bedops →
2.4.35+dfsg-1 →
armhf → 2018-05-29 04:59:50
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| bedops 2.4.35+dfsg-1 (armhf) Tue, 29 May 2018 04:39:32 +0000 |
+==============================================================================+
Package: bedops
Version: 2.4.35+dfsg-1
Source Version: 2.4.35+dfsg-1
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-724f6b88-7560-447d-b531-b8544ba4adb5' 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 [10.8 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.5 MB]
Fetched 23.3 MB in 14s (1683 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: 'bedops' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/bedops.git
Please use:
git clone https://salsa.debian.org/med-team/bedops.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 15.3 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main bedops 2.4.35+dfsg-1 (dsc) [2112 B]
Get:2 http://172.17.0.1/private buster-staging/main bedops 2.4.35+dfsg-1 (tar) [15.3 MB]
Get:3 http://172.17.0.1/private buster-staging/main bedops 2.4.35+dfsg-1 (diff) [6944 B]
Fetched 15.3 MB in 6s (2677 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bedops-EsrJj3/bedops-2.4.35+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bedops-EsrJj3' 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-wv3syF/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-wv3syF/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-wv3syF/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-wv3syF/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-wv3syF/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-wv3syF/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-wv3syF/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-wv3syF/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (9598 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 68 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-wv3syF/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15689 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), help2man, libbz2-dev, libjansson-dev, libjs-mathjax, python3-distutils, python3-sphinx, zlib1g-dev
Filtered Build-Depends: debhelper (>= 11~), help2man, libbz2-dev, libjansson-dev, libjs-mathjax, python3-distutils, python3-sphinx, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-bedops-dummy' in '/<<BUILDDIR>>/resolver-wv3syF/apt_archive/sbuild-build-depends-bedops-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-bedops-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-wv3syF/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-wv3syF/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-wv3syF/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-wv3syF/apt_archive ./ Sources [545 B]
Get:5 copy:/<<BUILDDIR>>/resolver-wv3syF/apt_archive ./ Packages [626 B]
Fetched 2504 B in 0s (12.4 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install bedops 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:
dbus dbus-user-session e2fsprogs-l10n libnss-systemd libpam-systemd
libsasl2-modules systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism docutils-common dwz file fonts-mathjax
gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl
libbsd0 libbz2-dev libcroco3 libelf1 libfile-stripnondeterminism-perl
libfreetype6 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu-le-hb0
libicu60 libjansson-dev libjansson4 libjs-jquery libjs-mathjax
libjs-sphinxdoc libjs-underscore liblocale-gettext-perl libmagic-mgc
libmagic1 libmpdec2 libncursesw6 libpipeline1 libpython3-stdlib
libpython3.6-minimal libpython3.6-stdlib libsigsegv2 libtimedate-perl
libtinfo6 libtool libxml2 m4 man-db mime-support po-debconf
python-babel-localedata python3 python3-alabaster python3-babel
python3-certifi python3-chardet python3-distutils python3-docutils
python3-idna python3-imagesize python3-jinja2 python3-lib2to3
python3-markupsafe python3-minimal python3-packaging python3-pkg-resources
python3-pygments python3-pyparsing python3-requests python3-roman
python3-six python3-sphinx python3-tz python3-urllib3 python3.6
python3.6-minimal sgml-base sphinx-common xml-core zlib1g zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
fonts-mathjax-extras fonts-stix libjs-mathjax-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv docutils-doc
fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french
texlive-latex-base texlive-latex-recommended python-jinja2-doc
python3-setuptools ttf-bitstream-vera python-pyparsing-doc
python3-cryptography python3-openssl python3-socks python3-sphinx-rtd-theme
dvipng texlive-latex-extra texlive-fonts-recommended texlive-generic-extra
latexmk imagemagick-6.q16 sphinx-doc python3.6-venv python3.6-doc
binfmt-support sgml-base-doc
Recommended packages:
curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs javascript-common libgpm2 libltdl-dev
libmail-sendmail-perl libpaper-utils python3-pil
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism docutils-common dwz file fonts-mathjax
gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl
libbsd0 libbz2-dev libcroco3 libelf1 libfile-stripnondeterminism-perl
libfreetype6 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu-le-hb0
libicu60 libjansson-dev libjansson4 libjs-jquery libjs-mathjax
libjs-sphinxdoc libjs-underscore liblocale-gettext-perl libmagic-mgc
libmagic1 libmpdec2 libncursesw6 libpipeline1 libpython3-stdlib
libpython3.6-minimal libpython3.6-stdlib libsigsegv2 libtimedate-perl
libtinfo6 libtool libxml2 m4 man-db mime-support po-debconf
python-babel-localedata python3 python3-alabaster python3-babel
python3-certifi python3-chardet python3-distutils python3-docutils
python3-idna python3-imagesize python3-jinja2 python3-lib2to3
python3-markupsafe python3-minimal python3-packaging python3-pkg-resources
python3-pygments python3-pyparsing python3-requests python3-roman
python3-six python3-sphinx python3-tz python3-urllib3 python3.6
python3.6-minimal sbuild-build-depends-bedops-dummy sgml-base sphinx-common
xml-core zlib1g-dev
The following packages will be upgraded:
zlib1g
1 upgraded, 84 newly installed, 0 to remove and 67 not upgraded.
Need to get 39.8 MB/40.6 MB of archives.
After this operation, 174 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-wv3syF/apt_archive ./ sbuild-build-depends-bedops-dummy 0.invalid.0 [916 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf liblocale-gettext-perl armhf 1.07-3+b2 [18.3 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf zlib1g armhf 1:1.2.11.dfsg-1 [87.3 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libpython3.6-minimal armhf 3.6.5-9 [565 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python3.6-minimal armhf 3.6.5-9 [1374 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.6.5-3 [36.2 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libtinfo6 armhf 6.1+20180210-4 [308 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libncursesw6 armhf 6.1+20180210-4 [103 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libpython3.6-stdlib armhf 3.6.5-9 [1651 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.5-9 [229 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.6.5-3 [19.7 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.6.5-3 [24.1 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf sgml-base all 1.29 [14.8 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-2 [234 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.33-2 [106 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-2 [64.7 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.041-1 [19.9 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.041-1 [12.0 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.4 [160 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.7.6-1+b1 [799 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.2 [994 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf xml-core all 0.18 [23.4 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf docutils-common all 0.14+dfsg-3 [204 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf fonts-mathjax all 2.7.4+dfsg-1 [2209 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf help2man armhf 1.47.6 [169 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-8.1 [26.9 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libjansson4 armhf 2.11-1 [26.3 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libjansson-dev armhf 2.11-1 [26.4 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libjs-mathjax all 2.7.4+dfsg-1 [5658 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libjs-underscore all 1.8.3~dfsg-1 [63.8 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libjs-sphinxdoc all 1.7.4-1 [89.7 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf python-babel-localedata all 2.4.0+dfsg.1-2 [3415 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf python3-pkg-resources all 39.1.0-1 [142 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf python3-tz all 2018.4-1 [26.9 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf python3-babel all 2.4.0+dfsg.1-2 [83.7 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf python3-certifi all 2018.1.18-3 [144 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf python3-chardet all 3.0.4-1 [80.2 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf python3-lib2to3 all 3.6.5-3 [78.7 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.6.5-3 [144 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf python3-roman all 2.0.0-3 [8768 B]
Get:66 http://172.17.0.1/private buster-staging/main armhf python3-docutils all 0.14+dfsg-3 [377 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf python3-idna all 2.6-1 [34.3 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf python3-imagesize all 1.0.0-1 [4960 B]
Get:69 http://172.17.0.1/private buster-staging/main armhf python3-markupsafe armhf 1.0-1+b1 [14.1 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf python3-jinja2 all 2.10-1 [106 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf python3-pyparsing all 2.2.0+dfsg1-2 [89.6 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf python3-six all 1.11.0-2 [15.2 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf python3-packaging all 17.1-1 [18.3 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf python3-pygments all 2.2.0+dfsg-1 [588 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf python3-urllib3 all 1.22-1 [97.9 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf python3-requests all 2.18.4-2 [77.1 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf python3-alabaster all 0.7.8-1 [18.4 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf sphinx-common all 1.7.4-1 [434 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf python3-sphinx all 1.7.4-1 [444 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking zlib1g:armhf (1:1.2.11.dfsg-1) over (1:1.2.8.dfsg-5) ...
Setting up zlib1g:armhf (1:1.2.11.dfsg-1) ...
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+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.30-15+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-12 gcc-7_7.3.0-12 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180414-1+rpi1 linux-libc-dev_4.15.17-1+rpi1
Package versions: adduser_3.117 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-2+b1 binutils_2.30-15+rpi1 binutils-arm-linux-gnueabihf_2.30-15+rpi1 binutils-common_2.30-15+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.5 build-essential_12.4+b1 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.3.0-12 dash_0.5.8-2.10 dbus_1.12.6-2 dbus-user-session_1.12.6-2 debconf_1.5.66 debhelper_11.3.2 debianutils_4.8.4 dh-autoreconf_19 dh-strip-nondeterminism_0.041-1 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1 docutils-common_0.14+dfsg-3 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.1-2 e2fsprogs_1.44.1-2 e2fsprogs-l10n_1.44.1-2 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.33-2 findutils_4.6.0+git+20171230-2 fonts-mathjax_2.7.4+dfsg-1 g++_4:7.2.0-1d1 g++-7_7.3.0-12 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_4.9.4-2+rpi1 gcc-5-base_5.5.0-8 gcc-7_7.3.0-12 gcc-7-base_7.3.0-12 gcc-8-base_8-20180414-1+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gnupg_2.2.5-1 gnupg-agent_2.2.5-1 gnupg-l10n_2.2.5-1 gnupg-utils_2.2.5-1 gpg_2.2.5-1 gpg-agent_2.2.5-1 gpg-wks-client_2.2.5-1 gpg-wks-server_2.2.5-1 gpgconf_2.2.5-1 gpgsm_2.2.5-1 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 help2man_1.47.6 hostname_3.20 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-4 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libasan4_7.3.0-12 libassuan0_2.5.1-2 libatomic1_8-20180414-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbinutils_2.30-15+rpi1 libblkid1_2.31.1-0.5 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libbz2-dev_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_8-20180414-1+rpi1 libcilkrts5_7.3.0-12 libcom-err2_1.44.1-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.6-2 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.91-2+rpi1 libdrm2_2.4.91-2+rpi1 libelf1_0.170-0.4 libexpat1_2.2.5-3 libext2fs2_1.44.1-2 libfakeroot_1.22-2 libfdisk1_2.31.1-0.5 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-1 libfreetype6_2.8.1-2 libgcc-7-dev_7.3.0-12 libgcc1_1:8-20180414-1+rpi1 libgcrypt20_1.8.2-2 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180414-1+rpi1 libgpg-error0_1.29-4 libgraphite2-3_1.3.11-2 libharfbuzz0b_1.7.6-1+b1 libhogweed4_3.4-1 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl15_0.18-4 libjansson-dev_2.11-1 libjansson4_2.11-1 libjs-jquery_3.2.1-1 libjs-mathjax_2.7.4+dfsg-1 libjs-sphinxdoc_1.7.4-1 libjs-underscore_1.8.3~dfsg-1 libjson-c3_0.12.1-1.3 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_1.8.1.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-2 libmagic1_1:5.33-2 libmount1_2.31.1-0.5 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libncurses5_6.1-1 libncursesw5_6.1-1 libncursesw6_6.1+20180210-4 libnettle6_3.4-1 libnpth0_1.5-3 libnss-systemd_238-4 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-4 libpam0g_1.1.8-3.7 libpcre3_2:8.39-9 libperl5.24_5.24.1-7 libperl5.26_5.26.2-2 libpipeline1_1.5.0-1 libplymouth4_0.9.3-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.14-1 libpython3-stdlib_3.6.5-3 libpython3.6-minimal_3.6.5-9 libpython3.6-stdlib_3.6.5-9 libreadline7_7.0-3 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-2 libsmartcols1_2.31.1-0.5 libsqlite3-0_3.23.1-1 libss2_1.44.1-2 libssl1.1_1.1.0h-2 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180414-1+rpi1 libsystemd0_238-4 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.1-1 libtinfo6_6.1+20180210-4 libtool_2.4.6-2.1 libubsan0_7.3.0-12 libudev1_238-4 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.5 libxml2_2.9.4+dfsg1-7 libzstd1_1.3.3+dfsg-2+rpi1 linux-base_4.5 linux-libc-dev_4.15.17-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mime-support_3.60 mount_2.31.1-0.5 multiarch-support_2.27-3+rpi1 nano_2.9.5-1 ncurses-base_6.1-1 ncurses-bin_6.1-1 netbase_5.4 openssl_1.1.0h-2 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-2 perl-base_5.26.2-2 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-3 pinentry-curses_1.1.0-1 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.14-1 python-babel-localedata_2.4.0+dfsg.1-2 python3_3.6.5-3 python3-alabaster_0.7.8-1 python3-babel_2.4.0+dfsg.1-2 python3-certifi_2018.1.18-3 python3-chardet_3.0.4-1 python3-distutils_3.6.5-3 python3-docutils_0.14+dfsg-3 python3-idna_2.6-1 python3-imagesize_1.0.0-1 python3-jinja2_2.10-1 python3-lib2to3_3.6.5-3 python3-markupsafe_1.0-1+b1 python3-minimal_3.6.5-3 python3-packaging_17.1-1 python3-pkg-resources_39.1.0-1 python3-pygments_2.2.0+dfsg-1 python3-pyparsing_2.2.0+dfsg1-2 python3-requests_2.18.4-2 python3-roman_2.0.0-3 python3-six_1.11.0-2 python3-sphinx_1.7.4-1 python3-tz_2018.4-1 python3-urllib3_1.22-1 python3.6_3.6.5-9 python3.6-minimal_3.6.5-9 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-bedops-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 sgml-base_1.29 sphinx-common_1.7.4-1 systemd_238-4 systemd-sysv_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018d-1 udev_238-4 util-linux_2.31.1-0.5 xml-core_0.18 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed May 23 15:54:16 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./bedops_2.4.35+dfsg-1.dsc
dpkg-source: info: extracting bedops in /<<BUILDDIR>>/bedops-2.4.35+dfsg
dpkg-source: info: unpacking bedops_2.4.35+dfsg.orig.tar.xz
dpkg-source: info: unpacking bedops_2.4.35+dfsg-1.debian.tar.xz
dpkg-source: info: applying use_debian_libs
dpkg-source: info: applying hardening.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-724f6b88-7560-447d-b531-b8544ba4adb5
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package bedops
dpkg-buildpackage: info: source version 2.4.35+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build bedops-2.4.35+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with sphinxdoc
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg'
make clean -j 8 -f system.mk/Makefile.linux
make[2]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg'
make[2]: warning: -jN forced in submake: disabling jobserver mode.
rm -rf bin
rm -rf bin
rm -rf bin
make -C applications/bed/bedmap/src -f Makefile clean
make -C applications/bed/sort-bed/src -f Makefile clean
make -C applications/bed/bedops/src -f Makefile clean
make -C applications/bed/closestfeats/src -f Makefile clean
make -C applications/bed/bedextract/src -f Makefile clean
make -C applications/bed/starch/src -f Makefile clean
make -C applications/bed/conversion/src -f Makefile clean
rm -rf modules
make[3]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/sort-bed/src'
make[3]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/bedops/src'
rm -rf objects_typical
make[3]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/bedmap/src'
rm -rf objects_typical
rm -rf ../bin
make[3]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/closestfeats/src'
make[3]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/conversion/src'
rm -rf objects_typical
rm -rf ../bin
make[3]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/bedextract/src'
rm -rf objects_typical
rm -rf objects-typical
rm -rf objects
rm -rf ../bin
make[3]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/starch/src'
make[3]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/bedops/src'
rm -rf ../lib
rm -rf ../bin
rm -rf ../bin
rm -rf ../bin
make[3]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/bedmap/src'
make[3]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/sort-bed/src'
make[3]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/closestfeats/src'
rm -f ../lib/libstarch_debug.a
rm -rf *.so *~
make[3]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/bedextract/src'
rm -f ../lib/libstarch_gprof.a
rm -rf objects
make[3]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/conversion/src'
rm -rf ../bin
make[3]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/starch/src'
rm -rf third-party/bzip2-1.0.6
rm -f third-party/bzip2
rm -rf third-party/jansson-2.6
rm -f third-party/jansson
rm -rf third-party/zlib-1.2.7
rm -f third-party/zlib
rm -rf bin
make[2]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg'
dh_clean
debian/rules build-arch
dh build-arch --with sphinxdoc
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
dh_auto_build -a
make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg'
make -j 8 -f system.mk/Makefile.linux
make[2]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg'
make[2]: warning: -jN forced in submake: disabling jobserver mode.
#bzcat | tar -x -C third-party
#cd third-party/jansson-2.6 && ./configure --prefix=/<<BUILDDIR>>/bedops-2.4.35+dfsg/third-party/jansson-2.6 && make && make install && cd /<<BUILDDIR>>/bedops-2.4.35+dfsg && rm -f jansson && ln -sf jansson-2.6 third-party/jansson
#bzcat | tar -x -C third-party
#cd third-party/bzip2-1.0.6 && make libbz2.a && cd /<<BUILDDIR>>/bedops-2.4.35+dfsg && rm -f bzip2 && ln -sf bzip2-1.0.6 third-party/bzip2
#bzcat | tar -x -C third-party
#cd third-party/zlib-1.2.7 && ./configure --static && make && cd /<<BUILDDIR>>/bedops-2.4.35+dfsg && rm -f zlib && ln -sf zlib-1.2.7 third-party/zlib
make build -f /<<BUILDDIR>>/bedops-2.4.35+dfsg/system.mk/Makefile.linux
make[3]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg'
make -C applications/bed/bedmap/src -f Makefile build
make -C applications/bed/sort-bed/src -f Makefile build
make -C applications/bed/bedops/src -f Makefile build
make -C applications/bed/closestfeats/src -f Makefile build
make -C applications/bed/bedextract/src -f Makefile build
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/bedmap/src'
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/sort-bed/src'
make -C applications/bed/starch/src -f Makefile build
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers
make -C applications/bed/conversion/src -f Makefile build
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/closestfeats/src'
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/starch/src'
mkdir -p objects
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects-typical/starchConstants.o -iquote../../../../interfaces/general-headers
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/bedops/src'
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchConstants.c -o objects/starchConstants.o -iquote../../../../interfaces/general-headers -iquote../../../..
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/conversion/src'
mkdir -p ../bin && gcc -Wall -Wextra -pedantic -std=c99 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -O3 -iquote"/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/conversion/src" -iquote"../../../../interfaces/general-headers" convert2bed.c -o ../bin/convert2bed-typical -lpthread
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/bedextract/src'
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects-typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects/unstarchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects-typical/starchHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects-typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)':
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:982:24: warning: comparison is always true due to limited range of data type [-Wtype-limits]
} while (currC != EOF);
^
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
../../../../interfaces/src/data/starch/starchHelpers.c:1976:77: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchHelpers.c:2666:57: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
convert2bed.c: In function 'c2b_process_intermediate_bytes_by_lines':
convert2bed.c:6086:103: warning: format '%zu' expects argument of type 'size_t', but argument 3 has type 'long unsigned int' [-Wformat=]
fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity);
~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
%lu
convert2bed.c:6086:109: warning: format '%zu' expects argument of type 'size_t', but argument 4 has type 'long unsigned int' [-Wformat=]
fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity);
~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
%lu
convert2bed.c:6086:115: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'long unsigned int' [-Wformat=]
fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity);
~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
%lu
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
../../../../interfaces/src/data/starch/starchHelpers.c:3135:77: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchHelpers.c:3843:57: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
../../../../interfaces/src/data/starch/starchHelpers.c:1976:77: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchHelpers.c:2666:57: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
../../../../interfaces/src/data/starch/starchHelpers.c:3135:77: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchHelpers.c:3843:57: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
../../../../interfaces/src/data/starch/starchHelpers.c:1976:77: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
mkdir -p objects
../../../../interfaces/src/data/starch/starchHelpers.c:2666:57: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchHelpers.c -o objects/starchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p objects
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../..
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
../../../../interfaces/src/data/starch/starchHelpers.c:3135:77: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
../../../../interfaces/src/data/starch/starchHelpers.c:1976:77: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchHelpers.c:3843:57: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchHelpers.c:2666:57: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
../../../../interfaces/src/data/starch/starchHelpers.c:3135:77: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchHelpers.c:3843:57: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)':
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:982:24: warning: comparison is always true due to limited range of data type [-Wtype-limits]
} while (currC != EOF);
^
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
../../../../interfaces/src/data/starch/starchHelpers.c:1976:77: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchHelpers.c:2666:57: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
../../../../interfaces/src/data/starch/starchHelpers.c:3135:77: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
../../../../interfaces/src/data/starch/starchHelpers.c:1976:77: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchHelpers.c:3843:57: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchHelpers.c:2666:57: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
../../../../interfaces/src/data/starch/starchHelpers.c:3135:77: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
../../../../interfaces/src/data/starch/starchHelpers.c:3843:57: warning: left shift count >= width of type [-Wshift-count-overflow]
bzBytesWritten = (size_t) bzBytesWrittenHi32 << 32 | bzBytesWrittenLo32;
^~
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects-typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects-typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects/starchFileHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers
mkdir -p objects
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects/starchSha1Digest.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 SortDetails.cpp -o objects-typical/SortDetails.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers
rm -rf objects
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/conversion/src'
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers
mkdir -p objects
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects/starchBase64Coding.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p ../bin && g++ -o ../bin/bedmap-typical -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 Bedmap.cpp
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers
mkdir -p ../bin
cp starchcluster_gnuParallel.tcsh ../bin/starchcluster_gnuParallel-typical
mkdir -p ../bin
cp starchcluster_sge.tcsh ../bin/starchcluster_sge-typical
mkdir -p ../bin
cp starchcluster_slurm.tcsh ../bin/starchcluster_slurm-typical
mkdir -p ../bin
cp starch-diff.py ../bin/starch-diff-typical
mkdir -p ../lib
ar rcs ../lib/libstarch.a objects/starchConstants.o objects/unstarchHelpers.o objects/starchHelpers.o objects/starchMetadataHelpers.o objects/starchFileHelpers.o objects/starchSha1Digest.o objects/starchBase64Coding.o
mkdir -p ../bin
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starch.c -o objects/starch.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starch.o -o ../bin/starch-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now
mkdir -p ../bin
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c unstarch.c -o objects/unstarch.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p ../bin && g++ -o ../bin/closest-features-typical -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 ClosestFeature.cpp
mkdir -p ../bin
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starchcat.c -o objects/starchcat.o -iquote../../../../interfaces/general-headers -iquote../../../..
starchcat.c:6672:5: warning: this use of "defined" may not be portable [-Wexpansion-to-defined]
#if CLANG_COMPILER
^~~~~~~~~~~~~~
starchcat.c:6678:5: warning: this use of "defined" may not be portable [-Wexpansion-to-defined]
#if CLANG_COMPILER
^~~~~~~~~~~~~~
starchcat.c: In function 'int starch::STARCHCAT2_rewriteInputRecordToOutput(starch::Metadata**, const char*, starch::CompressionType, const char*, const MetadataRecord*, size_t*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
starchcat.c:2038:67: warning: left shift count >= width of type [-Wshift-count-overflow]
bzOutBytesWritten = (size_t) bzOutBytesWrittenHi32 << 32 | bzOutBytesWrittenLo32;
^~
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/unstarch.o -o ../bin/unstarch-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers
mkdir -p ../bin
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starchstrip.c -o objects/starchstrip.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p ../bin && g++ -o ../bin/bedextract-typical -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 ExtractRows.cpp
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers
mkdir -p ../bin && g++ -o ../bin/bedops-typical -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 Bedops.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starchstrip.o -o ../bin/starchstrip-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now
mkdir -p ../bin && cp update-sort-bed-slurm.py ../bin/update-sort-bed-slurm-typical
mkdir -p ../bin && cp update-sort-bed-starch-slurm.py ../bin/update-sort-bed-starch-slurm-typical
mkdir -p ../bin && cp update-sort-bed-migrate-candidates.py ../bin/update-sort-bed-migrate-candidates-typical
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starchcat.o -o ../bin/starchcat-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now
rm -rf objects
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/starch/src'
mkdir -p ../bin && g++ -o ../bin/sort-bed-typical -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now objects-typical/starchConstants.o objects-typical/starchFileHelpers.o objects-typical/starchHelpers.o objects-typical/starchMetadataHelpers.o objects-typical/unstarchHelpers.o objects-typical/starchSha1Digest.o objects-typical/starchBase64Coding.o objects-typical/SortDetails.o objects-typical/Sort.o objects-typical/CheckSort.o -ljansson -lz -lbz2
rm -rf objects-typical
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/sort-bed/src'
rm -rf objects_typical
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/bedextract/src'
rm -rf objects_typical
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/closestfeats/src'
rm -rf objects_typical
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/bedops/src'
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:28,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:35:
/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, std::allocator<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, std::allocator<double> > >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:28,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:35:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introselect(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1977:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
__introselect(_RandomAccessIterator __first, _RandomAccessIterator __nth,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1977:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1977:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::nth_element(_RAIter, _RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >]':
/usr/include/c++/7/bits/stl_algo.h:4750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
nth_element(_RandomAccessIterator __first, _RandomAccessIterator __nth,
^~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:4750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:4750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:4765:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
std::__introselect(__first, __nth, __last,
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__gnu_cxx::__ops::__iter_less_iter());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/algorithm/visitors/NumericalVisitors.hpp:32:0,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:34,
from Bedmap.cpp:35:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::Visitor<Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::Visitor<Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapMapping, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapMapping, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::Visitor<Bed::BasicCoords<true, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::Visitor<Bed::NoPool::BasicCoords<true, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapMapping, Bed::BasicCoords<true, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapMapping, Bed::NoPool::BasicCoords<true, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapReference, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapReference, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapReference, Bed::BasicCoords<true, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapReference, Bed::NoPool::BasicCoords<true, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapBoth, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapBoth, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapBoth, Bed::BasicCoords<true, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapBoth, Bed::NoPool::BasicCoords<true, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapEither, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapEither, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapEither, Bed::BasicCoords<true, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapEither, Bed::NoPool::BasicCoords<true, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::RangedDist, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::RangedDist, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::RangedDist, Bed::BasicCoords<true, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::RangedDist, Bed::NoPool::BasicCoords<true, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::Overlapping, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::Overlapping, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::Overlapping, Bed::BasicCoords<true, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function 'void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::Overlapping, Bed::NoPool::BasicCoords<true, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]':
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
std::nth_element(vec.begin(), n, vec.end());
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
rm -rf objects_typical
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg/applications/bed/bedmap/src'
make[3]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --with sphinxdoc
dh_testroot -a
dh_prep -a
dh_auto_install -a
make -j4 install DESTDIR=/<<BUILDDIR>>/bedops-2.4.35\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg'
mkdir -p bin
cp applications/bed/conversion/src/wrappers/gvf2starch applications/bed/conversion/src/wrappers/bam2bed_gnuParallel applications/bed/conversion/src/wrappers/bam2starch_sge applications/bed/conversion/src/wrappers/bam2starch_slurm applications/bed/conversion/src/wrappers/psl2bed applications/bed/conversion/src/wrappers/bam2starch_gnuParallel applications/bed/conversion/src/wrappers/gff2starch applications/bed/conversion/src/wrappers/wig2bed applications/bed/conversion/src/wrappers/sam2bed applications/bed/conversion/src/wrappers/psl2starch applications/bed/conversion/src/wrappers/rmsk2bed applications/bed/conversion/src/wrappers/gtf2bed applications/bed/conversion/src/wrappers/vcf2bed applications/bed/conversion/src/wrappers/wig2starch applications/bed/conversion/src/wrappers/sam2starch applications/bed/conversion/src/wrappers/vcf2starch applications/bed/conversion/src/wrappers/rmsk2starch applications/bed/conversion/src/wrappers/bam2bed applications/bed/conversion/src/wrappers/gtf2starch applications/bed/conversion/src/wrappers/gff2bed applications/bed/conversion/src/wrappers/bam2starch applications/bed/conversion/src/wrappers/gvf2bed applications/bed/conversion/src/wrappers/bam2bed_sge applications/bed/conversion/src/wrappers/bam2bed_slurm bin
cp applications/bed/starch/bin/starchcluster_sge-typical bin/starchcluster_sge
cp applications/bed/starch/bin/starchcluster_gnuParallel-typical bin/starchcluster_gnuParallel
cp applications/bed/starch/bin/starchcluster_slurm-typical bin/starchcluster_slurm
cp applications/bed/starch/bin/starch-diff-typical bin/starch-diff
cp applications/bed/sort-bed/bin/sort-bed-typical bin/sort-bed
cp applications/bed/sort-bed/bin/update-sort-bed-slurm-typical bin/update-sort-bed-slurm
cp applications/bed/sort-bed/bin/update-sort-bed-starch-slurm-typical bin/update-sort-bed-starch-slurm
cp applications/bed/sort-bed/bin/update-sort-bed-migrate-candidates-typical bin/update-sort-bed-migrate-candidates
cp applications/bed/bedops/bin/bedops-typical bin/bedops
cp applications/bed/closestfeats/bin/closest-features-typical bin/closest-features
cp applications/bed/bedmap/bin/bedmap-typical bin/bedmap
cp applications/bed/bedextract/bin/bedextract-typical bin/bedextract
cp applications/bed/starch/bin/starch-typical bin/starch
cp applications/bed/starch/bin/unstarch-typical bin/unstarch
cp applications/bed/starch/bin/starchcat-typical bin/starchcat
cp applications/bed/starch/bin/starchstrip-typical bin/starchstrip
cp applications/bed/conversion/bin/convert2bed-typical bin/convert2bed
make[1]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg'
debian/rules override_dh_install-arch
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg'
dh_install -a
sed -i 's:/bin/tcsh:/usr/bin/tcsh:g' bin/*
mv bin/starch bin/bedops-starch
mkdir -p debian/bedops/usr/bin/
cp bin/* debian/bedops/usr/bin/
make[1]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg'
dh_installdocs -a
dh_sphinxdoc -a
dh_sphinxdoc: Sphinx documentation not found
dh_installchangelogs -a
debian/rules override_dh_installman-arch
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg'
cd bin && for f in * ; do help2man --no-discard-stderr --version-string="2.4.35+dfsg" -o $f.1 ./$f; done
help2man: can't get `--help' info from ./bam2bed_gnuParallel
help2man: can't get `--help' info from ./bam2bed_sge
help2man: can't get `--help' info from ./bam2bed_slurm
help2man: can't get `--help' info from ./bam2starch_gnuParallel
help2man: can't get `--help' info from ./bam2starch_sge
help2man: can't get `--help' info from ./bam2starch_slurm
help2man: can't get `--help' info from ./starchcluster_gnuParallel
help2man: can't get `--help' info from ./starchcluster_sge
help2man: can't get `--help' info from ./starchcluster_slurm
dh_installman -a
make[1]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.35+dfsg'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/bedops/usr/bin/sort-bed contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/bedops/usr/bin/bedops contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/bedops/usr/bin/bedmap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/bedops/usr/bin/closest-features contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/bedops/usr/bin/bedextract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/bedops/usr/bin/bedops debian/bedops/usr/bin/starchstrip debian/bedops/usr/bin/bedmap debian/bedops/usr/bin/unstarch debian/bedops/usr/bin/closest-features debian/bedops/usr/bin/bedops-starch debian/bedops/usr/bin/bedextract debian/bedops/usr/bin/starchcat were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.35+dfsg-1_armhf.deb'.
dpkg-deb: building package 'bedops' in '../bedops_2.4.35+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../bedops_2.4.35+dfsg-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build bedops-2.4.35+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-05-29T04:59:48Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
bedops_2.4.35+dfsg-1_armhf.changes:
-----------------------------------
Format: 1.8
Date: Wed, 23 May 2018 17:43:00 +0200
Source: bedops
Binary: bedops bedops-doc
Architecture: armhf
Version: 2.4.35+dfsg-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
bedops - high-performance genomic feature operations
bedops-doc - high-performance genomic feature operations (documentation)
Changes:
bedops (2.4.35+dfsg-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.4
Checksums-Sha1:
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10ba2157e18bb945d22bd8b0267a4a36d4682278 6356 bedops_2.4.35+dfsg-1_armhf.buildinfo
d0d9a88e12ecf5af45823e0000289cf5965c305e 812076 bedops_2.4.35+dfsg-1_armhf.deb
Checksums-Sha256:
8b7b28cd31759f0dc4a2f326c11edb1b09ee08b8861c8903ed910f58bc23691b 4152 bedops-dbgsym_2.4.35+dfsg-1_armhf.deb
29d49d1194f60f21ccc32a212eb111a58f3a6446681212e26125dbb40c808b2c 6356 bedops_2.4.35+dfsg-1_armhf.buildinfo
4d48a354941735156b8c706fe2eefa2047bbed5602e80d9929c84a3edfe9e2da 812076 bedops_2.4.35+dfsg-1_armhf.deb
Files:
d1deee0003ba21a5a52ec81cd6638504 4152 debug optional bedops-dbgsym_2.4.35+dfsg-1_armhf.deb
d6d78d05331e921149e26dae19f40484 6356 science optional bedops_2.4.35+dfsg-1_armhf.buildinfo
db5ea88db1bc925a30618c194f05a62d 812076 science optional bedops_2.4.35+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
bedops-dbgsym_2.4.35+dfsg-1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 4152 bytes: control archive=536 bytes.
377 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: bedops-dbgsym
Source: bedops
Version: 2.4.35+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 21
Depends: bedops (= 2.4.35+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for bedops
Build-Ids: 80824dbd28091ff26feea543fd235ac442d00c7b
drwxr-xr-x root/root 0 2018-05-23 15:43 ./
drwxr-xr-x root/root 0 2018-05-23 15:43 ./usr/
drwxr-xr-x root/root 0 2018-05-23 15:43 ./usr/lib/
drwxr-xr-x root/root 0 2018-05-23 15:43 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-05-23 15:43 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-05-23 15:43 ./usr/lib/debug/.build-id/80/
-rw-r--r-- root/root 10688 2018-05-23 15:43 ./usr/lib/debug/.build-id/80/824dbd28091ff26feea543fd235ac442d00c7b.debug
drwxr-xr-x root/root 0 2018-05-23 15:43 ./usr/share/
drwxr-xr-x root/root 0 2018-05-23 15:43 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-05-23 15:43 ./usr/share/doc/bedops-dbgsym -> bedops
bedops_2.4.35+dfsg-1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 812076 bytes: control archive=2580 bytes.
729 bytes, 15 lines control
4710 bytes, 76 lines md5sums
Package: bedops
Version: 2.4.35+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5948
Depends: libbz2-1.0, libc6 (>= 2.7), libgcc1 (>= 1:3.5), libjansson4 (>= 2.3), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), python, tcsh
Section: science
Priority: optional
Homepage: https://github.com/bedops/bedops
Description: high-performance genomic feature operations
BEDOPS is a suite of tools to address common questions raised in genomic
studies, mostly with regard to overlap and proximity relationships between
data sets.
It aims to be scalable and flexible, facilitating the efficient and accurate
analysis and management of large-scale genomic data.
drwxr-xr-x root/root 0 2018-05-23 15:43 ./
drwxr-xr-x root/root 0 2018-05-23 15:43 ./usr/
drwxr-xr-x root/root 0 2018-05-23 15:43 ./usr/bin/
-rwxr-xr-x root/root 4711 2018-05-23 15:43 ./usr/bin/bam2bed
-rwxr-xr-x root/root 4505 2018-05-23 15:43 ./usr/bin/bam2bed_gnuParallel
-rwxr-xr-x root/root 5030 2018-05-23 15:43 ./usr/bin/bam2bed_sge
-rwxr-xr-x root/root 5025 2018-05-23 15:43 ./usr/bin/bam2bed_slurm
-rwxr-xr-x root/root 5842 2018-05-23 15:43 ./usr/bin/bam2starch
-rwxr-xr-x root/root 4511 2018-05-23 15:43 ./usr/bin/bam2starch_gnuParallel
-rwxr-xr-x root/root 5084 2018-05-23 15:43 ./usr/bin/bam2starch_sge
-rwxr-xr-x root/root 5018 2018-05-23 15:43 ./usr/bin/bam2starch_slurm
-rwxr-xr-x root/root 161208 2018-05-23 15:43 ./usr/bin/bedextract
-rwxr-xr-x root/root 4425168 2018-05-23 15:43 ./usr/bin/bedmap
-rwxr-xr-x root/root 325048 2018-05-23 15:43 ./usr/bin/bedops
-rwxr-xr-x root/root 75332 2018-05-23 15:43 ./usr/bin/bedops-starch
-rwxr-xr-x root/root 193980 2018-05-23 15:43 ./usr/bin/closest-features
-rwxr-xr-x root/root 104660 2018-05-23 15:43 ./usr/bin/convert2bed
-rwxr-xr-x root/root 3773 2018-05-23 15:43 ./usr/bin/gff2bed
-rwxr-xr-x root/root 4904 2018-05-23 15:43 ./usr/bin/gff2starch
-rwxr-xr-x root/root 3532 2018-05-23 15:43 ./usr/bin/gtf2bed
-rwxr-xr-x root/root 4663 2018-05-23 15:43 ./usr/bin/gtf2starch
-rwxr-xr-x root/root 3773 2018-05-23 15:43 ./usr/bin/gvf2bed
-rwxr-xr-x root/root 4904 2018-05-23 15:43 ./usr/bin/gvf2starch
-rwxr-xr-x root/root 3976 2018-05-23 15:43 ./usr/bin/psl2bed
-rwxr-xr-x root/root 5107 2018-05-23 15:43 ./usr/bin/psl2starch
-rwxr-xr-x root/root 3776 2018-05-23 15:43 ./usr/bin/rmsk2bed
-rwxr-xr-x root/root 4907 2018-05-23 15:43 ./usr/bin/rmsk2starch
-rwxr-xr-x root/root 4711 2018-05-23 15:43 ./usr/bin/sam2bed
-rwxr-xr-x root/root 5842 2018-05-23 15:43 ./usr/bin/sam2starch
-rwxr-xr-x root/root 185780 2018-05-23 15:43 ./usr/bin/sort-bed
-rwxr-xr-x root/root 10260 2018-05-23 15:43 ./usr/bin/starch-diff
-rwxr-xr-x root/root 144948 2018-05-23 15:43 ./usr/bin/starchcat
-rwxr-xr-x root/root 4303 2018-05-23 15:43 ./usr/bin/starchcluster_gnuParallel
-rwxr-xr-x root/root 4818 2018-05-23 15:43 ./usr/bin/starchcluster_sge
-rwxr-xr-x root/root 4720 2018-05-23 15:43 ./usr/bin/starchcluster_slurm
-rwxr-xr-x root/root 79364 2018-05-23 15:43 ./usr/bin/starchstrip
-rwxr-xr-x root/root 107956 2018-05-23 15:43 ./usr/bin/unstarch
-rwxr-xr-x root/root 32771 2018-05-23 15:43 ./usr/bin/update-sort-bed-migrate-candidates
-rwxr-xr-x root/root 20786 2018-05-23 15:43 ./usr/bin/update-sort-bed-slurm
-rwxr-xr-x root/root 22767 2018-05-23 15:43 ./usr/bin/update-sort-bed-starch-slurm
-rwxr-xr-x root/root 4675 2018-05-23 15:43 ./usr/bin/vcf2bed
-rwxr-xr-x root/root 5806 2018-05-23 15:43 ./usr/bin/vcf2starch
-rwxr-xr-x root/root 4598 2018-05-23 15:43 ./usr/bin/wig2bed
-rwxr-xr-x root/root 5729 2018-05-23 15:43 ./usr/bin/wig2starch
drwxr-xr-x root/root 0 2018-05-23 15:43 ./usr/share/
drwxr-xr-x root/root 0 2018-05-23 15:43 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-05-23 15:43 ./usr/share/doc/bedops/
-rw-r--r-- root/root 267 2018-05-23 15:43 ./usr/share/doc/bedops/README.Debian
-rw-r--r-- root/root 787 2018-05-23 15:43 ./usr/share/doc/bedops/changelog.Debian.gz
-rw-r--r-- root/root 1129 2018-05-23 15:43 ./usr/share/doc/bedops/copyright
drwxr-xr-x root/root 0 2018-05-23 15:43 ./usr/share/man/
drwxr-xr-x root/root 0 2018-05-23 15:43 ./usr/share/man/man1/
-rw-r--r-- root/root 348 2018-05-23 15:43 ./usr/share/man/man1/bam2bed.1.gz
-rw-r--r-- root/root 355 2018-05-23 15:43 ./usr/share/man/man1/bam2starch.1.gz
-rw-r--r-- root/root 848 2018-05-23 15:43 ./usr/share/man/man1/bedextract.1.gz
-rw-r--r-- root/root 2506 2018-05-23 15:43 ./usr/share/man/man1/bedmap.1.gz
-rw-r--r-- root/root 1044 2018-05-23 15:43 ./usr/share/man/man1/bedops-starch.1.gz
-rw-r--r-- root/root 1391 2018-05-23 15:43 ./usr/share/man/man1/bedops.1.gz
-rw-r--r-- root/root 1277 2018-05-23 15:43 ./usr/share/man/man1/closest-features.1.gz
-rw-r--r-- root/root 1222 2018-05-23 15:43 ./usr/share/man/man1/convert2bed.1.gz
-rw-r--r-- root/root 348 2018-05-23 15:43 ./usr/share/man/man1/gff2bed.1.gz
-rw-r--r-- root/root 356 2018-05-23 15:43 ./usr/share/man/man1/gff2starch.1.gz
-rw-r--r-- root/root 348 2018-05-23 15:43 ./usr/share/man/man1/gtf2bed.1.gz
-rw-r--r-- root/root 355 2018-05-23 15:43 ./usr/share/man/man1/gtf2starch.1.gz
-rw-r--r-- root/root 349 2018-05-23 15:43 ./usr/share/man/man1/gvf2bed.1.gz
-rw-r--r-- root/root 356 2018-05-23 15:43 ./usr/share/man/man1/gvf2starch.1.gz
-rw-r--r-- root/root 347 2018-05-23 15:43 ./usr/share/man/man1/psl2bed.1.gz
-rw-r--r-- root/root 355 2018-05-23 15:43 ./usr/share/man/man1/psl2starch.1.gz
-rw-r--r-- root/root 350 2018-05-23 15:43 ./usr/share/man/man1/rmsk2bed.1.gz
-rw-r--r-- root/root 358 2018-05-23 15:43 ./usr/share/man/man1/rmsk2starch.1.gz
-rw-r--r-- root/root 348 2018-05-23 15:43 ./usr/share/man/man1/sam2bed.1.gz
-rw-r--r-- root/root 355 2018-05-23 15:43 ./usr/share/man/man1/sam2starch.1.gz
-rw-r--r-- root/root 739 2018-05-23 15:43 ./usr/share/man/man1/sort-bed.1.gz
-rw-r--r-- root/root 364 2018-05-23 15:43 ./usr/share/man/man1/starch-diff.1.gz
-rw-r--r-- root/root 988 2018-05-23 15:43 ./usr/share/man/man1/starchcat.1.gz
-rw-r--r-- root/root 1110 2018-05-23 15:43 ./usr/share/man/man1/starchstrip.1.gz
-rw-r--r-- root/root 1544 2018-05-23 15:43 ./usr/share/man/man1/unstarch.1.gz
-rw-r--r-- root/root 394 2018-05-23 15:43 ./usr/share/man/man1/update-sort-bed-migrate-candidates.1.gz
-rw-r--r-- root/root 380 2018-05-23 15:43 ./usr/share/man/man1/update-sort-bed-slurm.1.gz
-rw-r--r-- root/root 391 2018-05-23 15:43 ./usr/share/man/man1/update-sort-bed-starch-slurm.1.gz
-rw-r--r-- root/root 348 2018-05-23 15:43 ./usr/share/man/man1/vcf2bed.1.gz
-rw-r--r-- root/root 356 2018-05-23 15:43 ./usr/share/man/man1/vcf2starch.1.gz
-rw-r--r-- root/root 348 2018-05-23 15:43 ./usr/share/man/man1/wig2bed.1.gz
-rw-r--r-- root/root 356 2018-05-23 15:43 ./usr/share/man/man1/wig2starch.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 53920
Build-Time: 778
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 410
Job: bedops_2.4.35+dfsg-1
Machine Architecture: armhf
Package: bedops
Package-Time: 1216
Source-Version: 2.4.35+dfsg-1
Space: 53920
Status: successful
Version: 2.4.35+dfsg-1
--------------------------------------------------------------------------------
Finished at 2018-05-29T04:59:48Z
Build needed 00:20:16, 53920k disk space