bedops →
2.4.40+dfsg-1 →
armhf → 2021-10-26 05:59:57
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| bedops 2.4.40+dfsg-1 (armhf) Tue, 26 Oct 2021 05:35:26 +0000 |
+==============================================================================+
Package: bedops
Version: 2.4.40+dfsg-1
Source Version: 2.4.40+dfsg-1
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-2ff7c600-d96a-43a0-9cce-dce3ef52e2e0' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.5 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.9 MB in 10s (2690 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 13.5 MB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main bedops 2.4.40+dfsg-1 (dsc) [2178 B]
Get:2 http://172.17.0.1/private bookworm-staging/main bedops 2.4.40+dfsg-1 (tar) [13.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main bedops 2.4.40+dfsg-1 (diff) [10.3 kB]
Fetched 13.5 MB in 2s (6585 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bedops-Y0sts2/bedops-2.4.40+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bedops-Y0sts2' 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-7voAey/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-7voAey/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-7voAey/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-7voAey/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-7voAey/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-7voAey/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-7voAey/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-7voAey/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (9998 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 42 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-7voAey/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 (66.7 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12484 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, python3-distutils, zlib1g-dev
Filtered Build-Depends: debhelper-compat (= 12), help2man, libbz2-dev, libjansson-dev, python3-distutils, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-bedops-dummy' in '/<<BUILDDIR>>/resolver-7voAey/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-7voAey/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-7voAey/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-7voAey/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-7voAey/apt_archive ./ Sources [536 B]
Get:5 copy:/<<BUILDDIR>>/resolver-7voAey/apt_archive ./ Packages [614 B]
Fetched 2483 B in 0s (11.6 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install bedops build dependencies (apt-based resolver)
------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libbz2-dev
libdebhelper-perl libelf1 libexpat1 libffi8 libfile-stripnondeterminism-perl
libicu67 libjansson-dev libjansson4 libmagic-mgc libmagic1 libmpdec3
libpipeline1 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib
libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
media-types po-debconf python3 python3-distutils python3-lib2to3
python3-minimal python3.9 python3.9-minimal sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv python3.9-venv
python3.9-doc binfmt-support
Recommended packages:
curl | wget | lynx bzip2-doc libarchive-cpio-perl ca-certificates
libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libbz2-dev
libdebhelper-perl libelf1 libexpat1 libffi8 libfile-stripnondeterminism-perl
libicu67 libjansson-dev libjansson4 libmagic-mgc libmagic1 libmpdec3
libpipeline1 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib
libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
media-types po-debconf python3 python3-distutils python3-lib2to3
python3-minimal python3.9 python3.9-minimal
sbuild-build-depends-bedops-dummy sensible-utils zlib1g-dev
0 upgraded, 50 newly installed, 0 to remove and 42 not upgraded.
Need to get 23.0 MB of archives.
After this operation, 86.3 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-7voAey/apt_archive ./ sbuild-build-depends-bedops-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-4 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-minimal armhf 3.9.7-4+rpi1 [794 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.1-2 [80.3 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.7-4+rpi1 [1632 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libffi8 armhf 3.4.2-3 [21.3 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.7-4+rpi1 [1618 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf python3.9 armhf 3.9.7-4+rpi1 [480 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf python3 armhf 3.9.2-3 [37.9 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.5-1 [823 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-2 [26.3 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-2 [15.5 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf help2man armhf 1.48.5 [143 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libbz2-dev armhf 1.0.8-4 [28.0 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf libjansson4 armhf 2.13.1-1.1 [36.2 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf libjansson-dev armhf 2.13.1-1.1 [37.0 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf python3-lib2to3 all 3.9.7-1 [79.4 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf python3-distutils all 3.9.7-1 [146 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libjansson4:armhf.
Preparing to unpack .../29-libjansson4_2.13.1-1.1_armhf.deb ...
Unpacking libjansson4:armhf (2.13.1-1.1) ...
Selecting previously unselected package libjansson-dev:armhf.
Preparing to unpack .../30-libjansson-dev_2.13.1-1.1_armhf.deb ...
Unpacking libjansson-dev:armhf (2.13.1-1.1) ...
Selecting previously unselected package python3-lib2to3.
Preparing to unpack .../31-python3-lib2to3_3.9.7-1_all.deb ...
Unpacking python3-lib2to3 (3.9.7-1) ...
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Preparing to unpack .../32-python3-distutils_3.9.7-1_all.deb ...
Unpacking python3-distutils (3.9.7-1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../33-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package sbuild-build-depends-bedops-dummy.
Preparing to unpack .../34-sbuild-build-depends-bedops-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-bedops-dummy (0.invalid.0) ...
Setting up media-types (4.0.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up bsdextrautils (2.37.2-4) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.5.2) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up libjansson4:armhf (2.13.1-1.1) ...
Setting up help2man (1.48.5) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up autopoint (0.21-4) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libffi8:armhf (3.4.2-3) ...
Setting up sensible-utils (0.0.17) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libmpdec3:armhf (2.5.1-2+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libjansson-dev:armhf (2.13.1-1.1) ...
Setting up libpython3.9-stdlib:armhf (3.9.7-4+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.2-3) ...
Setting up libbz2-dev:armhf (1.0.8-4) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-2) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.0-2) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up python3.9 (3.9.7-4+rpi1) ...
Setting up automake (1:1.16.5-1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up python3 (3.9.2-3) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up python3-lib2to3 (3.9.7-1) ...
Setting up python3-distutils (3.9.7-1) ...
Setting up debhelper (13.5.2) ...
Setting up sbuild-build-depends-bedops-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-9+rpi1 gcc-10_10.3.0-9+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.5-1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-1 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-9+rpi1 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-2 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-9+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-9+rpi1 gcc-10-base_10.3.0-9+rpi1 gcc-11-base_11.2.0-4+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 help2man_1.48.5 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libasan6_11.2.0-4+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-4+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-1 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_11.2.0-4+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libexpat1_2.4.1-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.12.0-2 libgcc-10-dev_10.3.0-9+rpi1 libgcc-s1_11.2.0-4+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-4+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.23-1 libjansson-dev_2.13.1-1.1 libjansson4_2.13.1-1.1 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libpython3-stdlib_3.9.2-3 libpython3.9-minimal_3.9.7-4+rpi1 libpython3.9-stdlib_3.9.7-4+rpi1 libreadline8_8.1-2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-1 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.9-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.37.2-1 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 python3_3.9.2-3 python3-distutils_3.9.7-1 python3-lib2to3_3.9.7-1 python3-minimal_3.9.2-3 python3.9_3.9.7-4+rpi1 python3.9-minimal_3.9.7-4+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-bedops-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.37.2-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.ZHy9e77H/trustedkeys.kbx': General error
gpgv: Signature made Sun Oct 24 08:38:34 2021 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "nilesh@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./bedops_2.4.40+dfsg-1.dsc
dpkg-source: info: extracting bedops in /<<BUILDDIR>>/bedops-2.4.40+dfsg
dpkg-source: info: unpacking bedops_2.4.40+dfsg.orig.tar.xz
dpkg-source: info: unpacking bedops_2.4.40+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 parallel.patch
dpkg-source: info: applying adapt_to_new_sphinx.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-2ff7c600-d96a-43a0-9cce-dce3ef52e2e0
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package bedops
dpkg-buildpackage: info: source version 2.4.40+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg'
dh_auto_clean
make -j4 clean
make[2]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg'
make clean -f system.mk/Makefile.linux
make[3]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg'
rm -rf bin
rm -rf bin
rm -rf bin
make -C applications/bed/bedextract/src -f Makefile clean
rm -rf modules
make -C applications/bed/bedmap/src -f Makefile clean
make -C applications/bed/bedops/src -f Makefile clean
make -C applications/bed/closestfeats/src -f Makefile clean
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/bedextract/src'
rm -rf objects_typical
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/bedmap/src'
rm -rf objects_typical
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/bedops/src'
rm -rf objects_typical
rm -rf ../bin
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/closestfeats/src'
rm -rf objects_typical
rm -rf ../bin
rm -rf ../bin
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/bedextract/src'
rm -rf ../bin
make -C applications/bed/conversion/src -f Makefile clean
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/bedmap/src'
make -C applications/bed/sort-bed/src -f Makefile clean
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/bedops/src'
make -C applications/bed/starch/src -f Makefile clean
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/closestfeats/src'
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/sort-bed/src'
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/conversion/src'
rm -rf ../bin
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/starch/src'
rm -rf ../lib
rm -rf objects
rm -rf objects-typical
rm -f ../lib/libstarch_debug.a
rm -rf *.so *~
rm -rf ../bin
rm -f ../lib/libstarch_gprof.a
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/sort-bed/src'
rm -rf objects
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/conversion/src'
rm -rf ../bin
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+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-2.4.40+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg'
rm -rf docs/_build/
make[1]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
dh_auto_build -a
make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg'
make -f system.mk/Makefile.linux
make[2]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg'
#bzcat | tar -x -C third-party
#cd third-party/jansson-2.6 && ./configure --prefix=/<<BUILDDIR>>/bedops-2.4.40+dfsg/third-party/jansson-2.6 && make && make install && cd /<<BUILDDIR>>/bedops-2.4.40+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-2.4.40+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-2.4.40+dfsg && rm -f zlib && ln -sf zlib-1.2.7 third-party/zlib
make build -f /<<BUILDDIR>>/bedops-2.4.40+dfsg/system.mk/Makefile.linux
make[3]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg'
make -C applications/bed/bedextract/src -f Makefile build
make -C applications/bed/bedmap/src -f Makefile build
make -C applications/bed/bedops/src -f Makefile build
make -C applications/bed/closestfeats/src -f Makefile build
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/bedextract/src'
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-2.4.40+dfsg/applications/bed/bedmap/src'
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-2.4.40+dfsg/applications/bed/bedops/src'
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-2.4.40+dfsg/applications/bed/closestfeats/src'
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: 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:2171:88: 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:2171:88: 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:2171:88: 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:2908:68: 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:2908:68: 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:2908:68: 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:2908:68: 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:3434:88: 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: 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:3434:88: 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: 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:3434:88: 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: 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:3434:88: 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:4202:68: 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:4202:68: 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:4202:68: 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:4202:68: 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: 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: 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:359:87: note: length computed here
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:383:32: 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:383:32: 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:383:48: note: length computed here
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:485:16: 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:485:77: note: length computed here
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 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_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: 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: 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:560:83: note: length computed here
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::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: 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: 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:923:97: note: length computed here
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:964:28: 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:964:28: 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:964:98: note: length computed here
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);
| ~~~~~~^~~~~~~~~~~~
../../../../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: 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: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::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: 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: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:2464:28: 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: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);
| ~~~~~~^~~~~~~~~~~~
../../../../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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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: 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: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: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/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_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)':
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2221 | strncpy(recTokBuf, 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:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2221 | strncpy(recTokBuf, 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:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2221 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here
2221 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here
2221 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here
2221 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2237:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2237 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2237:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2237 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2237:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2237 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2237:65: note: length computed here
2237 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2237:65: note: length computed here
2237 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2237:65: note: length computed here
2237 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2249:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2249 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2249:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2249 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2249:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2249 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2249:59: note: length computed here
2249 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2249:59: note: length computed here
2249 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2249:59: note: length computed here
2249 | 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:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2221 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here
2221 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2237:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2237 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2237:65: note: length computed here
2237 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2249:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2249 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2249:59: note: length computed here
2249 | strncpy(recFilename, token, strlen(token) + 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:1677:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1677 | strncpy(*note, streamNote, strlen(streamNote) + 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:1677:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1677 | strncpy(*note, streamNote, strlen(streamNote) + 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:1677:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1677 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1677:50: note: length computed here
1677 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1677:50: note: length computed here
1677 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1677:50: note: length computed here
1677 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1660:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1660 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1660:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1660 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1660:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1660 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1660:52: note: length computed here
1660 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~^~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1660:52: note: length computed here
1660 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~^~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1660:52: note: length computed here
1660 | 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:1677:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1677 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1677:50: note: length computed here
1677 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1660:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1660 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1660:52: note: length computed here
1660 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~^~~~~~~~~~~~~
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/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: 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: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:1678:16: 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: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:1667:16: 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: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/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_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 )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../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 )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../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 )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+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 -ljansson -lz -lbz2 Bedops.cpp
mkdir -p ../bin && g++ -o ../bin/closest-features-typical -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+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 -ljansson -lz -lbz2 ClosestFeature.cpp
mkdir -p ../bin && g++ -o ../bin/bedextract-typical -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+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 -ljansson -lz -lbz2 ExtractRows.cpp
mkdir -p ../bin && g++ -o ../bin/bedmap-typical -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+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 -ljansson -lz -lbz2 Bedmap.cpp
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 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 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);
| ~~~~~~^~~~~
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);
| ~~~~~~^~~~~
../../../../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);
| ~~~~~~^~~~~
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-2.4.40+dfsg/applications/bed/bedextract/src'
make -C applications/bed/conversion/src -f Makefile build
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/conversion/src'
mkdir -p ../bin && cc -Wall -Wextra -pedantic -std=c99 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -iquote"/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/conversion/src" -iquote"../../../../interfaces/general-headers" convert2bed.c -o ../bin/convert2bed-typical -lpthread
convert2bed.c: In function 'c2b_process_intermediate_bytes_by_lines':
convert2bed.c:6631:103: warning: format '%zu' expects argument of type 'size_t', but argument 3 has type 'long unsigned int' [-Wformat=]
6631 | 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:6631:109: warning: format '%zu' expects argument of type 'size_t', but argument 4 has type 'long unsigned int' [-Wformat=]
6631 | 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:6631:115: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'long unsigned int' [-Wformat=]
6631 | 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
rm -rf objects
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/conversion/src'
make -C applications/bed/sort-bed/src -f Makefile build
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/sort-bed/src'
mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects-typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/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:2171:88: 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:2908:68: 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:3434:88: 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:4202:68: 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::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::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);
| ~~~~~~^~~~~~~~~~~~
mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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_JSONMetadataExists(FILE**, const char*)':
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1089:20: warning: comparison is always true due to limited range of data type [-Wtype-limits]
1089 | } while (currC != EOF);
| ^
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1090:63: warning: comparison is always false due to limited range of data type [-Wtype-limits]
1090 | if ((nReadBytes == STARCH_LEGACY_METADATA_SIZE) || (currC == EOF)) {
| ^
../../../../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:1306:24: warning: comparison is always true due to limited range of data type [-Wtype-limits]
1306 | } 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);
| ~~~~~~^~~~~~~~~~~
../../../../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:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2221 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here
2221 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2237:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2237 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2237:65: note: length computed here
2237 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2249:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2249 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2249:59: note: length computed here
2249 | strncpy(recFilename, token, strlen(token) + 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:1677:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1677 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1677:50: note: length computed here
1677 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1660:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1660 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1660:52: note: length computed here
1660 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~^~~~~~~~~~~~~
mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects-typical/unstarchHelpers.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:2276:13: 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:2278:13: 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:2640:33: 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:2642:33: 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/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_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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers
mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 SortDetails.cpp -o objects-typical/SortDetails.o -iquote../../../../interfaces/general-headers
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);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SortDetails.cpp:249:25: note: length computed here
249 | chromBufLen = strlen(chromBuf); // we know >= 1
| ~~~~~~^~~~~~~~~~
SortDetails.cpp: In function 'void lexSortBedData(BedData*)':
SortDetails.cpp:1343:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1343 | strncpy(chromBuf, beds->chroms[i]->chromName, chromBufLen);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SortDetails.cpp:1342:33: note: length computed here
1342 | 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)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
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 objects-typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers
mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers
rm -rf objects_typical
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/closestfeats/src'
mkdir -p ../bin && cp update-sort-bed-slurm.py ../bin/update-sort-bed-slurm-typical
make -C applications/bed/starch/src -f Makefile build
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/starch/src'
mkdir -p objects
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+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 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+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../../../..
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'void starch::UNSTARCH_printMetadataSignature(const unsigned char*)':
../../../../interfaces/src/data/starch/unstarchHelpers.c:2276:13: 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:2278:13: 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:2640:33: 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:2642:33: 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/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);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:1226:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1226 | static_cast<const CompressionType>( getArchiveType() ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1230:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1230 | static_cast<const Boolean>( getArchiveHeaderFlag() ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1231:40: 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:2003:51: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2003 | static_cast<const Boolean>( getArchiveHeaderFlag() )) != 0 ) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:2014:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2014 | static_cast<const Boolean>( getArchiveHeaderFlag() )) != 0 ) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~
../../../../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
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+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../../../..
../../../../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:2171:88: 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:2908:68: 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:3434:88: 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:4202:68: 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::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::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);
| ~~~~~~^~~~~~~~~~~~
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);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 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);
| ~~~~~~^~~~~
../../../../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
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../..
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_JSONMetadataExists(FILE**, const char*)':
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1089:20: warning: comparison is always true due to limited range of data type [-Wtype-limits]
1089 | } while (currC != EOF);
| ^
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1090:63: warning: comparison is always false due to limited range of data type [-Wtype-limits]
1090 | if ((nReadBytes == STARCH_LEGACY_METADATA_SIZE) || (currC == EOF)) {
| ^
../../../../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:1306:24: warning: comparison is always true due to limited range of data type [-Wtype-limits]
1306 | } 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);
| ~~~~~~^~~~~~~~~~~
../../../../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:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2221 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here
2221 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2237:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2237 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2237:65: note: length computed here
2237 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2249:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
2249 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2249:59: note: length computed here
2249 | strncpy(recFilename, token, strlen(token) + 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:1677:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1677 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1677:50: note: length computed here
1677 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1660:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
1660 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1660:52: note: length computed here
1660 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~^~~~~~~~~~~~~
mkdir -p objects
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects/starchFileHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p objects
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects/starchSha1Digest.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p objects
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+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 ../bin
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+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:106:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
106 | static_cast<const CompressionType>( type ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:121:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
121 | static_cast<const CompressionType>( type ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:123:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
123 | static_cast<const Boolean>( kStarchFinalizeTransformTrue ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:146:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
146 | static_cast<const CompressionType>( type ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:161:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
161 | static_cast<const CompressionType>( type ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:163:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
163 | static_cast<const Boolean>( kStarchFinalizeTransformTrue ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:191:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
191 | static_cast<const CompressionType>( type ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:194:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
194 | static_cast<const Boolean>( bedGeneratePerChrSignatureFlag ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:195:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
195 | static_cast<const Boolean>( bedHeaderFlag ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:196:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
196 | static_cast<const Boolean>( bedReportProgressFlag ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:197:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
197 | static_cast<const LineCountType>( bedReportProgressN )) != STARCH_EXIT_SUCCESS)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+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
mkdir -p ../bin
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+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:401:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
401 | static_cast<const unsigned long long>( metadataOffset ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:402:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
402 | static_cast<const Boolean>( headerFlag )) != 0) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:422:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
422 | static_cast<const unsigned long long>( metadataOffset ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:423:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
423 | static_cast<const Boolean>( headerFlag )) != 0) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:452:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
452 | static_cast<const unsigned long long>( sizeof(starchRevision2HeaderBytes) ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:453:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
453 | static_cast<const Boolean>( headerFlag )) != 0) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:473:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
473 | static_cast<const unsigned long long>( sizeof(starchRevision2HeaderBytes) ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:474:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
474 | static_cast<const Boolean>( headerFlag )) != 0) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:567:39: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
567 | UNSTARCH_printCompressionType(static_cast<const CompressionType>( type ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:798:78: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
798 | static_cast<const unsigned long long>( sizeof(starchRevision2HeaderBytes) ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:809:82: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
809 | static_cast<const unsigned long long>( sizeof(starchRevision2HeaderBytes) ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c: In function 'void starch::UNSTARCH_printMetadataSha1Signature(unsigned char*)':
unstarch.c:1334:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1334 | static_cast<const size_t>( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:1336:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1336 | static_cast<const size_t>( sha1BufferLength ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 'static bool starch::Starch::isStarch(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:678:25,
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: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: 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:541:76: note: length computed here
541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 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 'static bool starch::Starch::isStarch(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:678:25,
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 'static bool starch::Starch::isStarch(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:678:25,
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);
| ~~~~~~^~~~~
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+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
mkdir -p ../bin
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+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../../../..
In file included from /usr/include/c++/10/cassert:44,
from starchcat.c:33:
starchcat.c: In function 'int main(int, char**)':
starchcat.c:136:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
136 | assert( STARCHCAT_allocMetadataRecords ( &mdRecords, static_cast<const unsigned int>( numRecords ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:137:75: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
137 | assert( STARCHCAT_allocMetadataJSONObjects ( &metadataJSONs, static_cast<const unsigned int>( numRecords ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:138:87: 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:138:133: 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:139:75: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
139 | assert( STARCHCAT_checkMetadataJSONVersions ( &metadataJSONs, static_cast<const unsigned int>( numRecords ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:140:145: 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:141:69: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
141 | assert( STARCHCAT_allocChromosomeSummary ( &summary, static_cast<const unsigned int>( numChromosomes ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:142:124: 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:142:213: 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:143:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
143 | assert( STARCHCAT_allocChromosomeSummaries ( &summaries, static_cast<const unsigned int>( numChromosomes ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:144:127: 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:164:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
164 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:178:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
178 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:223:60: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
223 | assert( STARCHCAT_freeMetadataRecords( &mdRecords, static_cast<const unsigned int>( numRecords ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:233:68: 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:1338:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1338 | UNSTARCH_reverseTransformCoordinates( static_cast<const LineCountType>( t_lineIdx ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:1806:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1806 | UNSTARCH_reverseTransformCoordinates( static_cast<const LineCountType>( t_lineIdx ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:2131:78: 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:2450:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2450 | static_cast<const uint64_t>( inRec->mdOffset ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:2451:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2451 | static_cast<const Boolean>( inRec->hFlag )) != 0 ) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:2471:28: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2471 | static_cast<const uint64_t>( inRec->mdOffset ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:2472:28: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2472 | static_cast<const Boolean>( inRec->hFlag )) != 0 ) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:2509:23: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2509 | static_cast<const CompressionType>( outType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:2511:23: 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:3152:54: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
3152 | if (STARCHCAT2_setupBzip2InputStream(static_cast<const size_t>( inRecIdx ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:3316:69: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
3316 | static_cast<const size_t>( summary->numRecords ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:3455:77: 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:4265:43: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4265 | static_cast<const CompressionType>( outType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:4267:43: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4267 | static_cast<const Boolean>( kStarchFinalizeTransformFalse ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/cassert:44,
from starchcat.c:33:
starchcat.c: In function 'int starch::STARCHCAT_mergeChromosomeStreams(const ChromosomeSummaries*, starch::CompressionType, const char*)':
starchcat.c:4402:60: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4402 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:4420:63: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4420 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:4447:57: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4447 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:4479:39: 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:4541:62: 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++/10/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:5902:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
5902 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:5929:64: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
5929 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:5952:64: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
5952 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:5990:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
5990 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:6025:38: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
6025 | static_cast<const Boolean>( hFlag ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:6053:13: 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:6055:13: 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:6719:55: 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:7060:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
7060 | UNSTARCH_reverseTransformCoordinates( static_cast<const LineCountType>( *t_lineIdxPtr ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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::bed_check_iterator<BedType*, Sz>::operator++(int) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36,
inlined from 'int checkSort(const char**, unsigned int)' at CheckSort.cpp:51:28:
../../../../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 'int checkSort(const char**, unsigned int)':
../../../../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::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);
| ~~~~~~^~~~~~~~~~~~~~~~~~~
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);
| ~~~~~~^~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+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
mkdir -p ../bin
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+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../../../..
starchstrip.c: In function 'void starch::STARCHSTRIP_write_updated_metadata(FILE*)':
starchstrip.c:124:13: 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:126:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
126 | static_cast<const size_t>( STARCH2_MD_FOOTER_SHA1_LENGTH ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+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
rm -rf objects
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/starch/src'
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
mkdir -p ../bin && g++ -o ../bin/sort-bed-typical -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -iquote../../../../interfaces/general-headers 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-2.4.40+dfsg/applications/bed/sort-bed/src'
rm -rf objects_typical
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/bedops/src'
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/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++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
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 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 file included from /usr/include/c++/10/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++/10/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++/10/bits/stl_algo.h:4778:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
4778 | nth_element(_RandomAccessIterator __first, _RandomAccessIterator __nth,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:4778:5: 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++/10/bits/stl_algo.h:4778:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from Bedmap.cpp:35:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:121:21: 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 ../../../../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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | 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:100:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
100 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
103 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
108 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
rm -rf objects_typical
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg/applications/bed/bedmap/src'
make[3]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
make -j4 install DESTDIR=/<<BUILDDIR>>/bedops-2.4.40\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg'
mkdir -p bin
cp applications/bed/conversion/src/wrappers/bam2bed applications/bed/conversion/src/wrappers/bam2bed_gnuParallel applications/bed/conversion/src/wrappers/bam2bed_sge applications/bed/conversion/src/wrappers/bam2bed_slurm applications/bed/conversion/src/wrappers/bam2starch applications/bed/conversion/src/wrappers/bam2starch_gnuParallel applications/bed/conversion/src/wrappers/bam2starch_sge applications/bed/conversion/src/wrappers/bam2starch_slurm applications/bed/conversion/src/wrappers/gff2bed applications/bed/conversion/src/wrappers/gff2starch applications/bed/conversion/src/wrappers/gtf2bed applications/bed/conversion/src/wrappers/gtf2starch applications/bed/conversion/src/wrappers/gvf2bed applications/bed/conversion/src/wrappers/gvf2starch applications/bed/conversion/src/wrappers/psl2bed applications/bed/conversion/src/wrappers/psl2starch applications/bed/conversion/src/wrappers/rmsk2bed applications/bed/conversion/src/wrappers/rmsk2starch applications/bed/conversion/src/wrappers/sam2bed applications/bed/conversion/src/wrappers/sam2starch applications/bed/conversion/src/wrappers/vcf2bed applications/bed/conversion/src/wrappers/vcf2starch applications/bed/conversion/src/wrappers/wig2bed applications/bed/conversion/src/wrappers/wig2starch 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-2.4.40+dfsg'
debian/rules override_dh_install-arch
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg'
dh_install -a
mv bin/starch bin/bedops-starch
mkdir -p debian/bedops/usr/bin/
cp bin/* debian/bedops/usr/bin/
make[1]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installman-arch
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.40+dfsg'
cd bin && for f in * ; do help2man --no-discard-stderr --version-string="2.4.40+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-2.4.40+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-2.4.40+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-2.4.40+dfsg'
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
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/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/sort-bed contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/bedops/usr/bin/bedops contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/bedops/usr/bin/closest-features 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/bedextract debian/bedops/usr/bin/bedmap debian/bedops/usr/bin/sort-bed debian/bedops/usr/bin/bedops debian/bedops/usr/bin/convert2bed debian/bedops/usr/bin/closest-features debian/bedops/usr/bin/starchstrip debian/bedops/usr/bin/unstarch debian/bedops/usr/bin/bedops-starch debian/bedops/usr/bin/starchcat were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.40+dfsg-1_armhf.deb'.
dpkg-deb: building package 'bedops' in '../bedops_2.4.40+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../bedops_2.4.40+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 2021-10-26T05:59:54Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
bedops_2.4.40+dfsg-1_armhf.changes:
-----------------------------------
Format: 1.8
Date: Sun, 24 Oct 2021 13:20:15 +0530
Source: bedops
Binary: bedops bedops-dbgsym
Architecture: armhf
Version: 2.4.40+dfsg-1
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Description:
bedops - high-performance genomic feature operations
Closes: 997157
Changes:
bedops (2.4.40+dfsg-1) unstable; urgency=medium
.
* Team Upload.
[ Steffen Möller ]
* Update metadata - indent plus ref to guix
.
[ Nilesh Patra ]
* Add patch to fix FTBFS with new sphinx (Closes: #997157)
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547907903a56e78aecfd01946aef164eb25b35c3 1045692 bedops_2.4.40+dfsg-1_armhf.deb
Checksums-Sha256:
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ca32df792e7f59a9ec14c762dd26c50e9addb946b437c22cf6407b674d9c62d1 5588 bedops_2.4.40+dfsg-1_armhf.buildinfo
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Files:
2dcfb6cc4d9df4c75e8745081992bbdc 78188 debug optional bedops-dbgsym_2.4.40+dfsg-1_armhf.deb
392a684c71f915c99994571b2ef349ef 5588 science optional bedops_2.4.40+dfsg-1_armhf.buildinfo
d89ba2d292f7e6750cd2ffd2c2186a1e 1045692 science optional bedops_2.4.40+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
bedops-dbgsym_2.4.40+dfsg-1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 78188 bytes: control archive=536 bytes.
377 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: bedops-dbgsym
Source: bedops
Version: 2.4.40+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 95
Depends: bedops (= 2.4.40+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for bedops
Build-Ids: 9eb07fa2c8f71eb286d10a447770c7aea5cc1035
drwxr-xr-x root/root 0 2021-10-24 07:50 ./
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/lib/debug/.build-id/9e/
-rw-r--r-- root/root 86120 2021-10-24 07:50 ./usr/lib/debug/.build-id/9e/b07fa2c8f71eb286d10a447770c7aea5cc1035.debug
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops-dbgsym -> bedops
bedops_2.4.40+dfsg-1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 1045692 bytes: control archive=6152 bytes.
731 bytes, 15 lines control
21485 bytes, 236 lines md5sums
Package: bedops
Version: 2.4.40+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7093
Depends: libbz2-1.0, libc6 (>= 2.28), libgcc-s1 (>= 3.5), libjansson4 (>= 2.3), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), python3, 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 2021-10-24 07:50 ./
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/bin/
-rwxr-xr-x root/root 4711 2021-10-24 07:50 ./usr/bin/bam2bed
-rwxr-xr-x root/root 4501 2021-10-24 07:50 ./usr/bin/bam2bed_gnuParallel
-rwxr-xr-x root/root 5022 2021-10-24 07:50 ./usr/bin/bam2bed_sge
-rwxr-xr-x root/root 5021 2021-10-24 07:50 ./usr/bin/bam2bed_slurm
-rwxr-xr-x root/root 5842 2021-10-24 07:50 ./usr/bin/bam2starch
-rwxr-xr-x root/root 4507 2021-10-24 07:50 ./usr/bin/bam2starch_gnuParallel
-rwxr-xr-x root/root 5076 2021-10-24 07:50 ./usr/bin/bam2starch_sge
-rwxr-xr-x root/root 5014 2021-10-24 07:50 ./usr/bin/bam2starch_slurm
-rwxr-xr-x root/root 174136 2021-10-24 07:50 ./usr/bin/bedextract
-rwxr-xr-x root/root 5290160 2021-10-24 07:50 ./usr/bin/bedmap
-rwxr-xr-x root/root 378996 2021-10-24 07:50 ./usr/bin/bedops
-rwxr-xr-x root/root 75668 2021-10-24 07:50 ./usr/bin/bedops-starch
-rwxr-xr-x root/root 215108 2021-10-24 07:50 ./usr/bin/closest-features
-rwxr-xr-x root/root 113016 2021-10-24 07:50 ./usr/bin/convert2bed
-rwxr-xr-x root/root 3773 2021-10-24 07:50 ./usr/bin/gff2bed
-rwxr-xr-x root/root 4904 2021-10-24 07:50 ./usr/bin/gff2starch
-rwxr-xr-x root/root 3532 2021-10-24 07:50 ./usr/bin/gtf2bed
-rwxr-xr-x root/root 4663 2021-10-24 07:50 ./usr/bin/gtf2starch
-rwxr-xr-x root/root 3773 2021-10-24 07:50 ./usr/bin/gvf2bed
-rwxr-xr-x root/root 4904 2021-10-24 07:50 ./usr/bin/gvf2starch
-rwxr-xr-x root/root 3976 2021-10-24 07:50 ./usr/bin/psl2bed
-rwxr-xr-x root/root 5107 2021-10-24 07:50 ./usr/bin/psl2starch
-rwxr-xr-x root/root 3776 2021-10-24 07:50 ./usr/bin/rmsk2bed
-rwxr-xr-x root/root 4907 2021-10-24 07:50 ./usr/bin/rmsk2starch
-rwxr-xr-x root/root 4711 2021-10-24 07:50 ./usr/bin/sam2bed
-rwxr-xr-x root/root 5842 2021-10-24 07:50 ./usr/bin/sam2starch
-rwxr-xr-x root/root 186436 2021-10-24 07:50 ./usr/bin/sort-bed
-rwxr-xr-x root/root 10163 2021-10-24 07:50 ./usr/bin/starch-diff
-rwxr-xr-x root/root 145316 2021-10-24 07:50 ./usr/bin/starchcat
-rwxr-xr-x root/root 4299 2021-10-24 07:50 ./usr/bin/starchcluster_gnuParallel
-rwxr-xr-x root/root 4810 2021-10-24 07:50 ./usr/bin/starchcluster_sge
-rwxr-xr-x root/root 4716 2021-10-24 07:50 ./usr/bin/starchcluster_slurm
-rwxr-xr-x root/root 79700 2021-10-24 07:50 ./usr/bin/starchstrip
-rwxr-xr-x root/root 108308 2021-10-24 07:50 ./usr/bin/unstarch
-rwxr-xr-x root/root 32686 2021-10-24 07:50 ./usr/bin/update-sort-bed-migrate-candidates
-rwxr-xr-x root/root 20701 2021-10-24 07:50 ./usr/bin/update-sort-bed-slurm
-rwxr-xr-x root/root 22682 2021-10-24 07:50 ./usr/bin/update-sort-bed-starch-slurm
-rwxr-xr-x root/root 4675 2021-10-24 07:50 ./usr/bin/vcf2bed
-rwxr-xr-x root/root 5806 2021-10-24 07:50 ./usr/bin/vcf2starch
-rwxr-xr-x root/root 4598 2021-10-24 07:50 ./usr/bin/wig2bed
-rwxr-xr-x root/root 5729 2021-10-24 07:50 ./usr/bin/wig2starch
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops/
-rw-r--r-- root/root 267 2021-10-24 07:33 ./usr/share/doc/bedops/README.Debian
-rw-r--r-- root/root 1618 2021-10-24 07:50 ./usr/share/doc/bedops/changelog.Debian.gz
-rw-r--r-- root/root 22054 2021-07-27 21:43 ./usr/share/doc/bedops/changelog.gz
-rw-r--r-- root/root 1156 2021-10-24 07:33 ./usr/share/doc/bedops/copyright
drwxr-xr-x root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/
-rw-r--r-- root/root 954 2021-07-27 21:43 ./usr/share/doc/bedops/tests/Makefile
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops/tests/bedops/
-rw-r--r-- root/root 2166 2021-10-24 07:50 ./usr/share/doc/bedops/tests/bedops/Makefile.gz
drwxr-xr-x root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/
-rw-r--r-- root/root 197 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001.expected
-rw-r--r-- root/root 44 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001a.test
-rw-r--r-- root/root 53 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001b.test
-rw-r--r-- root/root 24 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.chrom.001.expected
-rw-r--r-- root/root 26 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.complement.001.expected
-rw-r--r-- root/root 31 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.difference.001.expected
-rw-r--r-- root/root 23 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.ec.001a.test
-rw-r--r-- root/root 69 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.element-of.001.expected
-rw-r--r-- root/root 91 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001.expected
-rw-r--r-- root/root 52 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001a.test
-rw-r--r-- root/root 104 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001b.test
-rw-r--r-- root/root 37 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.merge.001.expected
-rw-r--r-- root/root 111 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.merge.001.test
-rw-r--r-- root/root 368 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.named-pipe.001.expected
-rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.not-element-of.001.expected
-rw-r--r-- root/root 148 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001.expected
-rw-r--r-- root/root 39 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001a.test
-rw-r--r-- root/root 56 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001b.test
-rw-r--r-- root/root 40 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001c.test
-rw-r--r-- root/root 257 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.stdin.001.expected
-rw-r--r-- root/root 130 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.symdiff.001.expected
-rw-r--r-- root/root 134 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.union.001.expected
-rw-r--r-- root/root 126 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.union.001.test
-rw-r--r-- root/root 171 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.chop.002.expected
-rw-r--r-- root/root 20 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.chrom.002.expected
-rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.complement.002.expected
-rw-r--r-- root/root 2172 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002.expected
-rw-r--r-- root/root 3033 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002a.test
-rw-r--r-- root/root 2941 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002b.test
-rw-r--r-- root/root 18 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.element-of.002.expected
-rw-r--r-- root/root 13 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.intersection.002.expected
-rw-r--r-- root/root 26 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.intersection.002.test
-rw-r--r-- root/root 11 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.merge.002.expected
-rw-r--r-- root/root 11 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.not-element-of.002.expected
-rw-r--r-- root/root 376 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002.expected
-rw-r--r-- root/root 48 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002a.test
-rw-r--r-- root/root 49 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002b.test
-rw-r--r-- root/root 101 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002c.test
-rw-r--r-- root/root 39 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002d.test
-rw-r--r-- root/root 131 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002e.test
-rw-r--r-- root/root 118 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.symdiff.002.expected
-rw-r--r-- root/root 56 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.union.002.expected
-rw-r--r-- root/root 368 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.chop.003.expected
-rw-r--r-- root/root 24 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.chrom.003.expected
-rw-r--r-- root/root 61 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.complement.003.expected
-rw-r--r-- root/root 3794 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.difference.003.expected
-rw-r--r-- root/root 42 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.element-of.003.expected
-rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.intersection.003.expected
-rw-r--r-- root/root 35 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.merge.003.expected
-rw-r--r-- root/root 46 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.merge.003.test
-rw-r--r-- root/root 21 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003.expected
-rw-r--r-- root/root 63 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003a.test
-rw-r--r-- root/root 42 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003b.test
-rw-r--r-- root/root 153 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.partition.003.expected
-rw-r--r-- root/root 398 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.partition.003.test
-rw-r--r-- root/root 22 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003.expected
-rw-r--r-- root/root 18 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003a.test
-rw-r--r-- root/root 29 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003b.test
-rw-r--r-- root/root 9 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003c.test
-rw-r--r-- root/root 11 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003d.test
-rw-r--r-- root/root 355 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.union.003.expected
-rw-r--r-- root/root 360 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.union.003.test
-rw-r--r-- root/root 257 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.chop.004.expected
-rw-r--r-- root/root 24 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.chrom.004.expected
-rw-r--r-- root/root 111 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004.expected
-rw-r--r-- root/root 46 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004a.test
-rw-r--r-- root/root 132 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004b.test
-rw-r--r-- root/root 94 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004c.test
-rw-r--r-- root/root 30 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004.expected
-rw-r--r-- root/root 30 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004a.test
-rw-r--r-- root/root 31 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004b.test
-rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004.expected
-rw-r--r-- root/root 92 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004a.test
-rw-r--r-- root/root 23 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004b.test
-rw-r--r-- root/root 49 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004.expected
-rw-r--r-- root/root 103 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004a.test
-rw-r--r-- root/root 85 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004b.test
-rw-r--r-- root/root 47 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004c.test
-rw-r--r-- root/root 72 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.merge.004.expected
-rw-r--r-- root/root 117 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.partition.004.expected
-rw-r--r-- root/root 117 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.partition.004.test
-rw-r--r-- root/root 52 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.symdiff.004.expected
-rw-r--r-- root/root 22 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.union.004.expected
-rw-r--r-- root/root 32 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.union.004.test
-rw-r--r-- root/root 385 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.chop.005.expected
-rw-r--r-- root/root 87 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.chop.005.test
-rw-r--r-- root/root 20 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.complement.005.expected
-rw-r--r-- root/root 40 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.complement.005.test
-rw-r--r-- root/root 31 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.difference.005.expected
-rw-r--r-- root/root 93 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.merge.005.expected
-rw-r--r-- root/root 43 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.merge.005.test
-rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.symdiff.005.expected
-rw-r--r-- root/root 11 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.union.005.expected
-rw-r--r-- root/root 35 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.complement.006.expected
-rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.difference.006.expected
-rw-r--r-- root/root 41 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006.expected
-rw-r--r-- root/root 37 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006a.test
-rw-r--r-- root/root 35 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006b.test
-rw-r--r-- root/root 31 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006c.test
-rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.union.006.expected
-rw-r--r-- root/root 9 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.complement.007.expected
-rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.difference.007.expected
-rw-r--r-- root/root 55 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007.expected
-rw-r--r-- root/root 56 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007a.test
-rw-r--r-- root/root 69 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007b.test
-rw-r--r-- root/root 33 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.union.007.expected
-rw-r--r-- root/root 79 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/008.complement.008.expected
-rw-r--r-- root/root 197 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/008.merge.008.expected
-rw-r--r-- root/root 33 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/008.union.008.expected
-rw-r--r-- root/root 175 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/009.complement.009.expected
-rw-r--r-- root/root 52 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/009.merge.009.expected
-rw-r--r-- root/root 33 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/009.union.009.expected
-rw-r--r-- root/root 43 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/009.union.009.test
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops/tests/conversion/
-rw-r--r-- root/root 1159 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/Makefile.gz
drwxr-xr-x root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/
-rw-r--r-- root/root 398 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/001.wig2bed_with_chr_prefix_no_header.001.expected
-rw-r--r-- root/root 352 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/001.wig2bed_with_chr_prefix_no_header.001.wig
-rw-r--r-- root/root 368 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/002.wig2bed_no_chr_prefix_no_header.001.expected
-rw-r--r-- root/root 322 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/002.wig2bed_no_chr_prefix_no_header.001.wig
-rw-r--r-- root/root 102 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.001.expected
-rw-r--r-- root/root 52 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.001.wig
-rw-r--r-- root/root 102 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.002.expected
-rw-r--r-- root/root 60 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.002.wig
-rw-r--r-- root/root 93 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.001.expected
-rw-r--r-- root/root 49 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.001.wig
-rw-r--r-- root/root 93 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.002.expected
-rw-r--r-- root/root 56 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.002.wig
-rw-r--r-- root/root 170 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.001.expected
-rw-r--r-- root/root 85 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.001.wig
-rw-r--r-- root/root 34 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.002.expected
-rw-r--r-- root/root 43 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.002.wig
-rw-r--r-- root/root 155 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.001.expected
-rw-r--r-- root/root 82 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.001.wig
-rw-r--r-- root/root 31 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.002.expected
-rw-r--r-- root/root 40 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.002.wig
-rw-r--r-- root/root 538 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.001.expected
-rw-r--r-- root/root 454 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.001.wig
-rw-r--r-- root/root 583 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.002.expected
-rw-r--r-- root/root 700 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.003.expected
-rw-r--r-- root/root 763 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.004.expected
-rw-r--r-- root/root 493 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.001.expected
-rw-r--r-- root/root 421 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.001.wig
-rw-r--r-- root/root 538 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.002.expected
-rw-r--r-- root/root 652 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.003.expected
-rw-r--r-- root/root 715 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.004.expected
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops/tests/starch/
-rw-r--r-- root/root 1078 2021-10-24 07:50 ./usr/share/doc/bedops/tests/starch/Makefile.gz
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops/tests/starch/data/
-rw-r--r-- root/root 1935 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.starch_api.bedmap.001.expected
-rw-r--r-- root/root 2813 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.starch_api.bedmap.001.test.gz
-rw-r--r-- root/root 772 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr1.001.test
-rw-r--r-- root/root 1166 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr1andChr2.001.expected
-rw-r--r-- root/root 772 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr2.001.test
-rw-r--r-- root/root 764 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.unstarch.signature.001.expected
-rw-r--r-- root/root 2851 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.unstarch.signature.001.test.gz
-rw-r--r-- root/root 218 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/002.unstarch.signature.001.expected
-rw-r--r-- root/root 2254 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/002.unstarch.signature.001.test.gz
-rw-r--r-- root/root 109 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/README
-rw-r--r-- root/root 426 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/hg38.bed
-rw-r--r-- root/root 1516 2021-10-24 07:50 ./usr/share/doc/bedops/tests/starch/generate_random_intervals.sh
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/man/
drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/man/man1/
-rw-r--r-- root/root 348 2021-10-24 07:50 ./usr/share/man/man1/bam2bed.1.gz
-rw-r--r-- root/root 355 2021-10-24 07:50 ./usr/share/man/man1/bam2starch.1.gz
-rw-r--r-- root/root 847 2021-10-24 07:50 ./usr/share/man/man1/bedextract.1.gz
-rw-r--r-- root/root 2561 2021-10-24 07:50 ./usr/share/man/man1/bedmap.1.gz
-rw-r--r-- root/root 1044 2021-10-24 07:50 ./usr/share/man/man1/bedops-starch.1.gz
-rw-r--r-- root/root 1392 2021-10-24 07:50 ./usr/share/man/man1/bedops.1.gz
-rw-r--r-- root/root 1279 2021-10-24 07:50 ./usr/share/man/man1/closest-features.1.gz
-rw-r--r-- root/root 1223 2021-10-24 07:50 ./usr/share/man/man1/convert2bed.1.gz
-rw-r--r-- root/root 348 2021-10-24 07:50 ./usr/share/man/man1/gff2bed.1.gz
-rw-r--r-- root/root 355 2021-10-24 07:50 ./usr/share/man/man1/gff2starch.1.gz
-rw-r--r-- root/root 348 2021-10-24 07:50 ./usr/share/man/man1/gtf2bed.1.gz
-rw-r--r-- root/root 355 2021-10-24 07:50 ./usr/share/man/man1/gtf2starch.1.gz
-rw-r--r-- root/root 349 2021-10-24 07:50 ./usr/share/man/man1/gvf2bed.1.gz
-rw-r--r-- root/root 355 2021-10-24 07:50 ./usr/share/man/man1/gvf2starch.1.gz
-rw-r--r-- root/root 347 2021-10-24 07:50 ./usr/share/man/man1/psl2bed.1.gz
-rw-r--r-- root/root 355 2021-10-24 07:50 ./usr/share/man/man1/psl2starch.1.gz
-rw-r--r-- root/root 350 2021-10-24 07:50 ./usr/share/man/man1/rmsk2bed.1.gz
-rw-r--r-- root/root 357 2021-10-24 07:50 ./usr/share/man/man1/rmsk2starch.1.gz
-rw-r--r-- root/root 348 2021-10-24 07:50 ./usr/share/man/man1/sam2bed.1.gz
-rw-r--r-- root/root 355 2021-10-24 07:50 ./usr/share/man/man1/sam2starch.1.gz
-rw-r--r-- root/root 741 2021-10-24 07:50 ./usr/share/man/man1/sort-bed.1.gz
-rw-r--r-- root/root 720 2021-10-24 07:50 ./usr/share/man/man1/starch-diff.1.gz
-rw-r--r-- root/root 988 2021-10-24 07:50 ./usr/share/man/man1/starchcat.1.gz
-rw-r--r-- root/root 1109 2021-10-24 07:50 ./usr/share/man/man1/starchstrip.1.gz
-rw-r--r-- root/root 1544 2021-10-24 07:50 ./usr/share/man/man1/unstarch.1.gz
-rw-r--r-- root/root 1764 2021-10-24 07:50 ./usr/share/man/man1/update-sort-bed-migrate-candidates.1.gz
-rw-r--r-- root/root 1330 2021-10-24 07:50 ./usr/share/man/man1/update-sort-bed-slurm.1.gz
-rw-r--r-- root/root 1383 2021-10-24 07:50 ./usr/share/man/man1/update-sort-bed-starch-slurm.1.gz
-rw-r--r-- root/root 348 2021-10-24 07:50 ./usr/share/man/man1/vcf2bed.1.gz
-rw-r--r-- root/root 356 2021-10-24 07:50 ./usr/share/man/man1/vcf2starch.1.gz
-rw-r--r-- root/root 348 2021-10-24 07:50 ./usr/share/man/man1/wig2bed.1.gz
-rw-r--r-- root/root 356 2021-10-24 07:50 ./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: 44604
Build-Time: 1200
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 247
Job: bedops_2.4.40+dfsg-1
Machine Architecture: armhf
Package: bedops
Package-Time: 1468
Source-Version: 2.4.40+dfsg-1
Space: 44604
Status: successful
Version: 2.4.40+dfsg-1
--------------------------------------------------------------------------------
Finished at 2021-10-26T05:59:54Z
Build needed 00:24:28, 44604k disk space