bedops →
2.4.41+dfsg-1 →
armhf → 2022-07-23 08:47:33
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| bedops 2.4.41+dfsg-1 (armhf) Sat, 23 Jul 2022 04:36:06 +0000 |
+==============================================================================+
Package: bedops
Version: 2.4.41+dfsg-1
Source Version: 2.4.41+dfsg-1
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-db50ee65-2cde-43b1-92e4-e4ec7a421c6b' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.1 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.0 MB]
Fetched 27.2 MB in 28s (971 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| 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://172.17.4.1/private bookworm-staging/main bedops 2.4.41+dfsg-1 (dsc) [2178 B]
Get:2 http://172.17.4.1/private bookworm-staging/main bedops 2.4.41+dfsg-1 (tar) [13.5 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main bedops 2.4.41+dfsg-1 (diff) [10.4 kB]
Fetched 13.5 MB in 1s (10.3 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bedops-ziV3CY/bedops-2.4.41+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bedops-ziV3CY' 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-Islnrs/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-Islnrs/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-Islnrs/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-Islnrs/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Islnrs/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Islnrs/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-Islnrs/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-Islnrs/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Islnrs/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (1958 B/s)
Reading package lists...
W: copy:/<<BUILDDIR>>/resolver-Islnrs/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-Islnrs/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 9 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Islnrs/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (11.4 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12817 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) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), help2man, libbz2-dev, libjansson-dev, python3-distutils, zlib1g-dev
Filtered Build-Depends: debhelper-compat (= 13), help2man, libbz2-dev, libjansson-dev, python3-distutils, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-bedops-dummy' in '/<<BUILDDIR>>/resolver-Islnrs/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-Islnrs/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Islnrs/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Islnrs/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-Islnrs/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-Islnrs/apt_archive ./ Sources [535 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Islnrs/apt_archive ./ Packages [614 B]
Fetched 2482 B in 1s (2171 B/s)
Reading package lists...
W: copy:/<<BUILDDIR>>/resolver-Islnrs/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-Islnrs/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install bedops build dependencies (apt-based resolver)
------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev 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 libfile-stripnondeterminism-perl
libicu71 libjansson-dev libjansson4 liblocale-gettext-perl libmagic-mgc
libmagic1 libmpdec3 libpipeline1 libpython3-stdlib libpython3.10-minimal
libpython3.10-stdlib libsigsegv2 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db media-types po-debconf python3 python3-distutils
python3-lib2to3 python3-minimal python3.10 python3.10-minimal 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 python3.10-venv
python3.10-doc binfmt-support
Recommended packages:
curl | wget | lynx bzip2-doc libarchive-cpio-perl 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 libfile-stripnondeterminism-perl
libicu71 libjansson-dev libjansson4 liblocale-gettext-perl libmagic-mgc
libmagic1 libmpdec3 libpipeline1 libpython3-stdlib libpython3.10-minimal
libpython3.10-stdlib libsigsegv2 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db media-types po-debconf python3 python3-distutils
python3-lib2to3 python3-minimal python3.10 python3.10-minimal
sbuild-build-depends-bedops-dummy zlib1g-dev
0 upgraded, 49 newly installed, 0 to remove and 9 not upgraded.
Need to get 23.8 MB of archives.
After this operation, 89.5 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Islnrs/apt_archive ./ sbuild-build-depends-bedops-dummy 0.invalid.0 [900 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf liblocale-gettext-perl armhf 1.07-4+b2 [18.3 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.5-1+b1 [815 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.8-1 [84.1 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf python3.10-minimal armhf 3.10.5-1+b1 [1637 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.4-1+b1 [38.9 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf media-types all 8.0.0 [33.4 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-stdlib armhf 3.10.5-1+b1 [1626 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf python3.10 armhf 3.10.5-1+b1 [542 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.10.4-1+b1 [21.9 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.10.4-1+b1 [38.4 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38-4 [137 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-1 [33.7 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.2-1 [1362 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-6 [171 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.14-1 [36.6 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-6 [510 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.8 [195 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-3 [10.4 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-1 [175 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-6 [1214 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.8 [1070 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf help2man armhf 1.49.2 [202 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libbz2-dev armhf 1.0.8-5+b2 [26.8 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libjansson4 armhf 2.14-2 [37.0 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libjansson-dev armhf 2.14-2 [38.0 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.9.12-1 [79.9 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.9.12-1 [146 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4+b2 [183 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libbz2-dev:armhf (1.0.8-5+b2) ...
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Unpacking libjansson4:armhf (2.14-2) ...
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Preparing to unpack .../38-sbuild-build-depends-bedops-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-bedops-dummy (0.invalid.0) ...
Setting up media-types (8.0.0) ...
Setting up libpipeline1:armhf (1.5.6-1) ...
Setting up libicu71:armhf (71.1-3) ...
Setting up bsdextrautils (2.38-4) ...
Setting up libmagic-mgc (1:5.41-4) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.8) ...
Setting up libmagic1:armhf (1:5.41-4) ...
Setting up gettext-base (0.21-6) ...
Setting up file (1:5.41-4) ...
Setting up libjansson4:armhf (2.14-2) ...
Setting up autotools-dev (20220109.1) ...
Setting up libsigsegv2:armhf (2.14-1) ...
Setting up autopoint (0.21-6) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-4+b2) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libmpdec3:armhf (2.5.1-2+rpi1) ...
Setting up libsub-override-perl (0.09-3) ...
Setting up libelf1:armhf (0.187-1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1) ...
Setting up libjansson-dev:armhf (2.14-2) ...
Setting up liblocale-gettext-perl (1.07-4+b2) ...
Setting up libbz2-dev:armhf (1.0.8-5+b2) ...
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up gettext (0.21-6) ...
Setting up libtool (2.4.7-4) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up help2man (1.49.2) ...
Setting up libpython3.10-stdlib:armhf (3.10.5-1+b1) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.13.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-8) ...
Setting up libpython3-stdlib:armhf (3.10.4-1+b1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up python3.10 (3.10.5-1+b1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up python3 (3.10.4-1+b1) ...
Setting up man-db (2.10.2-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up python3-lib2to3 (3.9.12-1) ...
Setting up python3-distutils (3.9.12-1) ...
Setting up debhelper (13.8) ...
Setting up sbuild-build-depends-bedops-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.33-7+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.38.50.20220707-1+rpi1 dpkg-dev_1.21.9+rpi1 g++-11_11.3.0-3+rpi1 gcc-11_11.3.0-3+rpi1 libc6-dev_2.33-7+rpi1 libstdc++-11-dev_11.3.0-3+rpi1 libstdc++6_12.1.0-5+rpi1 linux-libc-dev_5.18.5-1+rpi1
Package versions: adduser_3.121 apt_2.5.1 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2+rpi1 base-passwd_3.5.52 bash_5.1-6.1 binutils_2.38.50.20220707-1+rpi1 binutils-arm-linux-gnueabihf_2.38.50.20220707-1+rpi1 binutils-common_2.38.50.20220707-1+rpi1 bsdextrautils_2.38-4 bsdutils_1:2.38-4 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.3.0-3+rpi1 dash_0.5.11+git20210903+057cd650a4ed-8 debconf_1.5.79 debhelper_13.8 debianutils_5.7-0.2 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dirmngr_2.2.35-3 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.5-2 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:11.2.0-2+rpi1 g++-11_11.3.0-3+rpi1 gcc_4:11.2.0-2+rpi1 gcc-11_11.3.0-3+rpi1 gcc-11-base_11.3.0-3+rpi1 gcc-12-base_12.1.0-5+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_0.21-6 gettext-base_0.21-6 gnupg_2.2.35-3 gnupg-l10n_2.2.35-3 gnupg-utils_2.2.35-3 gpg_2.2.35-3 gpg-agent_2.2.35-3 gpg-wks-client_2.2.35-3 gpg-wks-server_2.2.35-3 gpgconf_2.2.35-3 gpgsm_2.2.35-3 gpgv_2.2.35-3 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 help2man_1.49.2 hostname_3.23 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20211215-1 libacl1_2.3.1-1 libapt-pkg6.0_2.5.1 libarchive-zip-perl_1.68-1 libasan6_11.3.0-3+rpi1 libassuan0_2.5.5-4 libatomic1_12.1.0-5+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1 libaudit1_1:3.0.7-1+b1 libbinutils_2.38.50.20220707-1+rpi1 libblkid1_2.38-4 libbz2-1.0_1.0.8-5+b2 libbz2-dev_1.0.8-5+b2 libc-bin_2.33-7+rpi1 libc-dev-bin_2.33-7+rpi1 libc6_2.33-7+rpi1 libc6-dev_2.33-7+rpi1 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.1.0-5+rpi1 libcom-err2_1.46.5-2 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.38.50.20220707-1+rpi1 libctf0_2.38.50.20220707-1+rpi1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.263 libdebhelper-perl_13.8 libdpkg-perl_1.21.9+rpi1 libelf1_0.187-1 libexpat1_2.4.8-1 libext2fs2_1.46.5-2 libfakeroot_1.29-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-11-dev_11.3.0-3+rpi1 libgcc-s1_12.1.0-5+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgmp10_2:6.2.1+dfsg1-1 libgnutls30_3.7.6-2 libgomp1_12.1.0-5+rpi1 libgpg-error0_1.45-2 libgssapi-krb5-2_1.19.2-2+b7 libhogweed6_3.7.3-1 libicu71_71.1-3 libidn2-0_2.3.3-1 libisl23_0.24-2 libjansson-dev_2.14-2 libjansson4_2.14-2 libk5crypto3_1.19.2-2+b7 libkeyutils1_1.6.3-1 libkrb5-3_1.19.2-2+b7 libkrb5support0_1.19.2-2+b7 libksba8_1.6.0-3 libldap-2.5-0_2.5.12+dfsg-2 liblocale-gettext-perl_1.07-4+b2 liblz4-1_1.9.3-2 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmount1_2.38-4 libmpc3_1.2.1-2 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncursesw6_6.3+20220423-2 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.4.0-13 libpam-modules-bin_1.4.0-13 libpam-runtime_1.4.0-13 libpam0g_1.4.0-13 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libperl5.34_5.34.0-5 libpipeline1_1.5.6-1 libpython3-stdlib_3.10.4-1+b1 libpython3.10-minimal_3.10.5-1+b1 libpython3.10-stdlib_3.10.5-1+b1 libreadline8_8.1.2-1.2 libsasl2-2_2.1.28+dfsg-6+b1 libsasl2-modules-db_2.1.28+dfsg-6+b1 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsigsegv2_2.14-1 libsmartcols1_2.38-4 libsqlite3-0_3.39.0-2 libss2_1.46.5-2 libssl1.1_1.1.1o-1 libssl3_3.0.4-2 libstdc++-11-dev_11.3.0-3+rpi1 libstdc++6_12.1.0-5+rpi1 libsub-override-perl_0.09-3 libsystemd0_251.2-5+rpi1 libtasn1-6_4.18.0-4 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.7-4 libubsan1_12.1.0-5+rpi1 libuchardet0_0.0.7-1 libudev1_251.2-5+rpi1 libunistring2_1.0-1 libuuid1_2.38-4 libxml2_2.9.14+dfsg-1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.18.5-1+rpi1 login_1:4.11.1+dfsg1-2 logsave_1.46.5-2 lsb-base_11.2+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.10.2-1 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38-4 nano_6.3-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.3 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-5 perl-base_5.34.0-5 perl-modules-5.34_5.34.0-5 pinentry-curses_1.2.0-2 po-debconf_1.0.21+nmu1 python3_3.10.4-1+b1 python3-distutils_3.9.12-1 python3-lib2to3_3.9.12-1 python3-minimal_3.10.4-1+b1 python3.10_3.10.5-1+b1 python3.10-minimal_3.10.5-1+b1 raspbian-archive-keyring_20120528.2 readline-common_8.1.2-1.2 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 sgml-base_1.30 sysvinit-utils_3.03-1 tar_1.34+dfsg-1 tzdata_2022a-1 util-linux_2.38-4 util-linux-extra_2.38-4 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4+b2 zlib1g-dev_1:1.2.11.dfsg-4+b2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.LSkL8V3d/trustedkeys.kbx': General error
gpgv: Signature made Mon Jul 18 09:03:24 2022 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./bedops_2.4.41+dfsg-1.dsc
dpkg-source: info: extracting bedops in /<<BUILDDIR>>/bedops-2.4.41+dfsg
dpkg-source: info: unpacking bedops_2.4.41+dfsg.orig.tar.xz
dpkg-source: info: unpacking bedops_2.4.41+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 disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-db50ee65-2cde-43b1-92e4-e4ec7a421c6b
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package bedops
dpkg-buildpackage: info: source version 2.4.41+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg'
dh_auto_clean
make -j4 clean
make[2]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg'
make clean -f system.mk/Makefile.linux
make[3]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg'
rm -rf bin
rm -rf bin
rm -rf bin
rm -rf modules
make -C applications/bed/bedextract/src -f Makefile clean
make -C applications/bed/bedmap/src -f Makefile clean
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/bedextract/src'
make -C applications/bed/bedops/src -f Makefile clean
rm -rf objects_typical
make -C applications/bed/closestfeats/src -f Makefile clean
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/bedmap/src'
rm -rf objects_typical
rm -rf ../bin
rm -rf ../bin
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/bedextract/src'
make -C applications/bed/conversion/src -f Makefile clean
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/bedmap/src'
make -C applications/bed/sort-bed/src -f Makefile clean
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/bedops/src'
rm -rf objects_typical
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/closestfeats/src'
rm -rf objects_typical
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/conversion/src'
rm -rf ../bin
rm -rf ../bin
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/sort-bed/src'
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/bedops/src'
make -C applications/bed/starch/src -f Makefile clean
rm -rf objects
rm -rf *.so *~
rm -rf objects-typical
rm -rf ../bin
rm -rf ../bin
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/conversion/src'
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/starch/src'
rm -rf ../lib
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/closestfeats/src'
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/sort-bed/src'
rm -f ../lib/libstarch_debug.a
rm -f ../lib/libstarch_gprof.a
rm -rf objects
rm -rf ../bin
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg'
rm -rf docs/_build/
make[1]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg'
dh_clean
debian/rules binary-arch
dh binary-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-2.4.41+dfsg'
make -f system.mk/Makefile.linux
make[2]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg'
#bzcat | tar -x -C third-party
#cd third-party/jansson-2.6 && ./configure --prefix=/<<BUILDDIR>>/bedops-2.4.41+dfsg/third-party/jansson-2.6 && make && make install && cd /<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+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-2.4.41+dfsg && rm -f zlib && ln -sf zlib-1.2.7 third-party/zlib
make build -f /<<BUILDDIR>>/bedops-2.4.41+dfsg/system.mk/Makefile.linux
make[3]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+dfsg/applications/bed/bedextract/src'
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+dfsg/applications/bed/bedmap/src'
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+dfsg/applications/bed/bedops/src'
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+dfsg/applications/bed/closestfeats/src'
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+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-2.4.41+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-2.4.41+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-2.4.41+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-2.4.41+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-2.4.41+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-2.4.41+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-2.4.41+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-2.4.41+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-2.4.41+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-2.4.41+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-2.4.41+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_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-truncation]
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-truncation]
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-truncation]
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-truncation]
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:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)':
../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)':
../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)':
../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
../../../../interfaces/src/data/starch/starchHelpers.c: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: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: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: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);
| ~~~~~~^~~~~~~~~~~~
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+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-2.4.41+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-2.4.41+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-truncation]
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-truncation]
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-truncation]
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: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-truncation]
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-truncation]
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-truncation]
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-truncation]
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-truncation]
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-truncation]
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: 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-truncation]
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: 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-truncation]
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: 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-truncation]
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);
| ~~~~~~^~~~~~~
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+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-2.4.41+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-truncation]
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-truncation]
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-truncation]
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-truncation]
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-truncation]
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-truncation]
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-truncation]
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-truncation]
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-truncation]
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-truncation]
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-truncation]
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-truncation]
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 )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+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
../../../../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-2.4.41+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
../../../../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-2.4.41+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-2.4.41+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-2.4.41+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/bedextract-typical -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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/bedops-typical -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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 objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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/closest-features-typical -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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 objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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/bedmap-typical -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-truncation]
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);
| ~~~~~~^~~~~~~~
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 '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-truncation]
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 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-truncation]
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);
| ~~~~~~^~~~~~~~
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 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-truncation]
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 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-truncation]
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);
| ~~~~~~^~~~~~~~
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 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-truncation]
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 '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-truncation]
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-2.4.41+dfsg/applications/bed/bedextract/src'
make -C applications/bed/conversion/src -f Makefile build
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -iquote"/<<BUILDDIR>>/bedops-2.4.41+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:6716:103: warning: format '%zu' expects argument of type 'size_t', but argument 3 has type 'long unsigned int' [-Wformat=]
6716 | 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:6716:109: warning: format '%zu' expects argument of type 'size_t', but argument 4 has type 'long unsigned int' [-Wformat=]
6716 | 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:6716:115: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'long unsigned int' [-Wformat=]
6716 | 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: In function 'c2b_line_convert_sam_to_bed_unsorted_with_split_operation':
convert2bed.c:5017:25: warning: 'sprintf' argument 3 overlaps destination object '<unknown>' [-Wrestrict]
5017 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
convert2bed.c:5043:21: warning: 'sprintf' argument 3 overlaps destination object '<unknown>' [-Wrestrict]
5043 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
convert2bed.c:5061:21: warning: 'sprintf' argument 3 overlaps destination object '<unknown>' [-Wrestrict]
5061 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
convert2bed.c:4950:25: warning: 'sprintf' argument 3 overlaps destination object '<unknown>' [-Wrestrict]
4950 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
convert2bed.c:4974:21: warning: 'sprintf' argument 3 overlaps destination object '<unknown>' [-Wrestrict]
4974 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rm -rf objects
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/conversion/src'
make -C applications/bed/sort-bed/src -f Makefile build
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/sort-bed/src'
mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+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-2.4.41+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_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-truncation]
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:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
../../../../interfaces/src/data/starch/starchHelpers.c: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);
| ~~~~~~^~~~~~~~~~~~
mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-truncation]
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-truncation]
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-truncation]
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);
| ~~~~~~^~~~~~~
mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-truncation]
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-truncation]
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-truncation]
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-2.4.41+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-2.4.41+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-2.4.41+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-truncation]
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-truncation]
250 | strncpy(chrom->chromName, chromBuf, chromBufLen);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SortDetails.cpp: In function 'int processData(const char**, unsigned int, double, char*, bool, bool)':
SortDetails.cpp:249:25: note: length computed here
249 | chromBufLen = strlen(chromBuf); // we know >= 1
| ~~~~~~^~~~~~~~~~
mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+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
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);
| ^~~~~~~~
rm -rf objects_typical
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/closestfeats/src'
make -C applications/bed/starch/src -f Makefile build
make[4]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/starch/src'
mkdir -p objects
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+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-truncation]
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-truncation]
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-truncation]
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 )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-truncation]
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);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mkdir -p objects
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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_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-truncation]
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:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)':
../../../../interfaces/src/data/starch/starchHelpers.c: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);
| ~~~~~~^~~~~~~~~~~~
mkdir -p objects
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-truncation]
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-truncation]
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-truncation]
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);
| ~~~~~~^~~~~~~
mkdir -p objects
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+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../../../..
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-truncation]
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 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-truncation]
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor 'Bed::bed_check_iterator<BedType*, Sz>::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory<BedType, SZ>&, const string&, bool) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
mkdir -p objects
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+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-2.4.41+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-2.4.41+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 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-truncation]
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);
| ~~~~~~^~~~~
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+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++/11/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++/11/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++/11/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 ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-truncation]
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-2.4.41+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 && cp update-sort-bed-slurm.py ../bin/update-sort-bed-slurm-typical
mkdir -p ../bin
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starchstrip.c -o objects/starchstrip.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p ../bin && 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
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 ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mkdir -p ../bin && g++ -o ../bin/sort-bed-typical -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+dfsg/applications/bed/sort-bed/src'
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+dfsg/applications/bed/starch/src'
rm -rf objects_typical
make[4]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg/applications/bed/bedops/src'
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/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++/11/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++/11/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-truncation]
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);
| ~~~~~~^~~~~~~~
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 '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-truncation]
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 file included from /usr/include/c++/11/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++/11/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++/11/bits/stl_algo.h:4754:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
4754 | nth_element(_RandomAccessIterator __first, _RandomAccessIterator __nth,
| ^~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:4754:5: 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++/11/bits/stl_algo.h:4754:5: 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++/11/vector:72,
from Bedmap.cpp:35:
/usr/include/c++/11/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++/11/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++/11/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++/11/bits/vector.tcc:121:28: 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-2.4.41+dfsg/applications/bed/bedmap/src'
make[3]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_auto_install -a
make -j4 install DESTDIR=/<<BUILDDIR>>/bedops-2.4.41\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+dfsg'
debian/rules override_dh_install-arch
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+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-2.4.41+dfsg'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installman-arch
make[1]: Entering directory '/<<BUILDDIR>>/bedops-2.4.41+dfsg'
cd bin && for f in * ; do help2man --no-discard-stderr --version-string="2.4.41+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-2.4.41+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-2.4.41+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-2.4.41+dfsg'
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/bedops/usr/bin/bedmap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/bedops/usr/bin/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: 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/bedextract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/bedops/usr/bin/bedmap debian/bedops/usr/bin/bedops debian/bedops/usr/bin/closest-features debian/bedops/usr/bin/starchcat debian/bedops/usr/bin/sort-bed debian/bedops/usr/bin/convert2bed debian/bedops/usr/bin/unstarch debian/bedops/usr/bin/starchstrip debian/bedops/usr/bin/bedextract debian/bedops/usr/bin/bedops-starch 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_2.4.41+dfsg-1_armhf.deb'.
dpkg-deb: building package 'bedops' in '../bedops_2.4.41+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any -O../bedops_2.4.41+dfsg-1_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> -O../bedops_2.4.41+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 2022-07-23T08:46:58Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
bedops_2.4.41+dfsg-1_armhf.changes:
-----------------------------------
Format: 1.8
Date: Mon, 18 Jul 2022 10:29:31 +0200
Source: bedops
Binary: bedops bedops-dbgsym
Architecture: armhf
Version: 2.4.41+dfsg-1
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
bedops - high-performance genomic feature operations
Changes:
bedops (2.4.41+dfsg-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
* Standards-Version: 4.6.1 (routine-update)
* debhelper-compat 13 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Set upstream metadata fields: Repository, Repository-Browse.
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9cf7cb0e37db71693fe97d44f64d09e5c59dac07 1056052 bedops_2.4.41+dfsg-1_armhf.deb
Checksums-Sha256:
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Files:
3c6831edcc6dbb391d641922ec09b01c 77888 debug optional bedops-dbgsym_2.4.41+dfsg-1_armhf.deb
e2a3faa4ae1c7c9e1483feaf6f37b6c6 5728 science optional bedops_2.4.41+dfsg-1_armhf.buildinfo
07d225e6e74eb97172d57451a642565c 1056052 science optional bedops_2.4.41+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
bedops-dbgsym_2.4.41+dfsg-1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 77888 bytes: control archive=536 bytes.
377 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: bedops-dbgsym
Source: bedops
Version: 2.4.41+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 94
Depends: bedops (= 2.4.41+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for bedops
Build-Ids: 8d7b3bd9e571a8eb0b6204f3d28db4c64ecee3fe
drwxr-xr-x root/root 0 2022-07-18 08:29 ./
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/lib/
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/lib/debug/.build-id/8d/
-rw-r--r-- root/root 85460 2022-07-18 08:29 ./usr/lib/debug/.build-id/8d/7b3bd9e571a8eb0b6204f3d28db4c64ecee3fe.debug
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-07-18 08:29 ./usr/share/doc/bedops-dbgsym -> bedops
bedops_2.4.41+dfsg-1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 1056052 bytes: control archive=6144 bytes.
731 bytes, 15 lines control
21485 bytes, 236 lines md5sums
Package: bedops
Version: 2.4.41+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7419
Depends: libbz2-1.0, libc6 (>= 2.33), libgcc-s1 (>= 3.5), libjansson4 (>= 2.14), libstdc++6 (>= 11), 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 2022-07-18 08:29 ./
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/bin/
-rwxr-xr-x root/root 4711 2022-07-18 08:29 ./usr/bin/bam2bed
-rwxr-xr-x root/root 4501 2022-07-18 08:29 ./usr/bin/bam2bed_gnuParallel
-rwxr-xr-x root/root 5022 2022-07-18 08:29 ./usr/bin/bam2bed_sge
-rwxr-xr-x root/root 5021 2022-07-18 08:29 ./usr/bin/bam2bed_slurm
-rwxr-xr-x root/root 5842 2022-07-18 08:29 ./usr/bin/bam2starch
-rwxr-xr-x root/root 4507 2022-07-18 08:29 ./usr/bin/bam2starch_gnuParallel
-rwxr-xr-x root/root 5076 2022-07-18 08:29 ./usr/bin/bam2starch_sge
-rwxr-xr-x root/root 5014 2022-07-18 08:29 ./usr/bin/bam2starch_slurm
-rwxr-xr-x root/root 198712 2022-07-18 08:29 ./usr/bin/bedextract
-rwxr-xr-x root/root 5310644 2022-07-18 08:29 ./usr/bin/bedmap
-rwxr-xr-x root/root 395384 2022-07-18 08:29 ./usr/bin/bedops
-rwxr-xr-x root/root 133012 2022-07-18 08:29 ./usr/bin/bedops-starch
-rwxr-xr-x root/root 264260 2022-07-18 08:29 ./usr/bin/closest-features
-rwxr-xr-x root/root 133496 2022-07-18 08:29 ./usr/bin/convert2bed
-rwxr-xr-x root/root 3773 2022-07-18 08:29 ./usr/bin/gff2bed
-rwxr-xr-x root/root 4904 2022-07-18 08:29 ./usr/bin/gff2starch
-rwxr-xr-x root/root 4061 2022-07-18 08:29 ./usr/bin/gtf2bed
-rwxr-xr-x root/root 5195 2022-07-18 08:29 ./usr/bin/gtf2starch
-rwxr-xr-x root/root 3773 2022-07-18 08:29 ./usr/bin/gvf2bed
-rwxr-xr-x root/root 4904 2022-07-18 08:29 ./usr/bin/gvf2starch
-rwxr-xr-x root/root 3976 2022-07-18 08:29 ./usr/bin/psl2bed
-rwxr-xr-x root/root 5107 2022-07-18 08:29 ./usr/bin/psl2starch
-rwxr-xr-x root/root 3776 2022-07-18 08:29 ./usr/bin/rmsk2bed
-rwxr-xr-x root/root 4907 2022-07-18 08:29 ./usr/bin/rmsk2starch
-rwxr-xr-x root/root 4711 2022-07-18 08:29 ./usr/bin/sam2bed
-rwxr-xr-x root/root 5842 2022-07-18 08:29 ./usr/bin/sam2starch
-rwxr-xr-x root/root 198724 2022-07-18 08:29 ./usr/bin/sort-bed
-rwxr-xr-x root/root 10163 2022-07-18 08:29 ./usr/bin/starch-diff
-rwxr-xr-x root/root 198564 2022-07-18 08:29 ./usr/bin/starchcat
-rwxr-xr-x root/root 4299 2022-07-18 08:29 ./usr/bin/starchcluster_gnuParallel
-rwxr-xr-x root/root 4810 2022-07-18 08:29 ./usr/bin/starchcluster_sge
-rwxr-xr-x root/root 4716 2022-07-18 08:29 ./usr/bin/starchcluster_slurm
-rwxr-xr-x root/root 132948 2022-07-18 08:29 ./usr/bin/starchstrip
-rwxr-xr-x root/root 132884 2022-07-18 08:29 ./usr/bin/unstarch
-rwxr-xr-x root/root 32686 2022-07-18 08:29 ./usr/bin/update-sort-bed-migrate-candidates
-rwxr-xr-x root/root 20701 2022-07-18 08:29 ./usr/bin/update-sort-bed-slurm
-rwxr-xr-x root/root 22682 2022-07-18 08:29 ./usr/bin/update-sort-bed-starch-slurm
-rwxr-xr-x root/root 4675 2022-07-18 08:29 ./usr/bin/vcf2bed
-rwxr-xr-x root/root 5806 2022-07-18 08:29 ./usr/bin/vcf2starch
-rwxr-xr-x root/root 4598 2022-07-18 08:29 ./usr/bin/wig2bed
-rwxr-xr-x root/root 5729 2022-07-18 08:29 ./usr/bin/wig2starch
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/doc/bedops/
-rw-r--r-- root/root 267 2022-07-18 08:29 ./usr/share/doc/bedops/README.Debian
-rw-r--r-- root/root 1699 2022-07-18 08:29 ./usr/share/doc/bedops/changelog.Debian.gz
-rw-r--r-- root/root 22675 2022-07-13 08:18 ./usr/share/doc/bedops/changelog.gz
-rw-r--r-- root/root 1156 2022-07-18 08:29 ./usr/share/doc/bedops/copyright
drwxr-xr-x root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/
-rw-r--r-- root/root 954 2022-07-13 08:18 ./usr/share/doc/bedops/tests/Makefile
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/doc/bedops/tests/bedops/
-rw-r--r-- root/root 2166 2022-07-18 08:29 ./usr/share/doc/bedops/tests/bedops/Makefile.gz
drwxr-xr-x root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/
-rw-r--r-- root/root 197 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001.expected
-rw-r--r-- root/root 44 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001a.test
-rw-r--r-- root/root 53 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001b.test
-rw-r--r-- root/root 24 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.chrom.001.expected
-rw-r--r-- root/root 26 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.complement.001.expected
-rw-r--r-- root/root 31 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.difference.001.expected
-rw-r--r-- root/root 23 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.ec.001a.test
-rw-r--r-- root/root 69 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.element-of.001.expected
-rw-r--r-- root/root 91 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001.expected
-rw-r--r-- root/root 52 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001a.test
-rw-r--r-- root/root 104 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001b.test
-rw-r--r-- root/root 37 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.merge.001.expected
-rw-r--r-- root/root 111 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.merge.001.test
-rw-r--r-- root/root 368 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.named-pipe.001.expected
-rw-r--r-- root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.not-element-of.001.expected
-rw-r--r-- root/root 148 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001.expected
-rw-r--r-- root/root 39 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001a.test
-rw-r--r-- root/root 56 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001b.test
-rw-r--r-- root/root 40 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001c.test
-rw-r--r-- root/root 257 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.stdin.001.expected
-rw-r--r-- root/root 130 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.symdiff.001.expected
-rw-r--r-- root/root 134 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.union.001.expected
-rw-r--r-- root/root 126 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.union.001.test
-rw-r--r-- root/root 171 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.chop.002.expected
-rw-r--r-- root/root 20 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.chrom.002.expected
-rw-r--r-- root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.complement.002.expected
-rw-r--r-- root/root 2172 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002.expected
-rw-r--r-- root/root 3033 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002a.test
-rw-r--r-- root/root 2941 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002b.test
-rw-r--r-- root/root 18 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.element-of.002.expected
-rw-r--r-- root/root 13 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.intersection.002.expected
-rw-r--r-- root/root 26 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.intersection.002.test
-rw-r--r-- root/root 11 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.merge.002.expected
-rw-r--r-- root/root 11 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.not-element-of.002.expected
-rw-r--r-- root/root 376 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002.expected
-rw-r--r-- root/root 48 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002a.test
-rw-r--r-- root/root 49 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002b.test
-rw-r--r-- root/root 101 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002c.test
-rw-r--r-- root/root 39 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002d.test
-rw-r--r-- root/root 131 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002e.test
-rw-r--r-- root/root 118 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.symdiff.002.expected
-rw-r--r-- root/root 56 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.union.002.expected
-rw-r--r-- root/root 368 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.chop.003.expected
-rw-r--r-- root/root 24 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.chrom.003.expected
-rw-r--r-- root/root 61 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.complement.003.expected
-rw-r--r-- root/root 3794 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.difference.003.expected
-rw-r--r-- root/root 42 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.element-of.003.expected
-rw-r--r-- root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.intersection.003.expected
-rw-r--r-- root/root 35 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.merge.003.expected
-rw-r--r-- root/root 46 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.merge.003.test
-rw-r--r-- root/root 21 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003.expected
-rw-r--r-- root/root 63 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003a.test
-rw-r--r-- root/root 42 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003b.test
-rw-r--r-- root/root 153 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.partition.003.expected
-rw-r--r-- root/root 398 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.partition.003.test
-rw-r--r-- root/root 22 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003.expected
-rw-r--r-- root/root 18 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003a.test
-rw-r--r-- root/root 29 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003b.test
-rw-r--r-- root/root 9 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003c.test
-rw-r--r-- root/root 11 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003d.test
-rw-r--r-- root/root 355 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.union.003.expected
-rw-r--r-- root/root 360 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.union.003.test
-rw-r--r-- root/root 257 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.chop.004.expected
-rw-r--r-- root/root 24 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.chrom.004.expected
-rw-r--r-- root/root 111 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004.expected
-rw-r--r-- root/root 46 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004a.test
-rw-r--r-- root/root 132 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004b.test
-rw-r--r-- root/root 94 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004c.test
-rw-r--r-- root/root 30 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004.expected
-rw-r--r-- root/root 30 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004a.test
-rw-r--r-- root/root 31 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004b.test
-rw-r--r-- root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004.expected
-rw-r--r-- root/root 92 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004a.test
-rw-r--r-- root/root 23 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004b.test
-rw-r--r-- root/root 49 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004.expected
-rw-r--r-- root/root 103 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004a.test
-rw-r--r-- root/root 85 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004b.test
-rw-r--r-- root/root 47 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004c.test
-rw-r--r-- root/root 72 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.merge.004.expected
-rw-r--r-- root/root 117 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.partition.004.expected
-rw-r--r-- root/root 117 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.partition.004.test
-rw-r--r-- root/root 52 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.symdiff.004.expected
-rw-r--r-- root/root 22 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.union.004.expected
-rw-r--r-- root/root 32 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.union.004.test
-rw-r--r-- root/root 385 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.chop.005.expected
-rw-r--r-- root/root 87 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.chop.005.test
-rw-r--r-- root/root 20 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.complement.005.expected
-rw-r--r-- root/root 40 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.complement.005.test
-rw-r--r-- root/root 31 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.difference.005.expected
-rw-r--r-- root/root 93 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.merge.005.expected
-rw-r--r-- root/root 43 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.merge.005.test
-rw-r--r-- root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.symdiff.005.expected
-rw-r--r-- root/root 11 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.union.005.expected
-rw-r--r-- root/root 35 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/006.complement.006.expected
-rw-r--r-- root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/006.difference.006.expected
-rw-r--r-- root/root 41 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006.expected
-rw-r--r-- root/root 37 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006a.test
-rw-r--r-- root/root 35 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006b.test
-rw-r--r-- root/root 31 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006c.test
-rw-r--r-- root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/006.union.006.expected
-rw-r--r-- root/root 9 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/007.complement.007.expected
-rw-r--r-- root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/007.difference.007.expected
-rw-r--r-- root/root 55 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007.expected
-rw-r--r-- root/root 56 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007a.test
-rw-r--r-- root/root 69 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007b.test
-rw-r--r-- root/root 33 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/007.union.007.expected
-rw-r--r-- root/root 79 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/008.complement.008.expected
-rw-r--r-- root/root 197 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/008.merge.008.expected
-rw-r--r-- root/root 33 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/008.union.008.expected
-rw-r--r-- root/root 175 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/009.complement.009.expected
-rw-r--r-- root/root 52 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/009.merge.009.expected
-rw-r--r-- root/root 33 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/009.union.009.expected
-rw-r--r-- root/root 43 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/009.union.009.test
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/doc/bedops/tests/conversion/
-rw-r--r-- root/root 1159 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/Makefile.gz
drwxr-xr-x root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/
-rw-r--r-- root/root 398 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/001.wig2bed_with_chr_prefix_no_header.001.expected
-rw-r--r-- root/root 352 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/001.wig2bed_with_chr_prefix_no_header.001.wig
-rw-r--r-- root/root 368 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/002.wig2bed_no_chr_prefix_no_header.001.expected
-rw-r--r-- root/root 322 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/002.wig2bed_no_chr_prefix_no_header.001.wig
-rw-r--r-- root/root 102 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.001.expected
-rw-r--r-- root/root 52 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.001.wig
-rw-r--r-- root/root 102 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.002.expected
-rw-r--r-- root/root 60 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.002.wig
-rw-r--r-- root/root 93 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.001.expected
-rw-r--r-- root/root 49 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.001.wig
-rw-r--r-- root/root 93 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.002.expected
-rw-r--r-- root/root 56 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.002.wig
-rw-r--r-- root/root 170 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.001.expected
-rw-r--r-- root/root 85 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.001.wig
-rw-r--r-- root/root 34 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.002.expected
-rw-r--r-- root/root 43 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.002.wig
-rw-r--r-- root/root 155 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.001.expected
-rw-r--r-- root/root 82 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.001.wig
-rw-r--r-- root/root 31 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.002.expected
-rw-r--r-- root/root 40 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.002.wig
-rw-r--r-- root/root 538 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.001.expected
-rw-r--r-- root/root 454 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.001.wig
-rw-r--r-- root/root 583 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.002.expected
-rw-r--r-- root/root 700 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.003.expected
-rw-r--r-- root/root 763 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.004.expected
-rw-r--r-- root/root 493 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.001.expected
-rw-r--r-- root/root 421 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.001.wig
-rw-r--r-- root/root 538 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.002.expected
-rw-r--r-- root/root 652 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.003.expected
-rw-r--r-- root/root 715 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.004.expected
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/doc/bedops/tests/starch/
-rw-r--r-- root/root 1078 2022-07-18 08:29 ./usr/share/doc/bedops/tests/starch/Makefile.gz
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/doc/bedops/tests/starch/data/
-rw-r--r-- root/root 1935 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/001.starch_api.bedmap.001.expected
-rw-r--r-- root/root 2813 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/001.starch_api.bedmap.001.test.gz
-rw-r--r-- root/root 772 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr1.001.test
-rw-r--r-- root/root 1166 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr1andChr2.001.expected
-rw-r--r-- root/root 772 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr2.001.test
-rw-r--r-- root/root 764 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/001.unstarch.signature.001.expected
-rw-r--r-- root/root 2851 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/001.unstarch.signature.001.test.gz
-rw-r--r-- root/root 218 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/002.unstarch.signature.001.expected
-rw-r--r-- root/root 2254 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/002.unstarch.signature.001.test.gz
-rw-r--r-- root/root 109 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/README
-rw-r--r-- root/root 426 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/hg38.bed
-rw-r--r-- root/root 1516 2022-07-18 08:29 ./usr/share/doc/bedops/tests/starch/generate_random_intervals.sh
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/man/
drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/man/man1/
-rw-r--r-- root/root 347 2022-07-18 08:29 ./usr/share/man/man1/bam2bed.1.gz
-rw-r--r-- root/root 354 2022-07-18 08:29 ./usr/share/man/man1/bam2starch.1.gz
-rw-r--r-- root/root 848 2022-07-18 08:29 ./usr/share/man/man1/bedextract.1.gz
-rw-r--r-- root/root 2561 2022-07-18 08:29 ./usr/share/man/man1/bedmap.1.gz
-rw-r--r-- root/root 1043 2022-07-18 08:29 ./usr/share/man/man1/bedops-starch.1.gz
-rw-r--r-- root/root 1392 2022-07-18 08:29 ./usr/share/man/man1/bedops.1.gz
-rw-r--r-- root/root 1288 2022-07-18 08:29 ./usr/share/man/man1/closest-features.1.gz
-rw-r--r-- root/root 1222 2022-07-18 08:29 ./usr/share/man/man1/convert2bed.1.gz
-rw-r--r-- root/root 347 2022-07-18 08:29 ./usr/share/man/man1/gff2bed.1.gz
-rw-r--r-- root/root 354 2022-07-18 08:29 ./usr/share/man/man1/gff2starch.1.gz
-rw-r--r-- root/root 347 2022-07-18 08:29 ./usr/share/man/man1/gtf2bed.1.gz
-rw-r--r-- root/root 353 2022-07-18 08:29 ./usr/share/man/man1/gtf2starch.1.gz
-rw-r--r-- root/root 347 2022-07-18 08:29 ./usr/share/man/man1/gvf2bed.1.gz
-rw-r--r-- root/root 354 2022-07-18 08:29 ./usr/share/man/man1/gvf2starch.1.gz
-rw-r--r-- root/root 346 2022-07-18 08:29 ./usr/share/man/man1/psl2bed.1.gz
-rw-r--r-- root/root 354 2022-07-18 08:29 ./usr/share/man/man1/psl2starch.1.gz
-rw-r--r-- root/root 349 2022-07-18 08:29 ./usr/share/man/man1/rmsk2bed.1.gz
-rw-r--r-- root/root 356 2022-07-18 08:29 ./usr/share/man/man1/rmsk2starch.1.gz
-rw-r--r-- root/root 347 2022-07-18 08:29 ./usr/share/man/man1/sam2bed.1.gz
-rw-r--r-- root/root 354 2022-07-18 08:29 ./usr/share/man/man1/sam2starch.1.gz
-rw-r--r-- root/root 740 2022-07-18 08:29 ./usr/share/man/man1/sort-bed.1.gz
-rw-r--r-- root/root 720 2022-07-18 08:29 ./usr/share/man/man1/starch-diff.1.gz
-rw-r--r-- root/root 988 2022-07-18 08:29 ./usr/share/man/man1/starchcat.1.gz
-rw-r--r-- root/root 1109 2022-07-18 08:29 ./usr/share/man/man1/starchstrip.1.gz
-rw-r--r-- root/root 1542 2022-07-18 08:29 ./usr/share/man/man1/unstarch.1.gz
-rw-r--r-- root/root 1763 2022-07-18 08:29 ./usr/share/man/man1/update-sort-bed-migrate-candidates.1.gz
-rw-r--r-- root/root 1329 2022-07-18 08:29 ./usr/share/man/man1/update-sort-bed-slurm.1.gz
-rw-r--r-- root/root 1383 2022-07-18 08:29 ./usr/share/man/man1/update-sort-bed-starch-slurm.1.gz
-rw-r--r-- root/root 347 2022-07-18 08:29 ./usr/share/man/man1/vcf2bed.1.gz
-rw-r--r-- root/root 355 2022-07-18 08:29 ./usr/share/man/man1/vcf2starch.1.gz
-rw-r--r-- root/root 346 2022-07-18 08:29 ./usr/share/man/man1/wig2bed.1.gz
-rw-r--r-- root/root 355 2022-07-18 08:29 ./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: 44932
Build-Time: 14524
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 467
Job: bedops_2.4.41+dfsg-1
Machine Architecture: armhf
Package: bedops
Package-Time: 15052
Source-Version: 2.4.41+dfsg-1
Space: 44932
Status: successful
Version: 2.4.41+dfsg-1
--------------------------------------------------------------------------------
Finished at 2022-07-23T08:46:58Z
Build needed 04:10:52, 44932k disc space