bedops →
2.4.37+dfsg-1 →
armhf → 2019-10-26 08:58:06
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| bedops 2.4.37+dfsg-1 (armhf) Sat, 26 Oct 2019 05:00:28 +0000 |
+==============================================================================+
Package: bedops
Version: 2.4.37+dfsg-1
Source Version: 2.4.37+dfsg-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-e92f4d8b-c867-4a09-8eec-cc8f1b122c21' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.4 MB in 27s (891 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 bullseye-staging/main bedops 2.4.37+dfsg-1 (dsc) [2144 B]
Get:2 http://172.17.0.1/private bullseye-staging/main bedops 2.4.37+dfsg-1 (tar) [15.3 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main bedops 2.4.37+dfsg-1 (diff) [9884 B]
Fetched 15.3 MB in 2s (9157 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bedops-iyoWng/bedops-2.4.37+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bedops-iyoWng' 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-8G0ry5/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-8G0ry5/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-8G0ry5/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-8G0ry5/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-8G0ry5/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-8G0ry5/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-8G0ry5/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-8G0ry5/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2825 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:
libpam-cap netbase
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 10 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-8G0ry5/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12228 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), help2man, libbz2-dev, libjansson-dev, libjs-mathjax, python3-distutils, python3-sphinx, zlib1g-dev
Filtered Build-Depends: debhelper-compat (= 12), 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-8G0ry5/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-8G0ry5/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-8G0ry5/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-8G0ry5/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-8G0ry5/apt_archive ./ Sources [548 B]
Get:5 copy:/<<BUILDDIR>>/resolver-8G0ry5/apt_archive ./ Packages [626 B]
Fetched 2507 B in 1s (3317 B/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:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils ca-certificates
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 libdebhelper-perl libelf1
libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu63
libjansson-dev libjansson4 libjs-jquery libjs-mathjax libjs-sphinxdoc
libjs-underscore liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2
libncurses6 libpipeline1 libpython3-stdlib libpython3.7-minimal
libpython3.7-stdlib libsigsegv2 libssl1.1 libsub-override-perl libtinfo5
libtool libuchardet0 libxml2 m4 man-db mime-support openssl po-debconf
python-babel-localedata python3 python3-alabaster python3-attr 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 python3.7
python3.7-minimal sensible-utils sgml-base sphinx-common xml-core 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 python-attr-doc
docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french
texlive-latex-base texlive-latex-recommended python-jinja2-doc
python3-setuptools python-pygments-doc ttf-bitstream-vera
python-pyparsing-doc python3-cryptography python3-openssl python3-socks
dvipng imagemagick-6.q16 latexmk python3-sphinx-rtd-theme python3-stemmer
sphinx-doc texlive-fonts-recommended texlive-latex-extra
texlive-plain-generic python3.7-venv python3.7-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 ca-certificates
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 libdebhelper-perl libelf1
libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu63
libjansson-dev libjansson4 libjs-jquery libjs-mathjax libjs-sphinxdoc
libjs-underscore liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2
libncurses6 libpipeline1 libpython3-stdlib libpython3.7-minimal
libpython3.7-stdlib libsigsegv2 libssl1.1 libsub-override-perl libtinfo5
libtool libuchardet0 libxml2 m4 man-db mime-support openssl po-debconf
python-babel-localedata python3 python3-alabaster python3-attr 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 python3.7
python3.7-minimal sbuild-build-depends-bedops-dummy sensible-utils sgml-base
sphinx-common xml-core zlib1g-dev
0 upgraded, 88 newly installed, 0 to remove and 10 not upgraded.
Need to get 41.7 MB of archives.
After this operation, 186 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-8G0ry5/apt_archive ./ sbuild-build-depends-bedops-dummy 0.invalid.0 [916 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf liblocale-gettext-perl armhf 1.07-3+b5 [18.3 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20190803-1 [314 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.8.7-3 [1254 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.5~rc1-2 [584 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3.7-minimal armhf 3.7.5~rc1-2 [1524 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.7.5-1 [36.6 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-stdlib armhf 3.7.5~rc1-2 [1667 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.5~rc1-2 [347 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.7.5-1 [20.1 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.7.5-1 [61.5 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf sgml-base all 1.29.1 [15.0 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-6 [253 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-6 [111 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf openssl armhf 1.1.1d-2 [806 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates all 20190110 [157 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.1-1 [23.5 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.1-1 [14.4 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-1 [69.7 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.7 [173 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.1-1 [1134 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b2 [571 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20190803-1 [79.3 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7 [995 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf xml-core all 0.18+nmu1 [23.8 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf docutils-common all 0.15.2+dfsg-1 [167 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf fonts-mathjax all 2.7.4+dfsg-1 [2209 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf help2man armhf 1.47.11 [180 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-2 [27.7 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libjansson4 armhf 2.12-1 [34.6 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libjansson-dev armhf 2.12-1 [35.0 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libjs-jquery all 3.3.1~dfsg-3 [332 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libjs-mathjax all 2.7.4+dfsg-1 [5658 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libjs-underscore all 1.9.1~dfsg-1 [99.4 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libjs-sphinxdoc all 1.8.5-3 [96.5 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf python-babel-localedata all 2.6.0+dfsg.1-1 [4083 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf python3-attr all 18.2.0-1 [37.3 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf python3-pkg-resources all 41.2.0-1 [154 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf python3-tz all 2019.3-1 [27.2 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf python3-babel all 2.6.0+dfsg.1-1 [96.7 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf python3-certifi all 2018.8.24-1 [140 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf python3-chardet all 3.0.4-4 [80.8 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.7.5-1 [78.3 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.7.5-1 [145 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf python3-roman all 2.0.0-3 [8768 B]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf python3-docutils all 0.15.2+dfsg-1 [381 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf python3-idna all 2.6-2 [34.4 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf python3-imagesize all 1.0.0-1 [4960 B]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf python3-markupsafe armhf 1.1.0-1 [14.4 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf python3-jinja2 all 2.10.1-1 [107 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf python3-pyparsing all 2.4.2-1 [106 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf python3-six all 1.12.0-2 [15.8 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf python3-packaging all 19.1-2 [23.9 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf python3-pygments all 2.3.1+dfsg-1 [594 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf python3-urllib3 all 1.24.1-1 [97.1 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf python3-requests all 2.21.0-1 [66.9 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf sphinx-common all 1.8.5-3 [501 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf python3-alabaster all 0.7.8-1 [18.4 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf python3-sphinx all 1.8.5-3 [482 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
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No schema files found: doing nothing.
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Setting up libtool (2.4.6-11) ...
Setting up m4 (1.4.18-2) ...
Setting up help2man (1.47.11) ...
Setting up ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
128 added, 0 removed; done.
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
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Setting up libjs-sphinxdoc (1.8.5-3) ...
Setting up autoconf (2.69-11) ...
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Setting up gettext (0.19.8.1-9) ...
Setting up python3 (3.7.5-1) ...
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Not building database; man-db/auto-update is not 'true'.
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Setting up python3-pkg-resources (41.2.0-1) ...
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Setting up python3-babel (2.6.0+dfsg.1-1) ...
update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode
Setting up python3-alabaster (0.7.8-1) ...
Setting up po-debconf (1.0.21) ...
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Setting up python3-chardet (3.0.4-4) ...
Setting up python3-requests (2.21.0-1) ...
Setting up dh-autoreconf (19) ...
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Setting up debhelper (12.7) ...
Processing triggers for libc-bin (2.29-2+rpi1) ...
Processing triggers for sgml-base (1.29.1) ...
Setting up docutils-common (0.15.2+dfsg-1) ...
Processing triggers for sgml-base (1.29.1) ...
Setting up python3-docutils (0.15.2+dfsg-1) ...
update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode
Setting up python3-sphinx (1.8.5-3) ...
update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-apidoc to provide /usr/bin/sphinx-apidoc (sphinx-apidoc) in auto mode
update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-autogen to provide /usr/bin/sphinx-autogen (sphinx-autogen) in auto mode
update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-build to provide /usr/bin/sphinx-build (sphinx-build) in auto mode
update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-quickstart to provide /usr/bin/sphinx-quickstart (sphinx-quickstart) in auto mode
Setting up sbuild-build-depends-bedops-dummy (0.invalid.0) ...
Processing triggers for ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.32.51.20190909-1+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-8+rpi1 gcc-9_9.2.1-8+rpi1 libc6-dev_2.29-2+rpi1 libstdc++-9-dev_9.2.1-8+rpi1 libstdc++6_9.2.1-8+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.46 bash_5.0-4 binutils_2.32.51.20190909-1+rpi1 binutils-arm-linux-gnueabihf_2.32.51.20190909-1+rpi1 binutils-common_2.32.51.20190909-1+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 ca-certificates_20190110 coreutils_8.30-3 cpp_4:9.2.1-3+rpi1 cpp-9_9.2.1-8+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7 debianutils_4.9 dh-autoreconf_19 dh-strip-nondeterminism_1.6.1-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 docutils-common_0.15.2+dfsg-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-1 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 fonts-mathjax_2.7.4+dfsg-1 g++_4:9.2.1-3+rpi1 g++-9_9.2.1-8+rpi1 gcc_4:9.2.1-3+rpi1 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1+b3 gcc-7-base_7.4.0-14 gcc-9_9.2.1-8+rpi1 gcc-9-base_9.2.1-8+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.17-3 gnupg-l10n_2.2.17-3 gnupg-utils_2.2.17-3+b1 gpg_2.2.17-3+b1 gpg-agent_2.2.17-3+b1 gpg-wks-client_2.2.17-3+b1 gpg-wks-server_2.2.17-3+b1 gpgconf_2.2.17-3+b1 gpgsm_2.2.17-3+b1 gpgv_2.2.17-3+b1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 help2man_1.47.11 hostname_3.22 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-8+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-8+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2 libbinutils_2.32.51.20190909-1+rpi1 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libbz2-dev_1.0.8-2 libc-bin_2.29-2+rpi1 libc-dev-bin_2.29-2+rpi1 libc6_2.29-2+rpi1 libc6-dev_2.29-2+rpi1 libcap-ng0_0.7.9-2 libcap2_1:2.25-2 libcap2-bin_1:2.25-2 libcc1-0_9.2.1-8+rpi1 libcom-err2_1.45.4-1 libcroco3_0.6.13-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.249 libdebhelper-perl_12.7 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.1-1 libgcc-9-dev_9.2.1-8+rpi1 libgcc1_1:9.2.1-8+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.1-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.9-5 libgomp1_9.2.1-8+rpi1 libgpg-error0_1.36-7 libhogweed4_3.4.1-1 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl19_0.20-2 libisl21_0.21-2 libjansson-dev_2.12-1 libjansson4_2.12-1 libjs-jquery_3.3.1~dfsg-3 libjs-mathjax_2.7.4+dfsg-1 libjs-sphinxdoc_1.8.5-3 libjs-underscore_1.9.1~dfsg-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.48+dfsg-1+b1 libldap-common_2.4.48+dfsg-1 liblocale-gettext-perl_1.07-3+b5 liblz4-1_1.9.1-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20190803-1 libncursesw6_6.1+20190803-1 libnettle6_3.4.1-1 libnpth0_1.6-1 libp11-kit0_0.23.17-2 libpam-cap_1:2.25-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre3_2:8.39-12 libperl5.30_5.30.0-6 libpipeline1_1.5.1-2 libpython3-stdlib_3.7.5-1 libpython3.7-minimal_3.7.5~rc1-2 libpython3.7-stdlib_3.7.5~rc1-2 libreadline7_7.0-5 libreadline8_8.0-3 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.4.1-2+rpi1 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.0-1 libss2_1.45.4-1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-8+rpi1 libstdc++6_9.2.1-8+rpi1 libsub-override-perl_0.09-2 libsystemd0_242-7+rpi1 libtasn1-6_4.14-3 libtinfo5_6.1+20190803-1 libtinfo6_6.1+20190803-1 libtool_2.4.6-11 libubsan1_9.2.1-8+rpi1 libuchardet0_0.0.6-3 libudev1_242-7+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.4+dfsg1-7+b2 libzstd1_1.4.3+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.7-3 mawk_1.3.3-17 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.1+20190803-1 ncurses-bin_6.1+20190803-1 netbase_5.6 openssl_1.1.1d-2 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-6 perl-base_5.30.0-6 perl-modules-5.30_5.30.0-6 pinentry-curses_1.1.0-3 po-debconf_1.0.21 python-babel-localedata_2.6.0+dfsg.1-1 python3_3.7.5-1 python3-alabaster_0.7.8-1 python3-attr_18.2.0-1 python3-babel_2.6.0+dfsg.1-1 python3-certifi_2018.8.24-1 python3-chardet_3.0.4-4 python3-distutils_3.7.5-1 python3-docutils_0.15.2+dfsg-1 python3-idna_2.6-2 python3-imagesize_1.0.0-1 python3-jinja2_2.10.1-1 python3-lib2to3_3.7.5-1 python3-markupsafe_1.1.0-1 python3-minimal_3.7.5-1 python3-packaging_19.1-2 python3-pkg-resources_41.2.0-1 python3-pygments_2.3.1+dfsg-1 python3-pyparsing_2.4.2-1 python3-requests_2.21.0-1 python3-roman_2.0.0-3 python3-six_1.12.0-2 python3-sphinx_1.8.5-3 python3-tz_2019.3-1 python3-urllib3_1.24.1-1 python3.7_3.7.5~rc1-2 python3.7-minimal_3.7.5~rc1-2 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 sbuild-build-depends-bedops-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sgml-base_1.29.1 sphinx-common_1.8.5-3 sysvinit-utils_2.96~beta-3 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xml-core_0.18+nmu1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Oct 23 15:12:11 2019 UTC
gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1
gpgv: issuer "moeller@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./bedops_2.4.37+dfsg-1.dsc
dpkg-source: info: extracting bedops in /<<BUILDDIR>>/bedops-2.4.37+dfsg
dpkg-source: info: unpacking bedops_2.4.37+dfsg.orig.tar.xz
dpkg-source: info: unpacking bedops_2.4.37+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying tests_use_installed_binaries.patch
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying use_debian_libs
dpkg-source: info: applying hardening.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-e92f4d8b-c867-4a09-8eec-cc8f1b122c21
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package bedops
dpkg-buildpackage: info: source version 2.4.37+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with sphinxdoc
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg'
dh_auto_clean
make -j4 clean
make[2]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg'
make clean -j 8 -f system.mk/Makefile.linux
make[3]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg'
make[3]: warning: -j8 forced in submake: resetting 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
rm -rf modules
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
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/sort-bed/src'
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/bedmap/src'
rm -rf objects_typical
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/bedops/src'
rm -rf objects_typical
rm -rf ../bin
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/bedextract/src'
rm -rf objects_typical
rm -rf ../bin
rm -rf objects-typical
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/bedmap/src'
rm -rf ../bin
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/starch/src'
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/conversion/src'
rm -rf ../bin
rm -rf ../lib
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/closestfeats/src'
rm -rf objects_typical
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/bedextract/src'
rm -rf ../bin
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/bedops/src'
rm -f ../lib/libstarch_debug.a
rm -rf objects
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/sort-bed/src'
rm -rf ../bin
rm -f ../lib/libstarch_gprof.a
rm -rf *.so *~
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/closestfeats/src'
rm -rf objects
rm -rf ../bin
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/conversion/src'
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+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[3]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg'
rm -rf docs/_build/
make[1]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+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-2.4.37+dfsg'
make -j 8 -f system.mk/Makefile.linux
make[2]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg'
make[2]: warning: -j8 forced in submake: resetting jobserver mode.
#bzcat | tar -x -C third-party
#cd third-party/jansson-2.6 && ./configure --prefix=/<<BUILDDIR>>/bedops-2.4.37+dfsg/third-party/jansson-2.6 && make && make install && cd /<<BUILDDIR>>/bedops-2.4.37+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-2.4.37+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-2.4.37+dfsg && rm -f zlib && ln -sf zlib-1.2.7 third-party/zlib
make build -f /<<BUILDDIR>>/bedops-2.4.37+dfsg/system.mk/Makefile.linux
make[3]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+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[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/sort-bed/src'
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+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 -C applications/bed/closestfeats/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/bedextract/src -f Makefile build
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+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
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 -C applications/bed/starch/src -f Makefile build
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
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+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-2.4.37+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
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/starch/src'
mkdir -p objects
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.37+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../../../..
mkdir -p objects
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.37+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 -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 -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects-typical/starchHelpers.o -iquote../../../../interfaces/general-headers
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'void starch::UNSTARCH_printMetadataSignature(const unsigned char*)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:2276:85: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2276 | static_cast<const size_t>( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
| ^
../../../../interfaces/src/data/starch/unstarchHelpers.c:2278:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2278 | static_cast<const size_t>( mdSha1BufferLength ));
| ^
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:2640:105: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2640 | static_cast<const size_t>( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
| ^
../../../../interfaces/src/data/starch/unstarchHelpers.c:2642:90: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2642 | static_cast<const size_t>( STARCH2_MD_FOOTER_SHA1_LENGTH ));
| ^
../../../../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:2171:91: warning: left shift count >= width of type [-Wshift-count-overflow]
2171 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
../../../../interfaces/src/data/starch/starchHelpers.c:2908:71: warning: left shift count >= width of type [-Wshift-count-overflow]
2908 | bzBytesWritten = static_cast<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:3434:91: warning: left shift count >= width of type [-Wshift-count-overflow]
3434 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
mkdir -p objects
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.37+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../../../..
make -C applications/bed/conversion/src -f Makefile build
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+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-2.4.37+dfsg/applications/bed/conversion/src" -iquote"../../../../interfaces/general-headers" convert2bed.c -o ../bin/convert2bed-typical -lpthread
../../../../interfaces/src/data/starch/starchHelpers.c:4202:71: warning: left shift count >= width of type [-Wshift-count-overflow]
4202 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../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:2171:91: warning: left shift count >= width of type [-Wshift-count-overflow]
2171 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
../../../../interfaces/src/data/starch/starchHelpers.c:2908:71: warning: left shift count >= width of type [-Wshift-count-overflow]
2908 | bzBytesWritten = static_cast<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:3434:91: warning: left shift count >= width of type [-Wshift-count-overflow]
3434 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
../../../../interfaces/src/data/starch/starchHelpers.c:4202:71: warning: left shift count >= width of type [-Wshift-count-overflow]
4202 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)':
../../../../interfaces/src/data/starch/starchHelpers.c:359:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:383:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~^~~
../../../../interfaces/src/data/starch/starchHelpers.c:485:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
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::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)':
../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
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/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/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)':
../../../../interfaces/src/data/starch/starchHelpers.c:923:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../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:2171:91: warning: left shift count >= width of type [-Wshift-count-overflow]
2171 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
../../../../interfaces/src/data/starch/starchHelpers.c:2908:71: warning: left shift count >= width of type [-Wshift-count-overflow]
2908 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
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_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
../../../../interfaces/src/data/starch/starchHelpers.c:3434:91: warning: left shift count >= width of type [-Wshift-count-overflow]
3434 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
../../../../interfaces/src/data/starch/starchHelpers.c:4202:71: warning: left shift count >= width of type [-Wshift-count-overflow]
4202 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)':
../../../../interfaces/src/data/starch/starchHelpers.c:359:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:383:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~^~~
../../../../interfaces/src/data/starch/starchHelpers.c:485:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
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::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)':
../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
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/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)':
../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
../../../../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:2171:91: warning: left shift count >= width of type [-Wshift-count-overflow]
2171 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
../../../../interfaces/src/data/starch/starchHelpers.c:2908:71: warning: left shift count >= width of type [-Wshift-count-overflow]
2908 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)':
../../../../interfaces/src/data/starch/starchHelpers.c:923:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../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:3434:91: warning: left shift count >= width of type [-Wshift-count-overflow]
3434 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
../../../../interfaces/src/data/starch/starchHelpers.c:4202:71: warning: left shift count >= width of type [-Wshift-count-overflow]
4202 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)':
../../../../interfaces/src/data/starch/starchHelpers.c:359:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:383:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~^~~
../../../../interfaces/src/data/starch/starchHelpers.c:485:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
../../../../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:2171:91: warning: left shift count >= width of type [-Wshift-count-overflow]
2171 | bzBytesWritten = static_cast<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:2171:91: warning: left shift count >= width of type [-Wshift-count-overflow]
2171 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
../../../../interfaces/src/data/starch/starchHelpers.c:2908:71: warning: left shift count >= width of type [-Wshift-count-overflow]
2908 | bzBytesWritten = static_cast<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:3434:91: warning: left shift count >= width of type [-Wshift-count-overflow]
3434 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
../../../../interfaces/src/data/starch/starchHelpers.c:2908:71: warning: left shift count >= width of type [-Wshift-count-overflow]
2908 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
../../../../interfaces/src/data/starch/starchHelpers.c:4202:71: warning: left shift count >= width of type [-Wshift-count-overflow]
4202 | bzBytesWritten = static_cast<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:3434:91: warning: left shift count >= width of type [-Wshift-count-overflow]
3434 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ^~
../../../../interfaces/src/data/starch/starchHelpers.c:4202:71: warning: left shift count >= width of type [-Wshift-count-overflow]
4202 | bzBytesWritten = static_cast<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:2416:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)':
../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)':
../../../../interfaces/src/data/starch/starchHelpers.c:923:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)':
../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)':
../../../../interfaces/src/data/starch/starchHelpers.c:359:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:383:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~^~~
../../../../interfaces/src/data/starch/starchHelpers.c:485:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
2559 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)':
../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)':
../../../../interfaces/src/data/starch/starchHelpers.c:359:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:383:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~^~~
../../../../interfaces/src/data/starch/starchHelpers.c:485:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)':
../../../../interfaces/src/data/starch/starchHelpers.c:359:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:383:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~^~~
../../../../interfaces/src/data/starch/starchHelpers.c:485:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)':
../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)':
../../../../interfaces/src/data/starch/starchHelpers.c:923:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)':
../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)':
../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
../../../../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:2416:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)':
../../../../interfaces/src/data/starch/starchHelpers.c:923:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)':
../../../../interfaces/src/data/starch/starchHelpers.c:923:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
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
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)':
../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../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:2416:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../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:3695:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)':
../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)':
../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../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:2416:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../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:2416:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../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:2416:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../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:3695:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../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:3695:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
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:1222:24: warning: comparison is always true due to limited range of data type [-Wtype-limits]
1222 | } while (currC != EOF);
| ^
../../../../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:3695:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
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=]
6086 | 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);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| unsigned int long unsigned int
| %lu
convert2bed.c:6086:109: warning: format '%zu' expects argument of type 'size_t', but argument 4 has type 'long unsigned int' [-Wformat=]
6086 | 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);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| unsigned int long unsigned int
| %lu
convert2bed.c:6086:115: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'long unsigned int' [-Wformat=]
6086 | 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);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| unsigned int long unsigned int
| %lu
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)':
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../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:3695:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~^~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~^~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)':
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~^~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~^~~~~~~~~~~
../../../../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:3695:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
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
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)':
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2137:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2137 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2137:57: note: length computed here
2137 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2153:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2153 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2153:65: note: length computed here
2153 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2165:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2165 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2165:59: note: length computed here
2165 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)':
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2137:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2137 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2137:57: note: length computed here
2137 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2153:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2153 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2153:65: note: length computed here
2153 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2165:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2165 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2165:59: note: length computed here
2165 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
mkdir -p objects
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.37+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../../../..
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
../../../../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:1593:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1593 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1593:50: note: length computed here
1593 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1576:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1576 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1576:52: note: length computed here
1576 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~^~~~~~~~~~~~~
../../../../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:1593:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1593 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1593:50: note: length computed here
1593 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1576:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1576 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1576:52: note: length computed here
1576 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~^~~~~~~~~~~~~
../../../../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:1222:24: warning: comparison is always true due to limited range of data type [-Wtype-limits]
1222 | } while (currC != EOF);
| ^
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)':
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~^~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~^~~~~~~~~~~
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
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)':
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~^~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~^~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)':
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~^~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~^~~~~~~~~~~
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/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)':
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2137:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2137 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2137:57: note: length computed here
2137 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2153:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2153 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2153:65: note: length computed here
2153 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2165:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2165 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2165:59: note: length computed here
2165 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'void starch::UNSTARCH_printMetadataSignature(const unsigned char*)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:2276:85: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2276 | static_cast<const size_t>( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
| ^
../../../../interfaces/src/data/starch/unstarchHelpers.c:2278:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2278 | static_cast<const size_t>( mdSha1BufferLength ));
| ^
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:2640:105: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2640 | static_cast<const size_t>( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
| ^
../../../../interfaces/src/data/starch/unstarchHelpers.c:2642:90: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2642 | static_cast<const size_t>( STARCH2_MD_FOOTER_SHA1_LENGTH ));
| ^
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)':
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~^~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~^~~~~~~~~~~
../../../../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:1593:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1593 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1593:50: note: length computed here
1593 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1576:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1576 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1576:52: note: length computed here
1576 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~^~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)':
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2137:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2137 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2137:57: note: length computed here
2137 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2153:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2153 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2153:65: note: length computed here
2153 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2165:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2165 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2165:59: note: length computed here
2165 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)':
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2137:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2137 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2137:57: note: length computed here
2137 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2153:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2153 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2153:65: note: length computed here
2153 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2165:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2165 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2165:59: note: length computed here
2165 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../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:1593:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1593 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1593:50: note: length computed here
1593 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1576:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1576 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1576:52: note: length computed here
1576 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~^~~~~~~~~~~~~
../../../../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:1593:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1593 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1593:50: note: length computed here
1593 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1576:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1576 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1576:52: note: length computed here
1576 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~^~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)':
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2137:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2137 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2137:57: note: length computed here
2137 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2153:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2153 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2153:65: note: length computed here
2153 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2165:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2165 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2165:59: note: length computed here
2165 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
../../../../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:1593:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1593 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1593:50: note: length computed here
1593 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1576:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1576 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1576:52: note: length computed here
1576 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~^~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.37+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../../../..
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mkdir -p objects
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
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.37+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../../../..
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
2559 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
2559 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
2559 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 SortDetails.cpp -o objects-typical/SortDetails.o -iquote../../../../interfaces/general-headers
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
2559 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers
mkdir -p ../bin && g++ -o ../bin/closest-features-typical -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.37+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
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
2559 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-2.4.37+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
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 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/bedextract-typical -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.37+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 -Wextra -pedantic -ansi -O3 -std=c++11 Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers
mkdir -p ../bin
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.37+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../../../..
starch.c: In function 'int main(int, char**)':
starch.c:106:81: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
106 | static_cast<const CompressionType>( type ),
| ^
starch.c:121:91: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
121 | static_cast<const CompressionType>( type ),
| ^
starch.c:123:107: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
123 | static_cast<const Boolean>( kStarchFinalizeTransformTrue ),
| ^
starch.c:146:81: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
146 | static_cast<const CompressionType>( type ),
| ^
starch.c:161:91: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
161 | static_cast<const CompressionType>( type ),
| ^
SortDetails.cpp: In function 'ChromBedData* initializeChromBedData(char*, double*)':
SortDetails.cpp:250:12: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
250 | strncpy(chrom->chromName, chromBuf, chromBufLen);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:163:107: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
163 | static_cast<const Boolean>( kStarchFinalizeTransformTrue ),
| ^
starch.c:191:77: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
191 | static_cast<const CompressionType>( type ),
| ^
SortDetails.cpp:249:25: note: length computed here
249 | chromBufLen = strlen(chromBuf); // we know >= 1
| ~~~~~~^~~~~~~~~~
starch.c:194:95: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
194 | static_cast<const Boolean>( bedGeneratePerChrSignatureFlag ),
| ^
starch.c:195:78: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
195 | static_cast<const Boolean>( bedHeaderFlag ),
| ^
starch.c:196:86: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
196 | static_cast<const Boolean>( bedReportProgressFlag ),
| ^
starch.c:197:89: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
197 | static_cast<const LineCountType>( bedReportProgressN )) != STARCH_EXIT_SUCCESS)
| ^
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
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.37+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-2.4.37+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../../../..
unstarch.c: In function 'int main(int, char**)':
unstarch.c:410:113: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
410 | static_cast<const unsigned long long>( metadataOffset ),
| ^
unstarch.c:411:98: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
411 | static_cast<const Boolean>( headerFlag )) != 0) {
| ^
unstarch.c:431:112: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
431 | static_cast<const unsigned long long>( metadataOffset ),
| ^
unstarch.c:432:97: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
432 | static_cast<const Boolean>( headerFlag )) != 0) {
| ^
unstarch.c:461:133: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
461 | static_cast<const unsigned long long>( sizeof(starchRevision2HeaderBytes) ),
| ^
unstarch.c:462:98: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
462 | static_cast<const Boolean>( headerFlag )) != 0) {
| ^
unstarch.c:482:132: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
482 | static_cast<const unsigned long long>( sizeof(starchRevision2HeaderBytes) ),
| ^
unstarch.c:483:97: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
483 | static_cast<const Boolean>( headerFlag )) != 0) {
| ^
unstarch.c:576:80: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
576 | UNSTARCH_printCompressionType(static_cast<const CompressionType>( type ));
| ^
unstarch.c:807:152: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
807 | static_cast<const unsigned long long>( sizeof(starchRevision2HeaderBytes) ),
| ^
unstarch.c:818:156: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
818 | static_cast<const unsigned long long>( sizeof(starchRevision2HeaderBytes) ),
| ^
unstarch.c: In function 'void starch::UNSTARCH_printMetadataSha1Signature(unsigned char*)':
unstarch.c:1343:85: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1343 | static_cast<const size_t>( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
| ^
unstarch.c:1345:57: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1345 | static_cast<const size_t>( sha1BufferLength ));
| ^
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-2.4.37+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
SortDetails.cpp: In function 'void lexSortBedData(BedData*)':
SortDetails.cpp:1327:20: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
1327 | strncpy(chromBuf, beds->chroms[i]->chromName, chromBufLen);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SortDetails.cpp:1326:33: note: length computed here
1326 | chromBufLen = strlen(beds->chroms[i]->chromName); // we know >= 1
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'ChromBedData* initializeChromBedData(char*, double*)',
inlined from 'int processData(const char**, unsigned int, double, char*, bool, bool)' at SortDetails.cpp:909:59:
SortDetails.cpp:250:12: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
250 | strncpy(chrom->chromName, chromBuf, chromBufLen);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SortDetails.cpp: In function 'int processData(const char**, unsigned int, double, char*, bool, bool)':
SortDetails.cpp:249:25: note: length computed here
249 | chromBufLen = strlen(chromBuf); // we know >= 1
| ~~~~~~^~~~~~~~~~
mkdir -p ../bin && g++ -o ../bin/bedmap-typical -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.37+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
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.37+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 ../bin
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.37+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../../../..
rm -rf objects
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/conversion/src'
mkdir -p ../bin && cp update-sort-bed-slurm.py ../bin/update-sort-bed-slurm-typical
mkdir -p ../bin
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.37+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../../../..
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::listJSONMetadata(FILE*, FILE*)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1226:93: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1226 | static_cast<const CompressionType>( getArchiveType() ),
| ^
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1230:91: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1230 | static_cast<const Boolean>( getArchiveHeaderFlag() ),
| ^
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1231:96: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1231 | static_cast<const Boolean>( getArchiveShowNewlineFlag() ));
| ^
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractAllData(const string&, FILE*)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:2003:102: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2003 | static_cast<const Boolean>( getArchiveHeaderFlag() )) != 0 ) {
| ^
../../../../interfaces/general-headers/data/starch/starchApi.hpp:2014:101: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2014 | static_cast<const Boolean>( getArchiveHeaderFlag() )) != 0 ) {
| ^
starchstrip.c: In function 'void starch::STARCHSTRIP_write_updated_metadata(FILE*)':
starchstrip.c:124:85: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
124 | static_cast<const size_t>( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
| ^
starchstrip.c:126:70: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
126 | static_cast<const size_t>( STARCH2_MD_FOOTER_SHA1_LENGTH ));
| ^
In file included from /usr/include/c++/9/cassert:44,
from starchcat.c:33:
starchcat.c: In function 'int main(int, char**)':
starchcat.c:136:115: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
136 | assert( STARCHCAT_allocMetadataRecords ( &mdRecords, static_cast<const unsigned int>( numRecords ) ) );
| ^
starchcat.c:137:119: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
137 | assert( STARCHCAT_allocMetadataJSONObjects ( &metadataJSONs, static_cast<const unsigned int>( numRecords ) ) );
| ^
starchcat.c:138:130: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
138 | assert( STARCHCAT_buildMetadataRecords ( &metadataJSONs, &mdRecords, static_cast<const unsigned int>( firstArgc ), static_cast<const int>( argc ), const_cast<const char **>( argv ) ) );
| ^
starchcat.c:138:162: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
138 | assert( STARCHCAT_buildMetadataRecords ( &metadataJSONs, &mdRecords, static_cast<const unsigned int>( firstArgc ), static_cast<const int>( argc ), const_cast<const char **>( argv ) ) );
| ^
starchcat.c:139:119: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
139 | assert( STARCHCAT_checkMetadataJSONVersions ( &metadataJSONs, static_cast<const unsigned int>( numRecords ) ) );
| ^
starchcat.c:140:189: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
140 | assert( STARCHCAT_buildUniqueChromosomeList ( &chromosomes, &numChromosomes, reinterpret_cast<const MetadataRecord *>( mdRecords ), static_cast<const unsigned int>( numRecords ) ) );
| ^
starchcat.c:141:117: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
141 | assert( STARCHCAT_allocChromosomeSummary ( &summary, static_cast<const unsigned int>( numChromosomes ) ) );
| ^
starchcat.c:142:168: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
142 | assert( STARCHCAT_buildChromosomeSummary ( &summary, reinterpret_cast<const MetadataRecord *>( mdRecords ), static_cast<const unsigned int>( numRecords ), const_cast<const char **>( chromosomes ), static_cast<const unsigned int>( numChromosomes ) ) );
| ^
starchcat.c:142:261: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
142 | assert( STARCHCAT_buildChromosomeSummary ( &summary, reinterpret_cast<const MetadataRecord *>( mdRecords ), static_cast<const unsigned int>( numRecords ), const_cast<const char **>( chromosomes ), static_cast<const unsigned int>( numChromosomes ) ) );
| ^
starchcat.c:143:119: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
143 | assert( STARCHCAT_allocChromosomeSummaries ( &summaries, static_cast<const unsigned int>( numChromosomes ) ) );
| ^
starchcat.c:144:175: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
144 | assert( STARCHCAT_buildChromosomeSummaries ( &summaries, reinterpret_cast<const ChromosomeSummary *>( summary ), static_cast<const unsigned int>( numChromosomes ) ) );
| ^
starchcat.c:164:108: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
164 | static_cast<const CompressionType>( outputType ),
| ^
starchcat.c:178:108: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
178 | static_cast<const CompressionType>( outputType ),
| ^
starchcat.c:223:104: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
223 | assert( STARCHCAT_freeMetadataRecords( &mdRecords, static_cast<const unsigned int>( numRecords ) ) );
| ^
starchcat.c:233:112: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
233 | assert (STARCHCAT_freeMetadataJSONObjects( &metadataJSONs, static_cast<const unsigned int>( numRecords ) ) );
| ^
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:1338:115: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1338 | UNSTARCH_reverseTransformCoordinates( static_cast<const LineCountType>( t_lineIdx ),
| ^
starchcat.c:1806:115: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1806 | UNSTARCH_reverseTransformCoordinates( static_cast<const LineCountType>( t_lineIdx ),
| ^
starchcat.c:2131:81: warning: left shift count >= width of type [-Wshift-count-overflow]
2131 | bzOutBytesWritten = static_cast<size_t>( bzOutBytesWrittenHi32 ) << 32 | bzOutBytesWrittenLo32;
| ^~
starchcat.c: In function 'int starch::STARCHCAT_rewriteInputRecordToOutput(starch::Metadata**, const char*, starch::CompressionType, const char*, const MetadataRecord*)':
starchcat.c:2450:70: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2450 | static_cast<const uint64_t>( inRec->mdOffset ),
| ^
starchcat.c:2451:66: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2451 | static_cast<const Boolean>( inRec->hFlag )) != 0 ) {
| ^
starchcat.c:2471:73: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2471 | static_cast<const uint64_t>( inRec->mdOffset ),
| ^
starchcat.c:2472:69: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2472 | static_cast<const Boolean>( inRec->hFlag )) != 0 ) {
| ^
starchcat.c:2509:67: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2509 | static_cast<const CompressionType>( outType ),
| ^
starchcat.c:2511:81: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2511 | static_cast<const Boolean>( kStarchFinalizeTransformFalse ),
| ^
starchcat.c: In function 'int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)':
starchcat.c:3152:90: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
3152 | if (STARCHCAT2_setupBzip2InputStream(static_cast<const size_t>( inRecIdx ),
| ^
starchcat.c:3316:116: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
3316 | static_cast<const size_t>( summary->numRecords ),
| ^
starchcat.c:3455:122: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
3455 | static_cast<const Boolean>( flushZStreamFlag ),
| ^
starchcat.c: In function 'int starch::STARCHCAT_mergeInputRecordsToOutput(starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*)':
starchcat.c:4265:87: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4265 | static_cast<const CompressionType>( outType ),
| ^
starchcat.c:4267:101: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4267 | static_cast<const Boolean>( kStarchFinalizeTransformFalse ),
| ^
In file included from /usr/include/c++/9/cassert:44,
from starchcat.c:33:
starchcat.c: In function 'int starch::STARCHCAT_mergeChromosomeStreams(const ChromosomeSummaries*, starch::CompressionType, const char*)':
starchcat.c:4402:107: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4402 | static_cast<const CompressionType>( outputType ),
| ^
starchcat.c:4420:110: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4420 | static_cast<const CompressionType>( outputType ),
| ^
starchcat.c:4447:104: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4447 | static_cast<const CompressionType>( outputType ),
| ^
starchcat.c:4479:73: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4479 | static_cast<const Boolean>( hFlag ),
| ^
starchcat.c: In function 'int starch::STARCHCAT_freeChromosomeSummaries(starch::ChromosomeSummaries**)':
starchcat.c:4541:122: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4541 | STARCHCAT_freeChromosomeSummary( &((*chrSums)->summary), static_cast<const unsigned int>( (*chrSums)->numChromosomes ));
| ^
In file included from /usr/include/c++/9/cassert:44,
from starchcat.c:33:
starchcat.c: In function 'int starch::STARCHCAT2_mergeChromosomeStreams(const ChromosomeSummaries*, starch::CompressionType, const char*, size_t*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
starchcat.c:5902:108: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
5902 | static_cast<const CompressionType>( outputType ),
| ^
starchcat.c:5929:111: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
5929 | static_cast<const CompressionType>( outputType ),
| ^
starchcat.c:5952:111: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
5952 | static_cast<const CompressionType>( outputType ),
| ^
starchcat.c:5990:106: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
5990 | static_cast<const CompressionType>( outputType ),
| ^
starchcat.c:6025:72: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
6025 | static_cast<const Boolean>( hFlag ),
| ^
starchcat.c:6053:85: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
6053 | static_cast<const size_t>( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
| ^
starchcat.c:6055:70: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
6055 | static_cast<const size_t>( STARCH2_MD_FOOTER_SHA1_LENGTH ));
| ^
starchcat.c: In function 'int starch::STARCHCAT2_fillExtractionBufferFromBzip2Stream(starch::Boolean*, char*, char*, size_t*, BZFILE**, size_t*, char*, size_t*, starch::TransformState*)':
starchcat.c:6719:103: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
6719 | UNSTARCH_reverseTransformCoordinates( static_cast<const LineCountType>( *t_lineIdxPtr ),
| ^
starchcat.c: In function 'int starch::STARCHCAT2_fillExtractionBufferFromGzipStream(starch::Boolean*, FILE**, char*, char*, size_t*, z_stream*, size_t*, char**, size_t*, starch::TransformState*)':
starchcat.c:7060:107: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
7060 | UNSTARCH_reverseTransformCoordinates( static_cast<const LineCountType>( *t_lineIdxPtr ),
| ^
In file included from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp: In instantiation of 'Bed::bed_check_iterator<BedType*, Sz> Bed::bed_check_iterator<BedType*, Sz>::operator++(int) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]':
CheckSort.cpp:51:28: required from here
../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:268:12: warning: implicitly-declared 'Bed::bed_check_iterator<Bed::BasicCoords<true, true>*, 16>::bed_check_iterator(const Bed::bed_check_iterator<Bed::BasicCoords<true, true>*, 16>&)' is deprecated [-Wdeprecated-copy]
268 | auto __tmp = *this;
| ^~~~~
../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:308:10: note: because 'Bed::bed_check_iterator<Bed::BasicCoords<true, true>*, 16>' has user-provided 'bool Bed::bed_check_iterator<BedType*, Sz>::operator=(const Bed::bed_check_iterator<BedType*, Sz>&) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]'
308 | bool operator=(const bed_check_iterator& b);
| ^~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:295:14: warning: implicitly-declared 'Bed::bed_check_iterator<Bed::BasicCoords<true, true>*, 16>::bed_check_iterator(const Bed::bed_check_iterator<Bed::BasicCoords<true, true>*, 16>&)' is deprecated [-Wdeprecated-copy]
295 | return __tmp;
| ^~~~~
../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:308:10: note: because 'Bed::bed_check_iterator<Bed::BasicCoords<true, true>*, 16>' has user-provided 'bool Bed::bed_check_iterator<BedType*, Sz>::operator=(const Bed::bed_check_iterator<BedType*, Sz>&) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]'
308 | bool operator=(const bed_check_iterator& b);
| ^~~~~~~~
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-2.4.37+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
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1913 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here
1913 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function 'int starch::STARCHCAT_buildMetadataRecords(json_t***, starch::MetadataRecord**, unsigned int, int, const char**)':
starchcat.c:5368:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
5368 | strncpy(cTime, creationTimestamp, strlen(creationTimestamp) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:5368:53: note: length computed here
5368 | strncpy(cTime, creationTimestamp, strlen(creationTimestamp) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1521:82:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1712:86:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1758:40:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1769:45:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1576:86:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1620:40:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1628:45:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentRemainder(char*)',
inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here
899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here
541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here
551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1);
| ~~~~~~~~~~~^~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
556 | std::strncpy(_recFilename, _token, strlen(_token) + 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here
556 | std::strncpy(_recFilename, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::extractBEDLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from 'bool starch::Starch::extractBEDLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::extractBEDLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'void starch::Starch::setCurrentChromosome(char*)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1913 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here
1913 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1628:45:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentRemainder(char*)',
inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here
899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here
541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here
551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1);
| ~~~~~~~~~~~^~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
556 | std::strncpy(_recFilename, _token, strlen(_token) + 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here
556 | std::strncpy(_recFilename, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::isEOF()':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'void starch::Starch::setCurrentChromosome(char*)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from 'bool starch::Starch::extractBEDLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from 'bool starch::Starch::extractBEDLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from 'bool starch::Starch::extractBEDLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
starchcat.c: In function 'int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)':
starchcat.c:3123:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
3123 | strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:3123:78: note: length computed here
3123 | strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1913 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here
1913 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1628:45:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentRemainder(char*)',
inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here
899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1);
| ~~~~~~^~~~~~~~~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from 'bool starch::Starch::extractBEDLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from 'bool starch::Starch::extractBEDLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from 'bool starch::Starch::extractBEDLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.37+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-2.4.37+dfsg/applications/bed/starch/src'
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'Bed::bed_check_iterator<BedType*, Sz> Bed::bed_check_iterator<BedType*, Sz>::operator++(int) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'Bed::bed_check_iterator<BedType*, Sz> Bed::bed_check_iterator<BedType*, Sz>::operator++(int) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)',
inlined from 'static bool starch::Starch::hasStarchRevision1LegacyHeader(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:634:52,
inlined from 'static bool starch::Starch::isStarch(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:698:56,
inlined from 'Bed::bed_check_iterator<BedType*, Sz>::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory<BedType, SZ>&, const string&, bool) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:92:90:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor 'Bed::bed_check_iterator<BedType*, Sz>::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory<BedType, SZ>&, const string&, bool) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here
551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1);
| ~~~~~~~~~~~^~~~~~~~~~~~
In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)',
inlined from 'static bool starch::Starch::hasStarchRevision1LegacyHeader(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:634:52,
inlined from 'static bool starch::Starch::isStarch(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:698:56,
inlined from 'Bed::bed_check_iterator<BedType*, Sz>::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory<BedType, SZ>&, const string&, bool) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:92:90:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
556 | std::strncpy(_recFilename, _token, strlen(_token) + 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor 'Bed::bed_check_iterator<BedType*, Sz>::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory<BedType, SZ>&, const string&, bool) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here
556 | std::strncpy(_recFilename, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from 'Bed::bed_check_iterator<BedType*, Sz>::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory<BedType, SZ>&, const string&, bool) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor 'Bed::bed_check_iterator<BedType*, Sz>::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory<BedType, SZ>&, const string&, bool) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
mkdir -p ../bin && g++ -o ../bin/sort-bed-typical -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bedops-2.4.37+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-2.4.37+dfsg/applications/bed/sort-bed/src'
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here
541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here
551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1);
| ~~~~~~~~~~~^~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
556 | std::strncpy(_recFilename, _token, strlen(_token) + 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here
556 | std::strncpy(_recFilename, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::isEOF()':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'void starch::Starch::iterateArchiveMdIter()':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'void starch::Starch::setCurrentChromosome(char*)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1913 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here
1913 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void starch::Starch::setCurrentRemainder(char*)',
inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here
899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1);
| ~~~~~~^~~~~~~~~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from 'bool starch::Starch::extractBEDLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from 'bool starch::Starch::extractBEDLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from 'Bed::bed_check_iterator<BedType*, Sz>::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory<BedType, SZ>&, const string&, bool) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor 'Bed::bed_check_iterator<BedType*, Sz>::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory<BedType, SZ>&, const string&, bool) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
rm -rf objects_typical
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/bedextract/src'
rm -rf objects_typical
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/closestfeats/src'
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from 'Bed::allocate_iterator_starch_bed<BedType*, SZ>& Bed::allocate_iterator_starch_bed<BedType*, SZ>::operator++() [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36,
inlined from 'BedOperations::BedPadReader<IterType>::BedType* BedOperations::BedPadReader<IterType>::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, true>*, 512>]' at BedPadReader.hpp:140:11,
inlined from 'void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector<BedOperations::BedPadReader<Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, true>*, 512> >*, std::allocator<BedOperations::BedPadReader<Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, true>*, 512> >*> >; PQueue = std::priority_queue<Bed::BasicCoords<true, true>*, std::vector<Bed::BasicCoords<true, true>*>, Bed::InvertGenomicAddressCompare<Bed::BasicCoords<true, true>, Bed::BasicCoords<true, true> > >]' at Bedops.cpp:1389:10:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function 'void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector<BedOperations::BedPadReader<Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, true>*, 512> >*, std::allocator<BedOperations::BedPadReader<Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, true>*, 512> >*> >; PQueue = std::priority_queue<Bed::BasicCoords<true, true>*, std::vector<Bed::BasicCoords<true, true>*>, Bed::InvertGenomicAddressCompare<Bed::BasicCoords<true, true>, Bed::BasicCoords<true, true> > >]':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from 'Bed::allocate_iterator_starch_bed<BedType*, SZ>& Bed::allocate_iterator_starch_bed<BedType*, SZ>::operator++() [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36,
inlined from 'BedOperations::BedPadReader<IterType>::BedType* BedOperations::BedPadReader<IterType>::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, true>*, 512>]' at BedPadReader.hpp:140:11,
inlined from 'void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector<BedOperations::BedPadReader<Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, true>*, 512> >*, std::allocator<BedOperations::BedPadReader<Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, true>*, 512> >*> >; PQueue = std::priority_queue<Bed::BasicCoords<true, true>*, std::vector<Bed::BasicCoords<true, true>*>, Bed::InvertGenomicAddressCompare<Bed::BasicCoords<true, true>, Bed::BasicCoords<true, true> > >]' at Bedops.cpp:1411:16:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function 'void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector<BedOperations::BedPadReader<Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, true>*, 512> >*, std::allocator<BedOperations::BedPadReader<Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, true>*, 512> >*> >; PQueue = std::priority_queue<Bed::BasicCoords<true, true>*, std::vector<Bed::BasicCoords<true, true>*>, Bed::InvertGenomicAddressCompare<Bed::BasicCoords<true, true>, Bed::BasicCoords<true, true> > >]':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from 'Bed::allocate_iterator_starch_bed<BedType*, SZ>& Bed::allocate_iterator_starch_bed<BedType*, SZ>::operator++() [with BedType = Bed::BasicCoords<true, false>; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36,
inlined from 'BedOperations::BedPadReader<IterType>::BedType* BedOperations::BedPadReader<IterType>::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, false>*, 512>]' at BedPadReader.hpp:140:11,
inlined from 'void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector<BedOperations::BedPadReader<Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, false>*, 512> >*, std::allocator<BedOperations::BedPadReader<Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, false>*, 512> >*> >; PQueue = std::priority_queue<Bed::BasicCoords<true, false>*, std::vector<Bed::BasicCoords<true, false>*, std::allocator<Bed::BasicCoords<true, false>*> >, Bed::InvertGenomicAddressCompare<Bed::BasicCoords<true, false>, Bed::BasicCoords<true, false> > >]' at Bedops.cpp:1389:10:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function 'void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector<BedOperations::BedPadReader<Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, false>*, 512> >*, std::allocator<BedOperations::BedPadReader<Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, false>*, 512> >*> >; PQueue = std::priority_queue<Bed::BasicCoords<true, false>*, std::vector<Bed::BasicCoords<true, false>*, std::allocator<Bed::BasicCoords<true, false>*> >, Bed::InvertGenomicAddressCompare<Bed::BasicCoords<true, false>, Bed::BasicCoords<true, false> > >]':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from 'Bed::allocate_iterator_starch_bed<BedType*, SZ>& Bed::allocate_iterator_starch_bed<BedType*, SZ>::operator++() [with BedType = Bed::BasicCoords<true, false>; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36,
inlined from 'BedOperations::BedPadReader<IterType>::BedType* BedOperations::BedPadReader<IterType>::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, false>*, 512>]' at BedPadReader.hpp:140:11,
inlined from 'void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector<BedOperations::BedPadReader<Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, false>*, 512> >*, std::allocator<BedOperations::BedPadReader<Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, false>*, 512> >*> >; PQueue = std::priority_queue<Bed::BasicCoords<true, false>*, std::vector<Bed::BasicCoords<true, false>*, std::allocator<Bed::BasicCoords<true, false>*> >, Bed::InvertGenomicAddressCompare<Bed::BasicCoords<true, false>, Bed::BasicCoords<true, false> > >]' at Bedops.cpp:1411:16:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function 'void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector<BedOperations::BedPadReader<Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, false>*, 512> >*, std::allocator<BedOperations::BedPadReader<Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, false>*, 512> >*> >; PQueue = std::priority_queue<Bed::BasicCoords<true, false>*, std::vector<Bed::BasicCoords<true, false>*, std::allocator<Bed::BasicCoords<true, false>*> >, Bed::InvertGenomicAddressCompare<Bed::BasicCoords<true, false>, Bed::BasicCoords<true, false> > >]':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
rm -rf objects_typical
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/bedops/src'
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39,
from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here
541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here
551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1);
| ~~~~~~~~~~~^~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
556 | std::strncpy(_recFilename, _token, strlen(_token) + 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here
556 | std::strncpy(_recFilename, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39,
from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'void starch::Starch::setCurrentChromosome(char*)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1913 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here
1913 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void starch::Starch::setCurrentRemainder(char*)',
inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here
899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from Bedmap.cpp:35:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/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:37:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/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:37:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1976:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1976 | __introselect(_RandomAccessIterator __first, _RandomAccessIterator __nth,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1976:5: 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++/9/bits/stl_algo.h:1976:5: 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++/9/bits/stl_algo.h:1976:5: 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++/9/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++/9/bits/stl_algo.h:4775:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
4775 | nth_element(_RandomAccessIterator __first, _RandomAccessIterator __nth,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:4775:5: 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++/9/bits/stl_algo.h:4775:5: 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++/9/bits/stl_algo.h:4790:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
4790 | std::__introselect(__first, __nth, __last,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
4791 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
4792 | __gnu_cxx::__ops::__iter_less_iter());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/algorithm/visitors/NumericalVisitors.hpp:32,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:34,
from Bedmap.cpp:37:
../../../../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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | 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
99 | 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
102 | 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
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
rm -rf objects_typical
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg/applications/bed/bedmap/src'
make[3]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+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-2.4.37\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg'
mkdir -p bin
cp applications/bed/conversion/src/wrappers/gff2starch 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/gvf2starch 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/vcf2bed applications/bed/conversion/src/wrappers/gtf2bed 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/gvf2bed applications/bed/conversion/src/wrappers/bam2starch_gnuParallel applications/bed/conversion/src/wrappers/bam2starch applications/bed/conversion/src/wrappers/gff2bed 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-2.4.37+dfsg'
debian/rules override_dh_install-arch
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+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-2.4.37+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-2.4.37+dfsg'
cd bin && for f in * ; do help2man --no-discard-stderr --version-string="2.4.37+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-2.4.37+dfsg'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
debian/rules override_dh_dwz
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg'
# Work around: dwz: Too few files for multifile optimization
echo "Do not run dh_dwz"
Do not run dh_dwz
make[1]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.37+dfsg'
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
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/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/bedextract 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/sort-bed 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/bedmap debian/bedops/usr/bin/starchcat debian/bedops/usr/bin/bedops-starch debian/bedops/usr/bin/closest-features debian/bedops/usr/bin/bedops debian/bedops/usr/bin/bedextract debian/bedops/usr/bin/unstarch debian/bedops/usr/bin/starchstrip 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_2.4.37+dfsg-1_armhf.deb'.
dpkg-deb: building package 'bedops' in '../bedops_2.4.37+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../bedops_2.4.37+dfsg-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-10-26T08:57:50Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
bedops_2.4.37+dfsg-1_armhf.changes:
-----------------------------------
Format: 1.8
Date: Wed, 23 Oct 2019 16:44:58 +0200
Source: bedops
Binary: bedops bedops-dbgsym
Architecture: armhf
Version: 2.4.37+dfsg-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Steffen Moeller <moeller@debian.org>
Description:
bedops - high-performance genomic feature operations
Changes:
bedops (2.4.37+dfsg-1) unstable; urgency=medium
.
* Team upload.
* New upstream version - adjusted patches
* Improving cleanup after build
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eb868a883386cc4417e74508a159548f1e581c3f 6201 bedops_2.4.37+dfsg-1_armhf.buildinfo
b631627c0eb7cbe891f2ba1901d08c942e17c595 1009240 bedops_2.4.37+dfsg-1_armhf.deb
Checksums-Sha256:
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Files:
13deba1fbe627ae905baea44b259c429 4220 debug optional bedops-dbgsym_2.4.37+dfsg-1_armhf.deb
18574cfbd66f29325977732635b203b2 6201 science optional bedops_2.4.37+dfsg-1_armhf.buildinfo
e6294872029329ed24ec31f4161a2673 1009240 science optional bedops_2.4.37+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
bedops-dbgsym_2.4.37+dfsg-1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 4220 bytes: control archive=540 bytes.
377 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: bedops-dbgsym
Source: bedops
Version: 2.4.37+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 (= 2.4.37+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for bedops
Build-Ids: 1df1e86c28ef175d32b457356daf766d30d253f0
drwxr-xr-x root/root 0 2019-10-23 14:44 ./
drwxr-xr-x root/root 0 2019-10-23 14:44 ./usr/
drwxr-xr-x root/root 0 2019-10-23 14:44 ./usr/lib/
drwxr-xr-x root/root 0 2019-10-23 14:44 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-10-23 14:44 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-10-23 14:44 ./usr/lib/debug/.build-id/1d/
-rw-r--r-- root/root 10916 2019-10-23 14:44 ./usr/lib/debug/.build-id/1d/f1e86c28ef175d32b457356daf766d30d253f0.debug
drwxr-xr-x root/root 0 2019-10-23 14:44 ./usr/share/
drwxr-xr-x root/root 0 2019-10-23 14:44 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-10-23 14:44 ./usr/share/doc/bedops-dbgsym -> bedops
bedops_2.4.37+dfsg-1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 1009240 bytes: control archive=5376 bytes.
728 bytes, 15 lines control
17229 bytes, 204 lines md5sums
Package: bedops
Version: 2.4.37+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6933
Depends: libbz2-1.0, libc6 (>= 2.28), libgcc1 (>= 1:3.5), libjansson4 (>= 2.3), libstdc++6 (>= 9), 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 2019-10-23 14:44 ./
drwxr-xr-x root/root 0 2019-10-23 14:44 ./usr/
drwxr-xr-x root/root 0 2019-10-23 14:44 ./usr/bin/
-rwxr-xr-x root/root 4711 2019-10-23 14:44 ./usr/bin/bam2bed
-rwxr-xr-x root/root 4505 2019-10-23 14:44 ./usr/bin/bam2bed_gnuParallel
-rwxr-xr-x root/root 5030 2019-10-23 14:44 ./usr/bin/bam2bed_sge
-rwxr-xr-x root/root 5025 2019-10-23 14:44 ./usr/bin/bam2bed_slurm
-rwxr-xr-x root/root 5842 2019-10-23 14:44 ./usr/bin/bam2starch
-rwxr-xr-x root/root 4511 2019-10-23 14:44 ./usr/bin/bam2starch_gnuParallel
-rwxr-xr-x root/root 5084 2019-10-23 14:44 ./usr/bin/bam2starch_sge
-rwxr-xr-x root/root 5018 2019-10-23 14:44 ./usr/bin/bam2starch_slurm
-rwxr-xr-x root/root 169400 2019-10-23 14:44 ./usr/bin/bedextract
-rwxr-xr-x root/root 5227984 2019-10-23 14:44 ./usr/bin/bedmap
-rwxr-xr-x root/root 366008 2019-10-23 14:44 ./usr/bin/bedops
-rwxr-xr-x root/root 75332 2019-10-23 14:44 ./usr/bin/bedops-starch
-rwxr-xr-x root/root 206268 2019-10-23 14:44 ./usr/bin/closest-features
-rwxr-xr-x root/root 104660 2019-10-23 14:44 ./usr/bin/convert2bed
-rwxr-xr-x root/root 3773 2019-10-23 14:44 ./usr/bin/gff2bed
-rwxr-xr-x root/root 4904 2019-10-23 14:44 ./usr/bin/gff2starch
-rwxr-xr-x root/root 3532 2019-10-23 14:44 ./usr/bin/gtf2bed
-rwxr-xr-x root/root 4663 2019-10-23 14:44 ./usr/bin/gtf2starch
-rwxr-xr-x root/root 3773 2019-10-23 14:44 ./usr/bin/gvf2bed
-rwxr-xr-x root/root 4904 2019-10-23 14:44 ./usr/bin/gvf2starch
-rwxr-xr-x root/root 3976 2019-10-23 14:44 ./usr/bin/psl2bed
-rwxr-xr-x root/root 5107 2019-10-23 14:44 ./usr/bin/psl2starch
-rwxr-xr-x root/root 3776 2019-10-23 14:44 ./usr/bin/rmsk2bed
-rwxr-xr-x root/root 4907 2019-10-23 14:44 ./usr/bin/rmsk2starch
-rwxr-xr-x root/root 4711 2019-10-23 14:44 ./usr/bin/sam2bed
-rwxr-xr-x root/root 5842 2019-10-23 14:44 ./usr/bin/sam2starch
-rwxr-xr-x root/root 181684 2019-10-23 14:44 ./usr/bin/sort-bed
-rwxr-xr-x root/root 10166 2019-10-23 14:44 ./usr/bin/starch-diff
-rwxr-xr-x root/root 144948 2019-10-23 14:44 ./usr/bin/starchcat
-rwxr-xr-x root/root 4303 2019-10-23 14:44 ./usr/bin/starchcluster_gnuParallel
-rwxr-xr-x root/root 4818 2019-10-23 14:44 ./usr/bin/starchcluster_sge
-rwxr-xr-x root/root 4720 2019-10-23 14:44 ./usr/bin/starchcluster_slurm
-rwxr-xr-x root/root 79364 2019-10-23 14:44 ./usr/bin/starchstrip
-rwxr-xr-x root/root 107956 2019-10-23 14:44 ./usr/bin/unstarch
-rwxr-xr-x root/root 32689 2019-10-23 14:44 ./usr/bin/update-sort-bed-migrate-candidates
-rwxr-xr-x root/root 20704 2019-10-23 14:44 ./usr/bin/update-sort-bed-slurm
-rwxr-xr-x root/root 22685 2019-10-23 14:44 ./usr/bin/update-sort-bed-starch-slurm
-rwxr-xr-x root/root 4675 2019-10-23 14:44 ./usr/bin/vcf2bed
-rwxr-xr-x root/root 5806 2019-10-23 14:44 ./usr/bin/vcf2starch
-rwxr-xr-x root/root 4598 2019-10-23 14:44 ./usr/bin/wig2bed
-rwxr-xr-x root/root 5729 2019-10-23 14:44 ./usr/bin/wig2starch
drwxr-xr-x root/root 0 2019-10-23 14:44 ./usr/share/
drwxr-xr-x root/root 0 2019-10-23 14:44 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-10-23 14:44 ./usr/share/doc/bedops/
-rw-r--r-- root/root 267 2019-10-23 14:44 ./usr/share/doc/bedops/README.Debian
-rw-r--r-- root/root 1085 2019-10-23 14:44 ./usr/share/doc/bedops/changelog.Debian.gz
-rw-r--r-- root/root 1129 2019-10-23 14:44 ./usr/share/doc/bedops/copyright
drwxr-xr-x root/root 0 2019-10-12 00:53 ./usr/share/doc/bedops/tests/
-rw-r--r-- root/root 718 2019-10-12 00:53 ./usr/share/doc/bedops/tests/Makefile
drwxr-xr-x root/root 0 2019-10-23 14:44 ./usr/share/doc/bedops/tests/bedops/
-rw-r--r-- root/root 2166 2019-10-23 14:44 ./usr/share/doc/bedops/tests/bedops/Makefile.gz
drwxr-xr-x root/root 0 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/
-rw-r--r-- root/root 197 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001.expected
-rw-r--r-- root/root 44 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001a.test
-rw-r--r-- root/root 53 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001b.test
-rw-r--r-- root/root 24 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.chrom.001.expected
-rw-r--r-- root/root 26 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.complement.001.expected
-rw-r--r-- root/root 31 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.difference.001.expected
-rw-r--r-- root/root 23 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.ec.001a.test
-rw-r--r-- root/root 69 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.element-of.001.expected
-rw-r--r-- root/root 91 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001.expected
-rw-r--r-- root/root 52 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001a.test
-rw-r--r-- root/root 104 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001b.test
-rw-r--r-- root/root 37 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.merge.001.expected
-rw-r--r-- root/root 111 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.merge.001.test
-rw-r--r-- root/root 368 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.named-pipe.001.expected
-rw-r--r-- root/root 0 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.not-element-of.001.expected
-rw-r--r-- root/root 148 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001.expected
-rw-r--r-- root/root 39 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001a.test
-rw-r--r-- root/root 56 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001b.test
-rw-r--r-- root/root 40 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001c.test
-rw-r--r-- root/root 257 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.stdin.001.expected
-rw-r--r-- root/root 130 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.symdiff.001.expected
-rw-r--r-- root/root 134 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.union.001.expected
-rw-r--r-- root/root 126 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/001.union.001.test
-rw-r--r-- root/root 171 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.chop.002.expected
-rw-r--r-- root/root 20 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.chrom.002.expected
-rw-r--r-- root/root 0 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.complement.002.expected
-rw-r--r-- root/root 2172 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002.expected
-rw-r--r-- root/root 3033 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002a.test
-rw-r--r-- root/root 2941 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002b.test
-rw-r--r-- root/root 18 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.element-of.002.expected
-rw-r--r-- root/root 13 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.intersection.002.expected
-rw-r--r-- root/root 26 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.intersection.002.test
-rw-r--r-- root/root 11 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.merge.002.expected
-rw-r--r-- root/root 11 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.not-element-of.002.expected
-rw-r--r-- root/root 376 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002.expected
-rw-r--r-- root/root 48 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002a.test
-rw-r--r-- root/root 49 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002b.test
-rw-r--r-- root/root 101 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002c.test
-rw-r--r-- root/root 39 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002d.test
-rw-r--r-- root/root 131 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002e.test
-rw-r--r-- root/root 118 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.symdiff.002.expected
-rw-r--r-- root/root 56 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/002.union.002.expected
-rw-r--r-- root/root 368 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.chop.003.expected
-rw-r--r-- root/root 24 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.chrom.003.expected
-rw-r--r-- root/root 61 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.complement.003.expected
-rw-r--r-- root/root 3794 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.difference.003.expected
-rw-r--r-- root/root 42 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.element-of.003.expected
-rw-r--r-- root/root 0 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.intersection.003.expected
-rw-r--r-- root/root 35 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.merge.003.expected
-rw-r--r-- root/root 46 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.merge.003.test
-rw-r--r-- root/root 21 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003.expected
-rw-r--r-- root/root 63 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003a.test
-rw-r--r-- root/root 42 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003b.test
-rw-r--r-- root/root 153 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.partition.003.expected
-rw-r--r-- root/root 398 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.partition.003.test
-rw-r--r-- root/root 22 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003.expected
-rw-r--r-- root/root 18 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003a.test
-rw-r--r-- root/root 29 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003b.test
-rw-r--r-- root/root 9 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003c.test
-rw-r--r-- root/root 11 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003d.test
-rw-r--r-- root/root 355 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.union.003.expected
-rw-r--r-- root/root 360 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/003.union.003.test
-rw-r--r-- root/root 257 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.chop.004.expected
-rw-r--r-- root/root 24 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.chrom.004.expected
-rw-r--r-- root/root 111 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004.expected
-rw-r--r-- root/root 46 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004a.test
-rw-r--r-- root/root 132 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004b.test
-rw-r--r-- root/root 94 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004c.test
-rw-r--r-- root/root 30 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004.expected
-rw-r--r-- root/root 30 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004a.test
-rw-r--r-- root/root 31 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004b.test
-rw-r--r-- root/root 0 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004.expected
-rw-r--r-- root/root 92 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004a.test
-rw-r--r-- root/root 23 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004b.test
-rw-r--r-- root/root 49 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004.expected
-rw-r--r-- root/root 103 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004a.test
-rw-r--r-- root/root 85 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004b.test
-rw-r--r-- root/root 47 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004c.test
-rw-r--r-- root/root 72 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.merge.004.expected
-rw-r--r-- root/root 117 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.partition.004.expected
-rw-r--r-- root/root 117 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.partition.004.test
-rw-r--r-- root/root 52 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.symdiff.004.expected
-rw-r--r-- root/root 22 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.union.004.expected
-rw-r--r-- root/root 32 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/004.union.004.test
-rw-r--r-- root/root 385 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/005.chop.005.expected
-rw-r--r-- root/root 87 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/005.chop.005.test
-rw-r--r-- root/root 20 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/005.complement.005.expected
-rw-r--r-- root/root 40 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/005.complement.005.test
-rw-r--r-- root/root 31 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/005.difference.005.expected
-rw-r--r-- root/root 93 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/005.merge.005.expected
-rw-r--r-- root/root 43 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/005.merge.005.test
-rw-r--r-- root/root 0 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/005.symdiff.005.expected
-rw-r--r-- root/root 11 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/005.union.005.expected
-rw-r--r-- root/root 35 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/006.complement.006.expected
-rw-r--r-- root/root 0 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/006.difference.006.expected
-rw-r--r-- root/root 41 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006.expected
-rw-r--r-- root/root 37 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006a.test
-rw-r--r-- root/root 35 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006b.test
-rw-r--r-- root/root 31 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006c.test
-rw-r--r-- root/root 0 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/006.union.006.expected
-rw-r--r-- root/root 9 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/007.complement.007.expected
-rw-r--r-- root/root 0 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/007.difference.007.expected
-rw-r--r-- root/root 55 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007.expected
-rw-r--r-- root/root 56 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007a.test
-rw-r--r-- root/root 69 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007b.test
-rw-r--r-- root/root 33 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/007.union.007.expected
-rw-r--r-- root/root 79 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/008.complement.008.expected
-rw-r--r-- root/root 197 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/008.merge.008.expected
-rw-r--r-- root/root 33 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/008.union.008.expected
-rw-r--r-- root/root 175 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/009.complement.009.expected
-rw-r--r-- root/root 52 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/009.merge.009.expected
-rw-r--r-- root/root 33 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/009.union.009.expected
-rw-r--r-- root/root 43 2019-10-12 00:53 ./usr/share/doc/bedops/tests/bedops/data/009.union.009.test
drwxr-xr-x root/root 0 2019-10-23 14:44 ./usr/share/doc/bedops/tests/starch/
-rw-r--r-- root/root 1078 2019-10-23 14:44 ./usr/share/doc/bedops/tests/starch/Makefile.gz
drwxr-xr-x root/root 0 2019-10-23 14:44 ./usr/share/doc/bedops/tests/starch/data/
-rw-r--r-- root/root 1935 2019-10-12 00:53 ./usr/share/doc/bedops/tests/starch/data/001.starch_api.bedmap.001.expected
-rw-r--r-- root/root 2813 2019-10-12 00:53 ./usr/share/doc/bedops/tests/starch/data/001.starch_api.bedmap.001.test.gz
-rw-r--r-- root/root 772 2019-10-12 00:53 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr1.001.test
-rw-r--r-- root/root 1166 2019-10-12 00:53 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr1andChr2.001.expected
-rw-r--r-- root/root 772 2019-10-12 00:53 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr2.001.test
-rw-r--r-- root/root 764 2019-10-12 00:53 ./usr/share/doc/bedops/tests/starch/data/001.unstarch.signature.001.expected
-rw-r--r-- root/root 2851 2019-10-12 00:53 ./usr/share/doc/bedops/tests/starch/data/001.unstarch.signature.001.test.gz
-rw-r--r-- root/root 218 2019-10-12 00:53 ./usr/share/doc/bedops/tests/starch/data/002.unstarch.signature.001.expected
-rw-r--r-- root/root 2254 2019-10-12 00:53 ./usr/share/doc/bedops/tests/starch/data/002.unstarch.signature.001.test.gz
-rw-r--r-- root/root 109 2019-10-12 00:53 ./usr/share/doc/bedops/tests/starch/data/README
-rw-r--r-- root/root 426 2019-10-12 00:53 ./usr/share/doc/bedops/tests/starch/data/hg38.bed
-rw-r--r-- root/root 1511 2019-10-12 00:53 ./usr/share/doc/bedops/tests/starch/generate_random_intervals.sh
drwxr-xr-x root/root 0 2019-10-23 14:44 ./usr/share/man/
drwxr-xr-x root/root 0 2019-10-23 14:44 ./usr/share/man/man1/
-rw-r--r-- root/root 350 2019-10-23 14:44 ./usr/share/man/man1/bam2bed.1.gz
-rw-r--r-- root/root 357 2019-10-23 14:44 ./usr/share/man/man1/bam2starch.1.gz
-rw-r--r-- root/root 850 2019-10-23 14:44 ./usr/share/man/man1/bedextract.1.gz
-rw-r--r-- root/root 2563 2019-10-23 14:44 ./usr/share/man/man1/bedmap.1.gz
-rw-r--r-- root/root 1046 2019-10-23 14:44 ./usr/share/man/man1/bedops-starch.1.gz
-rw-r--r-- root/root 1393 2019-10-23 14:44 ./usr/share/man/man1/bedops.1.gz
-rw-r--r-- root/root 1280 2019-10-23 14:44 ./usr/share/man/man1/closest-features.1.gz
-rw-r--r-- root/root 1226 2019-10-23 14:44 ./usr/share/man/man1/convert2bed.1.gz
-rw-r--r-- root/root 349 2019-10-23 14:44 ./usr/share/man/man1/gff2bed.1.gz
-rw-r--r-- root/root 357 2019-10-23 14:44 ./usr/share/man/man1/gff2starch.1.gz
-rw-r--r-- root/root 349 2019-10-23 14:44 ./usr/share/man/man1/gtf2bed.1.gz
-rw-r--r-- root/root 357 2019-10-23 14:44 ./usr/share/man/man1/gtf2starch.1.gz
-rw-r--r-- root/root 350 2019-10-23 14:44 ./usr/share/man/man1/gvf2bed.1.gz
-rw-r--r-- root/root 358 2019-10-23 14:44 ./usr/share/man/man1/gvf2starch.1.gz
-rw-r--r-- root/root 348 2019-10-23 14:44 ./usr/share/man/man1/psl2bed.1.gz
-rw-r--r-- root/root 357 2019-10-23 14:44 ./usr/share/man/man1/psl2starch.1.gz
-rw-r--r-- root/root 352 2019-10-23 14:44 ./usr/share/man/man1/rmsk2bed.1.gz
-rw-r--r-- root/root 359 2019-10-23 14:44 ./usr/share/man/man1/rmsk2starch.1.gz
-rw-r--r-- root/root 349 2019-10-23 14:44 ./usr/share/man/man1/sam2bed.1.gz
-rw-r--r-- root/root 360 2019-10-23 14:44 ./usr/share/man/man1/sam2starch.1.gz
-rw-r--r-- root/root 743 2019-10-23 14:44 ./usr/share/man/man1/sort-bed.1.gz
-rw-r--r-- root/root 366 2019-10-23 14:44 ./usr/share/man/man1/starch-diff.1.gz
-rw-r--r-- root/root 989 2019-10-23 14:44 ./usr/share/man/man1/starchcat.1.gz
-rw-r--r-- root/root 1111 2019-10-23 14:44 ./usr/share/man/man1/starchstrip.1.gz
-rw-r--r-- root/root 1545 2019-10-23 14:44 ./usr/share/man/man1/unstarch.1.gz
-rw-r--r-- root/root 396 2019-10-23 14:44 ./usr/share/man/man1/update-sort-bed-migrate-candidates.1.gz
-rw-r--r-- root/root 382 2019-10-23 14:44 ./usr/share/man/man1/update-sort-bed-slurm.1.gz
-rw-r--r-- root/root 393 2019-10-23 14:44 ./usr/share/man/man1/update-sort-bed-starch-slurm.1.gz
-rw-r--r-- root/root 350 2019-10-23 14:44 ./usr/share/man/man1/vcf2bed.1.gz
-rw-r--r-- root/root 358 2019-10-23 14:44 ./usr/share/man/man1/vcf2starch.1.gz
-rw-r--r-- root/root 350 2019-10-23 14:44 ./usr/share/man/man1/wig2bed.1.gz
-rw-r--r-- root/root 358 2019-10-23 14:44 ./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: 57436
Build-Time: 12308
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 1877
Job: bedops_2.4.37+dfsg-1
Machine Architecture: armhf
Package: bedops
Package-Time: 14242
Source-Version: 2.4.37+dfsg-1
Space: 57436
Status: successful
Version: 2.4.37+dfsg-1
--------------------------------------------------------------------------------
Finished at 2019-10-26T08:57:50Z
Build needed 03:57:22, 57436k disc space