToolsIndex_p.cpp:10:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from src/api/BamAux.h:18,
from src/api/BamAlignment.h:14,
from src/api/internal/index/BamToolsIndex_p.cpp:10:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void BamTools::Internal::BamToolsIndex::ReadBlocks(const BamTools::Internal::BtiReferenceSummary&, BamTools::Internal::BtiBlockVector&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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 NewGenomeFile.cpp
In file included from /usr/include/c++/7/vector:69:0,
from src/api/BamAux.h:18,
from src/api/BamAlignment.h:14,
from src/api/internal/index/BamToolsIndex_p.cpp:10:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void BamTools::Internal::BamToolsIndex::InitializeFileSummary(const int&)':
/usr/include/c++/7/bits/vector.tcc:105:21: 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)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from src/api/BamAux.h:18,
from src/api/BamAlignment.h:14,
from src/api/internal/index/BamToolsIndex_p.cpp:10:
/usr/include/c++/7/bits/stl_vector.h: In member function 'virtual bool BamTools::Internal::BamToolsIndex::Create()':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
- Building in src/utils/ToolBase
* compiling ToolBase.cpp
* compiling BamDeviceFactory_p.cpp
In file included from /usr/include/c++/7/vector:69:0,
from src/api/BamAux.h:18,
from src/api/BamAlignment.h:14,
from src/api/internal/index/BamStandardIndex_p.cpp:10:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/vector:64:0,
from src/api/BamAux.h:18,
from src/api/BamAlignment.h:14,
from src/api/internal/index/BamStandardIndex_p.cpp:10:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void BamTools::Internal::BamStandardIndex::MergeAlignmentChunks(BamTools::Internal::BaiAlignmentChunkVector&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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++/7/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++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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++/7/vector:69:0,
from src/api/BamAux.h:18,
from src/api/BamAlignment.h:14,
from src/api/internal/index/BamStandardIndex_p.cpp:10:
/usr/include/c++/7/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++/7/bits/vector.tcc:458:5: 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++/7/vector:64:0,
from src/api/BamAux.h:18,
from src/api/BamAlignment.h:14,
from src/api/internal/index/BamStandardIndex_p.cpp:10:
/usr/include/c++/7/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++/7/bits/stl_vector.h:712:18: 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++/7/vector:69:0,
from src/api/BamAux.h:18,
from src/api/BamAlignment.h:14,
from src/api/internal/index/BamStandardIndex_p.cpp:10:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/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++/7/bits/vector.tcc:105:21: 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++/7/algorithm:62:0,
from src/api/internal/index/BamStandardIndex_p.cpp:21:
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from src/api/internal/index/BamStandardIndex_p.cpp:21:
/usr/include/c++/7/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++/7/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++/7/algorithm:62:0,
from src/api/internal/index/BamStandardIndex_p.cpp:21:
/usr/include/c++/7/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++/7/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++/7/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++/7/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);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'void BamTools::Internal::BamStandardIndex::GetOffset(const BamTools::BamRegion&, int64_t&, bool*)':
/usr/include/c++/7/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++/7/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++/7/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);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from src/api/internal/index/BamStandardIndex_p.cpp:21:
/usr/include/c++/7/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++/7/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,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from src/api/internal/index/BamStandardIndex_p.cpp:21:
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/bits/stl_algo.h: In member function 'void BamTools::Internal::BamStandardIndex::SortLinearOffsets(BamTools::Internal::BaiLinearOffsetVector&)':
/usr/include/c++/7/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++/7/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++/7/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);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling BamFile_p.cpp
* compiling BamFtp_p.cpp
* compiling BamHttp_p.cpp
- Building in src/utils/driver
* compiling BedtoolsDriver.cpp
* compiling BamPipe_p.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
* compiling BgzfStream_p.cpp
* compiling annotateBed.cpp
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;
^~~~~~~~~~
- Building in src/bamToBed
* compiling bamToBed.cpp
- Building in src/bamToFastq
* compiling bamToFastqMain.cpp
* compiling ByteArray_p.cpp
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;
^~~~~~~~~~~~~~~~~
- Building in src/bedToBam
* compiling bedToBam.cpp
* compiling HostAddress_p.cpp
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;
^~~~~~~~~~
src/api/internal/io/HostAddress_p.cpp: In member function 'bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const':
src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare]
return m_ip4Address < m_ip4Address;
~~~~~~~~~~~~~^~~~~~~~~~~~~~
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 bamToFastq.cpp
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 HostInfo_p.cpp
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
- Building in src/bedToIgv
* compiling bedToIgv.cpp
* compiling HttpHeader_p.cpp
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
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/closestFile
* compiling closestHelp.cpp
* compiling ILocalIODevice_p.cpp
- Building in src/clusterBed
* compiling clusterMain.cpp
- Building in src/complementFile
* compiling complementHelp.cpp
* compiling RollingBuffer_p.cpp
* compiling closestFile.cpp
* compiling complementFile.cpp
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;
^~~~~~~~~~~~~~~
* compiling clusterBed.cpp
* compiling TcpSocketEngine_p.cpp
- Building in src/coverageFile
* compiling coverageHelp.cpp
* compiling TcpSocketEngine_unix_p.cpp
* compiling TcpSocket_p.cpp
* compiling coverageFile.cpp
* compiling SamFormatParser_p.cpp
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
- Building in src/expand
* compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling BamException_p.cpp
- Building in src/flankBed
* compiling flankBedMain.cpp
* 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
ranlib lib/libbamtools.a
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling fastaFromBed.cpp
* compiling flankBed.cpp
- Building in src/getOverlap
* compiling getOverlap.cpp
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;
^~~~~~~~~~~
* compiling genomeCoverageBed.cpp
- Building in src/groupBy
* compiling groupBy.cpp
- Building in src/intersectFile
* compiling intersectHelp.cpp
* compiling intersectFile.cpp
genomeCoverageBed.cpp: In member function 'void BedGenomeCoverage::CoverageBam(std::__cxx11::string)':
genomeCoverageBed.cpp:322:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(end<_fragmentSize) { //sometimes fragmentSize is bigger :(
~~~^~~~~~~~~~~~~~
* compiling groupByHelp.cpp
- Building in src/fisher
* compiling fisherHelp.cpp
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
* compiling kfunc.cpp
- Building in src/jaccard
* compiling jaccardHelp.cpp
* compiling jaccard.cpp
- Building in src/linksBed
* compiling linksMain.cpp
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
- Building in src/mapFile
* compiling mapHelp.cpp
* compiling linksBed.cpp
- Building in src/mergeFile
* compiling mergeHelp.cpp
* compiling mapFile.cpp
* compiling mergeFile.cpp
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
* compiling multiIntersectBed.cpp
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;
^~~~~~~~~~~~
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/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
- Building in src/pairToBed
* compiling pairToBedMain.cpp
* compiling pairToBed.cpp
- Building in src/pairToPair
* compiling pairToPairMain.cpp
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;
^~~~~~~~~~~~
* compiling pairToPair.cpp
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;
^~~~~~~~~~~~
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;
^~~~~~~~~~
- Building in src/randomBed
* compiling randomBedMain.cpp
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;
^~~~~~
* compiling randomBed.cpp
In file included from /usr/include/c++/7/vector:69:0,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from pairToPair.cpp:12:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/vector:64:0,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from pairToPair.cpp:12:
/usr/include/c++/7/bits/stl_vector.h: In member function 'bool PairToPair::FindHitsOnBothEnds(const BEDPE&, const std::vector<MATE>&, const std::vector<MATE>&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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/regressTest
compiling RegressTest.cpp
/usr/include/c++/7/bits/stl_vector.h: In member function 'void PairToPair::FindHitsOnEitherEnd(const BEDPE&, const std::vector<MATE>&, const std::vector<MATE>&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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++/7/vector:69:0,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from pairToBed.cpp:12:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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>::
^~~~~~~~~~~~~~~~~~~
- Building in src/reldist
* compiling reldistMain.cpp
In file included from /usr/include/c++/7/vector:64:0,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from pairToBed.cpp:12:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void BedIntersectPE::FindOverlaps(const BEDPE&, std::vector<BED>&, std::vector<BED>&, const string&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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 src/sampleFile
* compiling sampleHelp.cpp
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 sampleFile.cpp
* compiling reldist.cpp
- Building in src/shiftBed
* compiling shiftBedMain.cpp
reldist.cpp: In member function 'void RelativeDistance::ReportDistanceSummary()':
reldist.cpp:73:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'unsigned int' [-Wformat=]
reldist.cpp:71:16:
freqItr->second,
~~~~~~~~~~~~~~~
reldist.cpp:73:62:
(float) freqItr->second / (float) _tot_queries);
^
reldist.cpp:73:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t {aka unsigned int}' [-Wformat=]
* compiling shiftBed.cpp
compiling regressTestMain.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
- Building in src/slopBed
* compiling slopBedMain.cpp
- Building in src/sortBed
* compiling sortMain.cpp
* compiling shuffleBed.cpp
* compiling slopBed.cpp
* compiling sortBed.cpp
- Building in src/spacingFile
* compiling spacingHelp.cpp
* compiling spacingFile.cpp
slopBed.cpp: In member function 'void BedSlop::AddSlop(BED&)':
slopBed.cpp:85:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( ((int)bed.end + (long)_leftSlop) <= chromSize ) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
slopBed.cpp:107:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( ((int)bed.end + (long)_rightSlop) <= chromSize )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
- Building in src/split
* compiling splitBed.cpp
* compiling splitBedMain.cpp
In file included from /usr/include/c++/7/vector:69:0,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from sortBed.cpp:13:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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>::
^~~~~~~~~~~~~~~~~~~
- Building in src/subtractFile
* compiling subtractHelp.cpp
In file included from /usr/include/c++/7/algorithm:62:0,
from ../utils//bedFile/bedFile.h:29,
from sortBed.h:12,
from sortBed.cpp:14:
/usr/include/c++/7/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++/7/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,
^~~~~~~~~~~~~~~~~~~~~~~~~
* compiling subtractFile.cpp
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from ../utils//bedFile/bedFile.h:29,
from sortBed.h:12,
from sortBed.cpp:14:
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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
- Building in src/tagBam
* compiling tagBamMain.cpp
In file included from /usr/include/c++/7/vector:69:0,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from splitBed.cpp:16:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/algorithm:62:0,
from ../utils//bedFile/bedFile.h:29,
from sortBed.h:12,
from sortBed.cpp:14:
/usr/include/c++/7/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++/7/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++/7/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++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from ../utils//bedFile/bedFile.h:29,
from sortBed.h:12,
from sortBed.cpp:14:
/usr/include/c++/7/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++/7/algorithm:62:0,
from ../utils//bedFile/bedFile.h:29,
from sortBed.h:12,
from sortBed.cpp:14:
/usr/include/c++/7/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++/7/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++/7/vector:64:0,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from splitBed.cpp:16:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void BedSplit::loadBed()':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++/7/algorithm:62:0,
from ../utils//bedFile/bedFile.h:29,
from splitBed.h:10,
from splitBed.cpp:18:
/usr/include/c++/7/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++/7/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,
^~~~~~~~~~~~~~~~~~~~~~~~~
- Building in src/unionBedGraphs
* compiling unionBedGraphsMain.cpp
/usr/include/c++/7/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++/7/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++/7/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++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from ../utils//bedFile/bedFile.h:29,
from splitBed.h:10,
from splitBed.cpp:18:
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/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
In file included from /usr/include/c++/7/vector:64:0,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from sortBed.cpp:13:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void BedSort::SortBedBySizeDesc()':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++/7/algorithm:62:0,
from ../utils//bedFile/bedFile.h:29,
from sortBed.h:12,
from sortBed.cpp:14:
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/bits/stl_algo.h: In member function 'void BedSort::SortBedByChromThenSizeDesc()':
/usr/include/c++/7/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++/7/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++/7/bits/stl_algo.h: In member function 'void BedSort::SortBedByChromThenSizeAsc()':
/usr/include/c++/7/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++/7/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++/7/bits/stl_algo.h: In member function 'void BedSort::SortBedByChromThenScoreDesc()':
/usr/include/c++/7/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++/7/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++/7/bits/stl_algo.h: In member function 'void BedSort::SortBedByChromThenScoreAsc()':
/usr/include/c++/7/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++/7/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++/7/vector:64:0,
from ../utils//lineFileUtilities/lineFileUtilities.h:4,
from sortBed.cpp:13:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void BedSort::SortBedBySizeAsc()':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++/7/algorithm:62:0,
from ../utils//bedFile/bedFile.h:29,
from sortBed.h:12,
from sortBed.cpp:14:
/usr/include/c++/7/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++/7/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 unionBedGraphs.cpp
In file included from /usr/include/c++/7/algorithm:62:0,
from ../utils//bedFile/bedFile.h:29,
from splitBed.h:10,
from splitBed.cpp:18:
/usr/include/c++/7/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++/7/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++/7/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++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from ../utils//bedFile/bedFile.h:29,
from splitBed.h:10,
from splitBed.cpp:18:
/usr/include/c++/7/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++/7/algorithm:62:0,
from ../utils//bedFile/bedFile.h:29,
from splitBed.h:10,
from splitBed.cpp:18:
/usr/include/c++/7/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++/7/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);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
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;
^~~~~~~~~~
* compiling tagBam.cpp
- Building in src/windowBed
* compiling windowMain.cpp
/usr/include/c++/7/bits/stl_algo.h: In member function 'int BedSplit::doEuristicSplitOnTotalSize()':
/usr/include/c++/7/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++/7/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++/7/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/windowMaker
* compiling windowMakerMain.cpp
* compiling windowMaker.cpp
* compiling windowBed.cpp
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
dh_auto_test -a
make -j4 test
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
Building BEDTools:
=========================================================
* Creating BamTools API
DETECTED_VERSION = v2.26.0
CURRENT_VERSION = v2.26.0
- Building in src/utils/FileRecordTools
- Building in src/utils/FileRecordTools/FileReaders
- Building in src/utils/FileRecordTools/Records
- Building in src/utils/bedFile
make[2]: Nothing to be done for 'all'.
make[2]: '../../../obj//bedFile.o' is up to date.
make[2]: Nothing to be done for 'all'.
- Building in FileReaders
- Building in src/utils/BinTree
- Building in Records
- Building in src/utils/version
make[3]: Nothing to be done for 'all'.
make[2]: '../../../obj//BinTree.o' is up to date.
make[3]: Nothing to be done for 'all'.
- Building in src/utils/bedGraphFile
- Building in src/utils/chromsweep
- Building in src/utils/Contexts
make[2]: Nothing to be done for 'all'.
- 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
- Building in src/utils/fileType
make[2]: Nothing to be done for 'all'.
- Building in src/utils/bedFilePE
make[2]: Nothing to be done for 'all'.
make[2]: '../../../obj//gzstream.o' is up to date.
- Building in src/utils/KeyListOps
make[2]: Nothing to be done for 'all'.
- Building in src/utils/NewChromsweep
make[2]: '../../../obj//bedFilePE.o' is up to date.
- Building in src/utils/sequenceUtilities
- Building in src/utils/tabFile
make[2]: Nothing to be done for 'all'.
- Building in src/utils/BamTools
make[2]: Nothing to be done for 'all'.
make[2]: '../../../obj//sequenceUtils.o' is up to date.
make[2]: '../../../obj//tabFile.o' is up to date.
- Building in src/utils/BamTools-Ancillary
- 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'.
make[2]: Nothing to be done for 'all'.
- Building in src/utils/VectorOps
- Building in src/utils/GenomeFile
- 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
make[2]: '../../../obj//ToolBase.o' is up to date.
- Building in src/annotateBed
- 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'.
make[2]: Nothing to be done for 'all'.
- Building in src/bedToBam
- 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'.
- Building in src/closestFile
make[2]: Nothing to be done for 'all'.
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
- Building in src/fastaFromBed
make[2]: Nothing to be done for 'all'.
- 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
- Building in src/maskFastaFromBed
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/mapFile
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/mergeFile
- Building in src/multiBamCov
- Building in src/multiIntersectBed
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/nucBed
make[2]: Nothing to be done for 'all'.
- Building in src/pairToBed
- Building in src/pairToPair
- Building in src/randomBed
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/regressTest
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
make[2]: Nothing to be done for 'all'.
compiling RegressTest.cpp
make[2]: Nothing to be done for 'all'.
- Building in src/shuffleBed
make[2]: Nothing to be done for 'all'.
- 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'.
make[2]: Nothing to be done for 'all'.
- Building in src/tagBam
- Building in src/unionBedGraphs
- Building in src/windowBed
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'.
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
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
Performing general tests:
general.t01...\c
ok
general.t02...\c
ok
general.t03...\c
ok
general.t05...\c
ok
general.t06...\c
ok
general.t07...\c
ok
general.t08...\c
ok
general.t09...\c
ok
general.t10...\c
ok
general.t11...\c
ok
general.t12...\c
ok
general.t13...\c
ok
general.t14...\c
ok
general.15...\c
ok
general.t16...\c
ok
general.t17...\c
ok
general.t18...\c
ok
general.t19...\c
ok
general.t20...\c
ok
general.t21...\c
ok
general.22...\c
ok
general.t23...\c
ok
general.t24...\c
ok
general.t25...\c
ok
general.t26...\c
ok
general.t27...\c
ok
general.t28...\c
ok
general.29...\c
ok
general.t30...\c
ok
general.t31...\c
ok
general.t32...\c
ok
general.t33...\c
ok
general.t34...\c
ok
general.t35...\c
ok
general.36...\c
ok
general.t37...\c
ok
general.t38...\c
ok
general.t39...\c
ok
general.t40...\c
ok
general.t41...\c
ok
general.t42...\c
ok
general.t43...\c
ok
Testing bedtools bed12tobed6:
bed12tobed6.t1...\c
ok
bed12tobed6.t2...\c
ok
bed12tobed6.t3...\c
ok
bed12tobed6.t4...\c
ok
bed12tobed6.t5...\c
ok
Testing bedtools bamtobed:
bamtobed.t1...\c
ok
bamtobed.t2...\c
ok
bamtobed.t3...\c
ok
bamtobed.t4...\c
ok
bamtobed.t5...\c
ok
bamtobed.t6...\c
ok
bamtobed.t7...\c
ok
bamtobed.t8...\c
ok
bamtobed.t9...\c
ok
bamtobed.t10...\c
ok
bamtobed.t9...\c
ok
bamtobed.t11...\c
ok
Testing bedtools closest:
closest.t1...\c
ok
closest.t2...\c
ok
closest.t3...\c
ok
closest.t4...\c
ok
closest.t5...\c
ok
closest.t6...\c
ok
closest.t7...\c
ok
closest.t8...\c
ok
closest.t9...\c
ok
closest.t10...\c
ok
closest.t11...\c
ok
closest.t13...\c
ok
closest.t14...\c
ok
closest.t15...\c
ok
closest.t16...\c
ok
closest.t17...\c
ok
closest.t18...\c
ok
closest.t19...\c
ok
closest.t20...\c
ok
closest.t21...\c
ok
closest.t22...\c
ok
closest.t23...\c
ok
closest.t24...\c
ok
closest.t25...\c
ok
closest.t26...\c
ok
closest.t27...\c
ok
closest.t28...\c
ok
closest.t29...\c
ok
closest.t30...\c
ok
closest.t31...\c
ok
closest.t32...\c
ok
closest.t33...\c
ok
closest.t34...\c
ok
closest.t35...\c
ok
closest.t36...\c
ok
closest.t37...\c
ok
closest.t38...\c
ok
closest.t39...\c
ok
closest.t40...\c
ok
closest.t41...\c
ok
closest.t42...\c
ok
closest.t43...\c
ok
closest.t44...\c
ok
closest.t45...\c
ok
closest.t46...\c
ok
closest.t47...\c
ok
closest.t48...\c
ok
closest.t49...\c
ok
closest.t50...\c
ok
closest.t51...\c
ok
closest.t52...\c
ok
closest.t53...\c
ok
closest.t54...\c
ok
closest.t55...\c
ok
closest.t56...\c
ok
closest.t57...\c
ok
closest.t58...\c
ok
closest.t59...\c
ok
closest.t60...\c
ok
closest.t61...\c
ok
closest.t62...\c
ok
closest.t63...\c
ok
closest.t64...\c
ok
closest.t65...\c
ok
closest.t66...\c
ok
closest.t67...\c
ok
closest.t68...\c
ok
closest.t69...\c
ok
closest.t70...\c
ok
closest.t71...\c
ok
###########################################################
#
# CHROMOSOME SORT ORDER AND NAMING CONVENTIONS
#
###########################################################
closest.t01...\c
ok
closest.t02...\c
ok
closest.t03...\c
ok
closest.t04...\c
ok
closest.t05...\c
ok
closest.t06...\c
ok
closest.t07...\c
ok
closest.t08...\c
ok
closest.t09...\c
ok
closest.t10...\c
ok
closest.t11...\c
ok
closest.t12...\c
ok
closest.t13...\c
ok
closest.t14...\c
ok
closest.t15...\c
ok
closest.t16...\c
ok
closest.t17...\c
ok
closest.t18...\c
ok
closest.t19...\c
ok
closest.20...\c
ok
closest.21...\c
ok
closest.22...\c
ok
closest.23...\c
ok
###########################################################
#
# K CLOSEST HITS TESTS
#
###########################################################
kclosest.t1...\c
ok
kclosest.t2...\c
ok
kclosest.t3...\c
ok
kclosest.t4...\c
ok
kclosest.t5...\c
ok
kclosest.t6...\c
ok
kclosest.t7...\c
ok
kclosest.t8...\c
ok
kclosest.t9...\c
ok
kclosest.t10...\c
ok
kclosest.t11...\c
ok
kclosest.t12...\c
ok
kclosest.t13...\c
ok
kclosest.t14...\c
ok
kclosest.t15...\c
ok
kclosest.t16...\c
ok
kclosest.t17...\c
ok
kclosest.t18...\c
ok
kclosest.t19...\c
ok
kclosest.t20...\c
ok
kclosest.t21...\c
ok
kclosest.t22...\c
ok
kclosest.t23...\c
ok
kclosest.t24...\c
ok
kclosest.t25...\c
ok
kclosest.t26...\c
ok
kclosest.t27...\c
ok
kclosest.t28...\c
ok
kclosest.t29...\c
ok
kclosest.t30...\c
ok
kclosest.t31...\c
ok
kclosest.t32...\c
ok
kclosest.t33...\c
ok
kclosest.t34...\c
ok
kclosest.t35...\c
ok
kclosest.t36...\c
ok
kclosest.t37...\c
ok
kclosest.t38...\c
ok
Testing bedtools cluster:
cluster.t1...\c
ok
cluster.t2...\c
ok
Testing bedtools coverage:
coverage.t1...\c
ok
ok
coverage.t2...\c
ok
ok
coverage.t3...\c
ok
ok
coverage.t4...\c
ok
ok
coverage.t5...\c
ok
ok
coverage.t6...\c
ok
ok
coverage.t7...\c
ok
ok
coverage.t8...\c
ok
ok
coverage.t9...\c
ok
ok
coverage.t10...\c
ok
ok
coverage.t11...\c
ok
ok
coverage.t12...\c
ok
ok
coverage.t13...\c
ok
ok
coverage.t14...\c
ok
ok
coverage.t15...\c
ok
ok
coverage.t16...\c
ok
ok
coverage.t17...\c
ok
ok
coverage.t18...\c
ok
ok
coverage.t19...\c
ok
ok
Testing bedtools expand:
expand.t1...\c
ok
expand.t2...\c
ok
expand.t3...\c
ok
Testing bedtools flank:
flank.t1...\c
ok
flank.t2...\c
ok
flank.t3...\c
ok
flank.t4...\c
ok
flank.t5...\c
ok
flank.t6...\c
ok
flank.t7...\c
ok
flank.t8...\c
ok
flank.t9...\c
ok
flank.t10...\c
ok
flank.t11...\c
ok
Testing bedtools fisher:
fisher.t1...\c
ok
fisher.t2...\c
ok
fisher.t3...\c
14c14
< 1 1 1 nan
---
> 1 1 1 -nan
fail
fisher.t4...\c
ok
Testing bedtools genomecov:
genomecov.t1...\c
ok
genomecov.t2...\c
ok
genomecov.t3...\c
ok
genomecov.t4...\c
ok
genomecov.t5...\c
ok
genomecov.t6...\c
ok
genomecov.t7...\c
ok
genomecov.t8...\c
ok
genomecov.t9...\c
ok
genomecov.t10...\c
ok
genomecov.t11...\c
ok
genomecov.t12...\c
ok
genomecov.t13...\c
ok
genomecov.t14...\c
ok
genomecov.t15...\c
ok
Testing bedtools getfasta:
getfasta.t01...\c
ok
getfasta.t02...\c
ok
getfasta.t03...\c
ok
getfasta.t04...\c
ok
getfasta.t05...\c
ok
getfasta.t06...\c
ok
getfasta.t07...\c
ok
getfasta.t08...\c
index file test.iupac.fa.fai not found, generating...
ok
getfasta.t09...\c
index file test.iupac.fa.fai not found, generating...
ok
getfasta.t10...\c
index file test.fa.fai not found, generating...
ok
getfasta.t11...\c
ok
getfasta.t12...\c
ok
getfasta.t13...\c
ok
getfasta.t134..\c
ok
Testing bedtools groupby:
test.sh: line 35: cd: groupby: No such file or directory
bash: test-groupby.sh: No such file or directory
Testing bedtools intersect:
test.sh: line 38: cd: intersect: No such file or directory
bash: test-intersect.sh: No such file or directory
bash: new_test-intersect.sh: No such file or directory
Testing bedtools jaccard:
test.sh: line 41: cd: jaccard: No such file or directory
bash: test-jaccard.sh: No such file or directory
Testing bedtools map:
test.sh: line 44: cd: map: No such file or directory
bash: test-map.sh: No such file or directory
Testing bedtools merge:
test.sh: line 47: cd: merge: No such file or directory
bash: test-merge.sh: No such file or directory
Testing bedtools multicov:
test.sh: line 50: cd: multicov: No such file or directory
bash: test-multicov.sh: No such file or directory
Testing bedtools reldist:
test.sh: line 53: cd: reldist: No such file or directory
bash: test-reldist.sh: No such file or directory
Testing bedtools shift:
test.sh: line 56: cd: shift: No such file or directory
bash: test-shift.sh: No such file or directory
Testing bedtools slop:
test.sh: line 59: cd: slop: No such file or directory
bash: test-slop.sh: No such file or directory
Testing bedtools sort:
test.sh: line 62: cd: slop: No such file or directory
bash: test-sort.sh: No such file or directory
Testing bedtools shuffle:
test.sh: line 65: cd: shuffle: No such file or directory
bash: test-shuffle.sh: No such file or directory
Testing bedtools subtract:
test.sh: line 68: cd: subtract: No such file or directory
bash: test-subtract.sh: No such file or directory
Testing bedtools sample:
test.sh: line 71: cd: sample: No such file or directory
bash: test-sample.sh: No such file or directory
Testing bedtools split: FIXME: This test is known to be broken and will be ignored by the Debian autopkgtest
test.sh: line 74: cd: split: No such file or directory
bash: test-split.sh: No such file or directory
Testing bedtools spacing:
test.sh: line 77: cd: spacing: No such file or directory
bash: test-spacing.sh: No such file or directory
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.26.0+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 debian/bedtools
make -j4 install DESTDIR=/<<BUILDDIR>>/bedtools-2.26.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
Building BEDTools:
=========================================================
* Creating BamTools API
DETECTED_VERSION = v2.26.0
CURRENT_VERSION = v2.26.0
- Building in src/utils/FileRecordTools
- Building in src/utils/FileRecordTools/FileReaders
- Building in src/utils/bedFile
- Building in src/utils/FileRecordTools/Records
make[2]: '../../../obj//bedFile.o' is up to date.
- Building in src/utils/BinTree
make[2]: Nothing to be done for 'all'.
- Building in FileReaders
make[2]: Nothing to be done for 'all'.
- Building in Records
- Building in src/utils/version
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all'.
make[2]: '../../../obj//BinTree.o' is up to date.
- Building in src/utils/bedGraphFile
- Building in src/utils/chromsweep
- Building in src/utils/Contexts
make[2]: Nothing to be done for 'all'.
- 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
- Building in src/utils/fileType
make[2]: Nothing to be done for 'all'.
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
make[2]: '../../../obj//bedFilePE.o' is up to date.
- Building in src/utils/sequenceUtilities
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.
make[2]: '../../../obj//tabFile.o' is up to date.
- Building in src/utils/BamTools-Ancillary
- 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'.
make[2]: Nothing to be done for 'all'.
- Building in src/utils/VectorOps
- Building in src/utils/GenomeFile
- Building in src/utils/RecordOutputMgr
- Building in src/utils/ToolBase
make[2]: '../../../obj//NewGenomeFile.o' is up to date.
make[2]: '../../../obj//VectorOps.o' is up to date.
make[2]: '../../../obj//RecordOutputMgr.o' is up to date.
make[2]: '../../../obj//ToolBase.o' is up to date.
- Building in src/utils/driver
- Building in src/annotateBed
- 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'.
make[2]: Nothing to be done for 'all'.
- Building in src/bedToBam
- 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'.
make[2]: Nothing to be done for 'all'.
- Building in src/closestFile
- 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'.
make[2]: Nothing to be done for 'all'.
- Building in src/expand
- 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'.
make[2]: Nothing to be done for 'all'.
- Building in src/getOverlap
- Building in src/groupBy
- 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
make[2]: Nothing to be done for 'all'.
- Building in src/linksBed
- 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'.
make[2]: Nothing to be done for 'all'.
- Building in src/mergeFile
- Building in src/multiBamCov
- Building in src/multiIntersectBed
- Building in src/nucBed
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/pairToBed
make[2]: Nothing to be done for 'all'.
- Building in src/pairToPair
- Building in src/randomBed
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/regressTest
make[2]: Nothing to be done for 'all'.
- Building in src/reldist
- Building in src/sampleFile
make[2]: Nothing to be done for 'all'.
- Building in src/shiftBed
make[2]: Nothing to be done for 'all'.
compiling RegressTest.cpp
make[2]: Nothing to be done for 'all'.
- Building in src/shuffleBed
- Building in src/slopBed
make[2]: Nothing to be done for 'all'.
- Building in src/sortBed
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/spacingFile
- Building in src/split
make[2]: Nothing to be done for 'all'.
- Building in src/subtractFile
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
- Building in src/tagBam
- Building in src/unionBedGraphs
make[2]: Nothing to be done for 'all'.
- 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
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
mkdir -p /<<BUILDDIR>>/bedtools-2.26.0+dfsg/debian/tmp/usr/local/bin
for file in bin/* ; do \
cp -f $file /<<BUILDDIR>>/bedtools-2.26.0+dfsg/debian/tmp/usr/local/bin; \
done
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.26.0+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-2.26.0+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-2.26.0+dfsg'
dh_installdocs -a
install -d debian/bedtools/usr/share/doc/bedtools
cp --reflink=auto -a ./README.md 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-2.26.0+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-2.26.0+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-2.26.0+dfsg'
rm -f debian/bedtools.debhelper.log
debian/rules override_dh_fixperms-arch
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.26.0+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 \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -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-2.26.0+dfsg/debian/bedtools/usr/share/bedtools/genomes/*.genome
find /<<BUILDDIR>>/bedtools-2.26.0+dfsg/debian -name "*.bed" -executable -exec chmod -x \{\} \;
find /<<BUILDDIR>>/bedtools-2.26.0+dfsg/debian -name "*.sh" -not -executable -exec chmod +x \{\} \;
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
dh_missing -a
dh_strip -a
install -d debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/18
objcopy --only-keep-debug --compress-debug-sections debian/bedtools/usr/bin/bedtools debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/18/ffb274a29e74cab7f40b21b6baa4665540af54.debug
chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/18/ffb274a29e74cab7f40b21b6baa4665540af54.debug
chown 0:0 -- debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/18/ffb274a29e74cab7f40b21b6baa4665540af54.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/18/ffb274a29e74cab7f40b21b6baa4665540af54.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 -DAuto-Built-Package=debug-symbols -DPackage=bedtools-dbgsym "-DDepends=bedtools (= \${binary:Version})" "-DDescription=debug symbols for bedtools" -DBuild-Ids=18ffb274a29e74cab7f40b21b6baa4665540af54 -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 ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
chmod 0644 -- debian/bedtools/DEBIAN/md5sums
chown 0:0 -- debian/bedtools/DEBIAN/md5sums
(cd debian/.debhelper/bedtools/dbgsym-root >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
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-dbgsym' in '../bedtools-dbgsym_2.26.0+dfsg-5_armhf.deb'.
dpkg-deb: building package 'bedtools' in '../bedtools_2.26.0+dfsg-5_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../bedtools_2.26.0+dfsg-5_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build bedtools-2.26.0+dfsg
dpkg-source: info: using options from bedtools-2.26.0+dfsg/debian/source/options: --single-debian-patch
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-10-02T07:10:26Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
bedtools_2.26.0+dfsg-5_armhf.changes:
-------------------------------------
Format: 1.8
Date: Tue, 26 Sep 2017 22:42:08 +0900
Source: bedtools
Binary: bedtools bedtools-test
Architecture: armhf
Version: 2.26.0+dfsg-5
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: 876802
Changes:
bedtools (2.26.0+dfsg-5) unstable; urgency=medium
.
* Use "override_dh_install-indep" to prevent failures when
architecture-independent packages are not built. Closes: #876802
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6994b867e858bc3048e3fca155b929072811ae3a 5427 bedtools_2.26.0+dfsg-5_armhf.buildinfo
d17e129841906080972e2b59e76f80260797769e 476226 bedtools_2.26.0+dfsg-5_armhf.deb
Checksums-Sha256:
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6e2c7879b09e0c47a11bbdcd592f2d1781583d4c667ac7d2b84c21bdc74e472f 5427 bedtools_2.26.0+dfsg-5_armhf.buildinfo
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Files:
e742011d90d828b205cd2324b4efd63d 63274 debug optional bedtools-dbgsym_2.26.0+dfsg-5_armhf.deb
9bb5b100bd15fb4341b8d1e4df47c11a 5427 science optional bedtools_2.26.0+dfsg-5_armhf.buildinfo
184787bb50d786f086588df18919c834 476226 science optional bedtools_2.26.0+dfsg-5_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
bedtools-dbgsym_2.26.0+dfsg-5_armhf.deb
---------------------------------------
new debian package, version 2.0.
size 63274 bytes: control archive=458 bytes.
386 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: bedtools-dbgsym
Source: bedtools
Version: 2.26.0+dfsg-5
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 364
Depends: bedtools (= 2.26.0+dfsg-5)
Section: debug
Priority: optional
Description: debug symbols for bedtools
Build-Ids: 18ffb274a29e74cab7f40b21b6baa4665540af54
drwxr-xr-x root/root 0 2017-09-26 13:42 ./
drwxr-xr-x root/root 0 2017-09-26 13:42 ./usr/
drwxr-xr-x root/root 0 2017-09-26 13:42 ./usr/lib/
drwxr-xr-x root/root 0 2017-09-26 13:42 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-09-26 13:42 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-09-26 13:42 ./usr/lib/debug/.build-id/18/
-rw-r--r-- root/root 361560 2017-09-26 13:42 ./usr/lib/debug/.build-id/18/ffb274a29e74cab7f40b21b6baa4665540af54.debug
drwxr-xr-x root/root 0 2017-09-26 13:42 ./usr/share/
drwxr-xr-x root/root 0 2017-09-26 13:42 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-09-26 13:42 ./usr/share/doc/bedtools-dbgsym -> bedtools
bedtools_2.26.0+dfsg-5_armhf.deb
--------------------------------
new debian package, version 2.0.
size 476226 bytes: control archive=2121 bytes.
871 bytes, 20 lines control
2845 bytes, 49 lines md5sums
Package: bedtools
Version: 2.26.0+dfsg-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1611
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 2017-09-26 13:42 ./
drwxr-xr-x root/root 0 2017-09-26 13:42 ./usr/
drwxr-xr-x root/root 0 2017-09-26 13:42 ./usr/bin/
-rwxr-xr-x root/root 41 2017-09-26 13:42 ./usr/bin/annotateBed
-rwxr-xr-x root/root 41 2017-09-26 13:42 ./usr/bin/bamToBed
-rwxr-xr-x root/root 43 2017-09-26 13:42 ./usr/bin/bamToFastq
-rwxr-xr-x root/root 44 2017-09-26 13:42 ./usr/bin/bed12ToBed6
-rwxr-xr-x root/root 41 2017-09-26 13:42 ./usr/bin/bedToBam
-rwxr-xr-x root/root 36 2017-09-26 13:42 ./usr/bin/bedToIgv
-rwxr-xr-x root/root 43 2017-09-26 13:42 ./usr/bin/bedpeToBam
-rwxr-xr-x root/root 1549964 2017-09-26 13:42 ./usr/bin/bedtools
-rwxr-xr-x root/root 40 2017-09-26 13:42 ./usr/bin/closestBed
-rwxr-xr-x root/root 40 2017-09-26 13:42 ./usr/bin/clusterBed
-rwxr-xr-x root/root 43 2017-09-26 13:42 ./usr/bin/complementBed
-rwxr-xr-x root/root 41 2017-09-26 13:42 ./usr/bin/coverageBed
-rwxr-xr-x root/root 39 2017-09-26 13:42 ./usr/bin/expandCols
-rwxr-xr-x root/root 41 2017-09-26 13:42 ./usr/bin/fastaFromBed
-rwxr-xr-x root/root 38 2017-09-26 13:42 ./usr/bin/flankBed
-rwxr-xr-x root/root 42 2017-09-26 13:42 ./usr/bin/genomeCoverageBed
-rwxr-xr-x root/root 40 2017-09-26 13:42 ./usr/bin/getOverlap
-rwxr-xr-x root/root 40 2017-09-26 13:42 ./usr/bin/groupBy
-rwxr-xr-x root/root 42 2017-09-26 13:42 ./usr/bin/intersectBed
-rwxr-xr-x root/root 38 2017-09-26 13:42 ./usr/bin/linksBed
-rwxr-xr-x root/root 36 2017-09-26 13:42 ./usr/bin/mapBed
-rwxr-xr-x root/root 42 2017-09-26 13:42 ./usr/bin/maskFastaFromBed
-rwxr-xr-x root/root 38 2017-09-26 13:42 ./usr/bin/mergeBed
-rwxr-xr-x root/root 41 2017-09-26 13:42 ./usr/bin/multiBamCov
-rwxr-xr-x root/root 43 2017-09-26 13:42 ./usr/bin/multiIntersectBed
-rwxr-xr-x root/root 36 2017-09-26 13:42 ./usr/bin/nucBed
-rwxr-xr-x root/root 42 2017-09-26 13:42 ./usr/bin/pairToBed
-rwxr-xr-x root/root 43 2017-09-26 13:42 ./usr/bin/pairToPair
-rwxr-xr-x root/root 39 2017-09-26 13:42 ./usr/bin/randomBed
-rwxr-xr-x root/root 38 2017-09-26 13:42 ./usr/bin/shiftBed
-rwxr-xr-x root/root 40 2017-09-26 13:42 ./usr/bin/shuffleBed
-rwxr-xr-x root/root 37 2017-09-26 13:42 ./usr/bin/slopBed
-rwxr-xr-x root/root 37 2017-09-26 13:42 ./usr/bin/sortBed
-rwxr-xr-x root/root 41 2017-09-26 13:42 ./usr/bin/subtractBed
-rwxr-xr-x root/root 36 2017-09-26 13:42 ./usr/bin/tagBam
-rwxr-xr-x root/root 42 2017-09-26 13:42 ./usr/bin/unionBedGraphs
-rwxr-xr-x root/root 39 2017-09-26 13:42 ./usr/bin/windowBed
-rwxr-xr-x root/root 44 2017-09-26 13:42 ./usr/bin/windowMaker
drwxr-xr-x root/root 0 2017-09-26 13:42 ./usr/share/
drwxr-xr-x root/root 0 2017-09-26 13:42 ./usr/share/bash-completion/
drwxr-xr-x root/root 0 2017-09-26 13:42 ./usr/share/bash-completion/completions/
-rw-r--r-- root/root 638 2016-07-20 00:12 ./usr/share/bash-completion/completions/bedtools
drwxr-xr-x root/root 0 2017-09-26 13:42 ./usr/share/bedtools/
drwxr-xr-x root/root 0 2016-07-06 22:23 ./usr/share/bedtools/genomes/
-rw-r--r-- root/root 868 2016-07-06 22:23 ./usr/share/bedtools/genomes/human.hg18.genome
-rw-r--r-- root/root 1984 2016-07-06 22:23 ./usr/share/bedtools/genomes/human.hg19.genome
-rw-r--r-- root/root 11684 2016-07-06 22:23 ./usr/share/bedtools/genomes/human.hg38.genome
-rw-r--r-- root/root 1417 2016-07-06 22:23 ./usr/share/bedtools/genomes/mouse.mm10.genome
-rw-r--r-- root/root 577 2016-07-06 22:23 ./usr/share/bedtools/genomes/mouse.mm8.genome
-rw-r--r-- root/root 596 2016-07-06 22:23 ./usr/share/bedtools/genomes/mouse.mm9.genome
drwxr-xr-x root/root 0 2017-09-26 13:42 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-09-26 13:42 ./usr/share/doc/bedtools/
-rw-r--r-- root/root 3244 2016-07-06 22:23 ./usr/share/doc/bedtools/README.md
-rw-r--r-- root/root 3023 2017-09-26 13:42 ./usr/share/doc/bedtools/changelog.Debian.gz
-rw-r--r-- root/root 15699 2016-07-06 22:23 ./usr/share/doc/bedtools/changelog.gz
-rw-r--r-- root/root 5570 2017-09-25 03:22 ./usr/share/doc/bedtools/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 68404
Build-Time: 240
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 118
Job: bedtools_2.26.0+dfsg-5
Machine Architecture: armhf
Package: bedtools
Package-Time: 378
Source-Version: 2.26.0+dfsg-5
Space: 68404
Status: successful
Version: 2.26.0+dfsg-5
--------------------------------------------------------------------------------
Finished at 2017-10-02T07:10:26Z
Build needed 00:06:18, 68404k disk space