I: pbuilder: network access will be disabled during build
I: Current time: Thu Apr 9 14:09:18 -12 2026
I: pbuilder-time-stamp: 1775786958
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [bedops_2.4.41+dfsg-3.dsc]
I: copying [./bedops_2.4.41+dfsg.orig.tar.xz]
I: copying [./bedops_2.4.41+dfsg-3.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./bedops_2.4.41+dfsg-3.dsc: unsupported subcommand
dpkg-source: info: extracting bedops in 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-3.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
dpkg-source: info: applying intersphinx
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/2776650/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='d47a74b0a3d746109d8ad19ac7807554'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='2776650'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wXtqkvxJ/pbuilderrc_fCw1 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wXtqkvxJ/b1 --logfile b1/build.log bedops_2.4.41+dfsg-3.dsc'
SUDO_GID='110'
SUDO_UID='105'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://213.165.73.152:3128'
I: uname -a
Linux ionos5-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/2776650/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), help2man, libbz2-dev, libjansson-dev, zlib1g-dev, tcsh, sphinx-common, dh-sequence-sphinxdoc, libjs-mathjax, python3-sphinx
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19783 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on help2man; however:
Package help2man is not installed.
pbuilder-satisfydepends-dummy depends on libbz2-dev; however:
Package libbz2-dev is not installed.
pbuilder-satisfydepends-dummy depends on libjansson-dev; however:
Package libjansson-dev is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on tcsh; however:
Package tcsh is not installed.
pbuilder-satisfydepends-dummy depends on sphinx-common; however:
Package sphinx-common is not installed.
pbuilder-satisfydepends-dummy depends on dh-sequence-sphinxdoc; however:
Package dh-sequence-sphinxdoc is not installed.
pbuilder-satisfydepends-dummy depends on libjs-mathjax; however:
Package libjs-mathjax is not installed.
pbuilder-satisfydepends-dummy depends on python3-sphinx; however:
Package python3-sphinx is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fonts-mathjax{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbz2-dev{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libicu72{a} libjansson-dev{a} libjs-jquery{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-snowballstemmer{a} python3-sphinx{a} python3-urllib3{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tcsh{a} tzdata{a} xml-core{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
bzip2-doc curl javascript-common libarchive-cpio-perl libjson-xs-perl libltdl-dev libmail-sendmail-perl libpaper-utils lynx python3-pil wget
0 packages upgraded, 81 newly installed, 0 to remove and 0 not upgraded.
Need to get 48.2 MB of archives. After unpacking 208 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 media-types all 12.0.0 [28.9 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-1 [745 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.2-2 [28.1 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.1-1 [1427 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-7 [294 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 40 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 41 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 43 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 44 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 46 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 47 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 48 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB]
Get: 51 http://deb.debian.org/debian unstable/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB]
Get: 52 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB]
Get: 53 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB]
Get: 54 http://deb.debian.org/debian unstable/main amd64 libjansson-dev amd64 2.14-2+b3 [43.2 kB]
Get: 55 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 56 http://deb.debian.org/debian unstable/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB]
Get: 57 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 58 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB]
Get: 59 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB]
Get: 60 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB]
Get: 61 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB]
Get: 62 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.17.0-1 [117 kB]
Get: 63 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B]
Get: 64 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB]
Get: 65 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.1-1+b1 [125 kB]
Get: 66 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB]
Get: 67 http://deb.debian.org/debian unstable/main amd64 python3-roman all 5.0-1 [10.6 kB]
Get: 68 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB]
Get: 69 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.10-1 [42.0 kB]
Get: 70 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B]
Get: 71 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB]
Get: 72 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.5-2 [107 kB]
Get: 73 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB]
Get: 74 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB]
Get: 75 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.3.0-1 [114 kB]
Get: 76 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-4 [72.1 kB]
Get: 77 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB]
Get: 78 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.1.3-5 [617 kB]
Get: 79 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.1.3-5 [468 kB]
Get: 80 http://deb.debian.org/debian unstable/main amd64 tcsh amd64 6.24.13-2 [454 kB]
Get: 81 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Fetched 48.2 MB in 1s (43.1 MB/s)
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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
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Current default time zone: 'Etc/UTC'
Local time is now: Fri Apr 10 02:10:29 UTC 2026.
Universal Time is now: Fri Apr 10 02:10:29 UTC 2026.
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/bedops-2.4.41+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bedops_2.4.41+dfsg-3_source.changes
dpkg-buildpackage: info: source package bedops
dpkg-buildpackage: info: source version 2.4.41+dfsg-3
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg'
dh_auto_clean
make -j42 clean
make[2]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg'
make clean -f system.mk/Makefile.linux
make[3]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg'
rm -rf bin
rm -rf bin
rm -rf bin
make -C applications/bed/bedextract/src -f Makefile clean
make -C applications/bed/bedmap/src -f Makefile clean
rm -rf modules
make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedmap/src'
make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedextract/src'
rm -rf objects_typical
rm -rf objects_typical
make -C applications/bed/bedops/src -f Makefile clean
rm -rf ../bin
make -C applications/bed/closestfeats/src -f Makefile clean
make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedops/src'
rm -rf objects_typical
make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedextract/src'
make -C applications/bed/conversion/src -f Makefile clean
make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/src'
rm -rf objects_typical
make -C applications/bed/sort-bed/src -f Makefile clean
make -C applications/bed/starch/src -f Makefile clean
make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/sort-bed/src'
make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/conversion/src'
rm -rf ../bin
rm -rf ../bin
rm -rf ../bin
rm -rf ../bin
rm -rf objects
make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedmap/src'
make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedops/src'
make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/starch/src'
rm -rf objects-typical
make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/src'
rm -rf ../bin
rm -rf ../lib
rm -rf *.so *~
rm -f ../lib/libstarch_debug.a
make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/sort-bed/src'
make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/conversion/src'
rm -f ../lib/libstarch_gprof.a
rm -rf objects
rm -rf ../bin
make[4]: Leaving directory '/build/reproducible-path/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 '/build/reproducible-path/bedops-2.4.41+dfsg'
make[2]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg'
rm -rf docs/_build/
make[1]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
dh_auto_build
make -j42 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg'
make -f system.mk/Makefile.linux
make[2]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg'
#bzcat | tar -x -C third-party
#cd third-party/jansson-2.6 && ./configure --prefix=/build/reproducible-path/bedops-2.4.41+dfsg/third-party/jansson-2.6 && make && make install && cd /build/reproducible-path/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 /build/reproducible-path/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 /build/reproducible-path/bedops-2.4.41+dfsg && rm -f zlib && ln -sf zlib-1.2.7 third-party/zlib
make build -f /build/reproducible-path/bedops-2.4.41+dfsg/system.mk/Makefile.linux
make[3]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg'
make -C applications/bed/bedextract/src -f Makefile build
make -C applications/bed/bedmap/src -f Makefile build
make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedextract/src'
make -C applications/bed/bedops/src -f Makefile build
make -C applications/bed/closestfeats/src -f Makefile build
make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedmap/src'
make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedops/src'
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers
make -C applications/bed/conversion/src -f Makefile build
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers
make -C applications/bed/sort-bed/src -f Makefile build
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers
make -C applications/bed/starch/src -f Makefile build
make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/src'
make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/sort-bed/src'
make[4]: Entering directory '/build/reproducible-path/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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -iquote"/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/conversion/src" -iquote"../../../../interfaces/general-headers" convert2bed.c -o ../bin/convert2bed-typical -lpthread
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/starch/src'
mkdir -p objects
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects-typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects/unstarchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects-typical/starchHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -pedantic -ansi -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchHelpers.c -o objects/starchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects-typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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
mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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
mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -pedantic -ansi -O3 -std=c++11 SortDetails.cpp -o objects-typical/SortDetails.o -iquote../../../../interfaces/general-headers
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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../../../..
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects/starchSha1Digest.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -pedantic -ansi -O3 -std=c++11 CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers
convert2bed.c: In function 'c2b_line_convert_rmsk_to_bed_unsorted':
convert2bed.c:3780:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=]
3780 | fprintf(stderr, "Error: Invalid query coordinates at line [%llu]\n", c2b_globals.rmsk->line);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long unsigned int uint64_t {aka long unsigned int}
| %lu
../../../../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*, 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 ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mkdir -p objects
../../../../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 ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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../../../..
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, 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 ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mkdir -p ../bin
cp starchcluster_gnuParallel.tcsh ../bin/starchcluster_gnuParallel-typical
mkdir -p ../bin && cp update-sort-bed-slurm.py ../bin/update-sort-bed-slurm-typical
mkdir -p ../bin
cp starchcluster_sge.tcsh ../bin/starchcluster_sge-typical
mkdir -p ../bin && cp update-sort-bed-starch-slurm.py ../bin/update-sort-bed-starch-slurm-typical
mkdir -p ../bin && cp update-sort-bed-migrate-candidates.py ../bin/update-sort-bed-migrate-candidates-typical
mkdir -p ../bin
cp starchcluster_slurm.tcsh ../bin/starchcluster_slurm-typical
mkdir -p ../bin
cp starch-diff.py ../bin/starch-diff-typical
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, Boolean, 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/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/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, Boolean, 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/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/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(Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, Boolean, 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(Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, Boolean, 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(Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, Boolean, 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/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/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, 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/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/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, Boolean, 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/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/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(Metadata**, const FILE*, 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_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/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, 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:200:32: note: length computed here
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../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:200:32: note: length computed here
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_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(Metadata**, const FILE*, 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_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(Metadata**, const FILE*, 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/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, 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/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, 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:200:32: note: length computed here
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../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:200:32: note: length computed here
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, 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:200:32: note: length computed here
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../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:200:32: note: length computed here
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(Metadata**, const FILE*, 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(Metadata**, const FILE*, 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_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/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, 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*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, 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/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, 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:200:32: note: length computed here
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../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:200:32: note: length computed here
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../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*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, 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/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, 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/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, 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:200:32: note: length computed here
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(Metadata**, const FILE*, 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/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, 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/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, 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/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, 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:200:32: note: length computed here
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../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:200:32: note: length computed here
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:38:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
38 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from CheckSort.cpp:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:52:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
52 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:77:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
77 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:88:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
88 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:101:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
101 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:165:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
165 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:242:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
242 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:254:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
254 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:264:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
264 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:274:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
274 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:284:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
284 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:294:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
294 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:302:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
302 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, 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*, Metadata**, CompressionType, const char*, const char*, Boolean, 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/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, 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:2559:40: note: length computed here
2559 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, 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*, Metadata**, CompressionType, const char*, const char*, Boolean, 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);
| ~~~~~~^~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44:
../../../../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 std::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 ) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, 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:2559:40: note: length computed here
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*, 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:2559:40: note: length computed here
2559 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../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>; long unsigned int SZ = 16]':
CheckSort.cpp:51:28: required from here
51 | pool.release(*start++);
| ^~
../../../../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>; long 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>; long unsigned int SZ = 16]'
308 | bool operator=(const bed_check_iterator& b);
| ^~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, 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:2559:40: note: length computed here
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*, 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:2559:40: note: length computed here
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*, 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:2559:40: note: length computed here
2559 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mkdir -p ../bin && g++ -o ../bin/bedmap-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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
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
| ~~~~~~^~~~~~~~~~
mkdir -p ../bin && g++ -o ../bin/bedextract-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 ../lib
mkdir -p ../bin && g++ -o ../bin/closest-features-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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
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=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starch.c -o objects/starch.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p ../bin
mkdir -p ../bin
mkdir -p ../bin
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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../../../..
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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../../../..
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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../../../..
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 ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mkdir -p ../bin && g++ -o ../bin/bedops-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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
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) ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 file included from /usr/include/c++/14/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(Metadata**, const char*, CompressionType, const char*, const MetadataRecord*, size_t*, Boolean, 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: In function 'int starch::STARCHCAT_rewriteInputRecordToOutput(Metadata**, const char*, 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*, Metadata**, const char*, 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(Metadata**, const char*, 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 ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function 'int starch::STARCHCAT_mergeChromosomeStreams(const ChromosomeSummaries*, 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(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 ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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
starchcat.c: In function 'int starch::STARCHCAT2_mergeChromosomeStreams(const ChromosomeSummaries*, CompressionType, const char*, size_t*, Boolean, 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(Boolean*, char*, char*, size_t*, BZFILE**, size_t*, char*, size_t*, 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(Boolean*, FILE**, char*, char*, size_t*, z_stream*, size_t*, char**, size_t*, 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_transformCompressionBuffer(const char*, char*, TransformState*)':
starchcat.c:7428:25: warning: the address of 'starch::transformState::r_chromosome' will never be NULL [-Waddress]
7428 | if ((!retransState->r_chromosome) || (strlen(retransState->r_chromosome) == 0))
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from starchcat.c:50:
starchcat.h:107:30: note: 'starch::transformState::r_chromosome' declared here
107 | char r_chromosome[TOKEN_CHR_MAX_LENGTH];
| ^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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
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:249:25: note: length computed here
249 | chromBufLen = strlen(chromBuf); // we know >= 1
| ~~~~~~^~~~~~~~~~
In file included from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:36,
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/bed/BedCompare.hpp:38:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
38 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from Bedmap.cpp:29:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:52:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
52 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:77:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
77 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:88:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
88 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:101:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
101 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:165:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
165 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:242:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
242 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:254:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
254 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:264:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
264 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:274:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
274 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:284:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
284 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:294:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
294 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:302:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
302 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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
In file included from ../../../../interfaces/general-headers/algorithm/visitors/NumericalVisitors.hpp:32,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:34:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:43:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
43 | struct abs_diff : std::binary_function<T, T, T> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:39,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:38:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
38 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/deque:67,
from ClosestFeature.cpp:27:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:52:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
52 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:77:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
77 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:88:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
88 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:101:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
101 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:165:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
165 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:242:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
242 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:254:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
254 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:264:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
264 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:274:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
274 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:284:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
284 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:294:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
294 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:302:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
302 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ExtractRows.cpp:40:
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:38:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
38 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from ExtractRows.cpp:29:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:52:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
52 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:77:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
77 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:88:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
88 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:101:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
101 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:165:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
165 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:242:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
242 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:254:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
254 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:264:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
264 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:274:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
274 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:284:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
284 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:294:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
294 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:302:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
302 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/algorithm/visitors/helpers/ProcessBedVisitorRow.hpp:33,
from Bedops.cpp:40:
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:38:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
38 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/deque:67,
from Bedops.cpp:27:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:52:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
52 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:77:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
77 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:88:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
88 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:101:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
101 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:165:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
165 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:242:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
242 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:254:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
254 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:264:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
264 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:274:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
274 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:284:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
284 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:294:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
294 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCompare.hpp:302:20: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
302 | : public std::binary_function<BedType1 const*, BedType2 const*, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../../../../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);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function 'int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, Metadata**, const char*, 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);
| ~~~~~~^~~~~~~
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 static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)',
inlined from 'static bool starch::Starch::hasStarchRevision1LegacyHeader(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:634:52,
inlined from 'static bool starch::Starch::isStarch(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:698:56,
inlined from 'Bed::bed_check_iterator<BedType*, Sz>::bed_check_iterator(std::istream&, const std::string&, Ext::PooledMemory<BedType, SZ>&, const std::string&, bool) [with BedType = Bed::BasicCoords<true, true>; long 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:541:76: note: length computed here
541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::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 std::string&, Ext::PooledMemory<BedType, SZ>&, const std::string&, bool) [with BedType = Bed::BasicCoords<true, true>; long 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:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-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);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42:
../../../../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);
| ~~~~~~^~~~~~~~
rm -rf objects
make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/starch/src'
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from '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>; long unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36,
inlined from 'Bed::bed_check_iterator<BedType*, Sz> Bed::bed_check_iterator<BedType*, Sz>::operator++(int) [with BedType = Bed::BasicCoords<true, true>; long unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:267:24,
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:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-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);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rm -rf objects
make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/conversion/src'
mkdir -p ../bin && g++ -o ../bin/sort-bed-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/sort-bed/src'
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from 'Bed::bed_check_iterator<BedType*, Sz>::bed_check_iterator(std::istream&, const std::string&, Ext::PooledMemory<BedType, SZ>&, const std::string&, bool) [with BedType = Bed::BasicCoords<true, true>; long 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:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from 'Bed::bed_check_iterator<BedType*, Sz> Bed::bed_check_iterator<BedType*, Sz>::operator++(int) [with BedType = Bed::BasicCoords<true, true>; long unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36,
inlined from 'Bed::bed_check_iterator<BedType*, Sz> Bed::bed_check_iterator<BedType*, Sz>::operator++(int) [with BedType = Bed::BasicCoords<true, true>; long unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:267:24,
inlined from 'std::pair<bool, long int> Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = bed_check_iterator<BasicCoords<true, true>*, 16>; Op = Visitors::BedHelpers::Println]' at ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:102:64:
../../../../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:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)':
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-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);
| ~~~~~~^~~~~~~~
../../../../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);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rm -rf objects_typical
make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedextract/src'
rm -rf objects_typical
make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/src'
In member function 'void starch::Starch::setCurrentChromosome(char*)',
inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from 'Bed::bed_check_iterator<BedType*, Sz>& Bed::bed_check_iterator<BedType*, Sz>::operator++() [with BedType = Bed::BasicCoords<true, false>; long unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:261:36,
inlined from 'BedOperations::BedPadReader<IterType>::BedType* BedOperations::BedPadReader<IterType>::ReadLine() [with IterType = Bed::bed_check_iterator<Bed::BasicCoords<true, false>*, 512>]' at BedPadReader.hpp:140:11,
inlined from 'void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector<BedPadReader<Bed::bed_check_iterator<Bed::BasicCoords<true, false>*, 512> >*, std::allocator<BedPadReader<Bed::bed_check_iterator<Bed::BasicCoords<true, false>*, 512> >*> >; PQueue = std::priority_queue<Bed::BasicCoords<true, false>*, std::vector<Bed::BasicCoords<true, false>*, std::allocator<Bed::BasicCoords<true, false>*> >, Bed::InvertGenomicAddressCompare<Bed::BasicCoords<true, false>, Bed::BasicCoords<true, false> > >]' at Bedops.cpp:1411:39:
../../../../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:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
rm -rf objects_typical
make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedops/src'
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39:
../../../../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);
| ~~~~~~^~~~~~~~
../../../../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);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rm -rf objects_typical
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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
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cp applications/bed/starch/bin/starchstrip-typical bin/starchstrip
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copying images... [ 87%] assets/reference/statistics/reference_bedmap_inputs.png
copying images... [ 88%] assets/reference/statistics/reference_bedmap_mapref_all.png
copying images... [ 90%] assets/reference/statistics/reference_bedmap_mapref_ref1.png
copying images... [ 92%] assets/reference/statistics/reference_bedmap_mapref_ref2.png
copying images... [ 93%] assets/reference/statistics/reference_bedmap_mapref_ref3.png
copying images... [ 95%] assets/reference/statistics/reference_bedmap_mapref_ref3_padded.png
copying images... [ 97%] assets/usage-examples/SNP_DHS_matrix.png
copying images... [ 98%] assets/usage-examples/SNP_DHS_matrix_diseaseSorted.png
copying images... [100%] assets/reference/file-management/compression/starchcluster_mechanism.png
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 3 warnings.
The HTML pages are in _build/html.
find _build/../assets -type f -name "*.png" -exec cp -f "{}" _build/html/_static \;
Build finished. The HTML pages are in _build/html.
make[2]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/docs'
mkdir -p debian/bedops-doc/usr/share/doc/bedops
cp -r docs/_build/html debian/bedops-doc/usr/share/doc/bedops
find debian/bedops-doc/usr/share/doc/bedops/html/content/usage-examples -type f | xargs sed -i 's;https://cdn[js]*\..*/MathJax.js;../../_static/mathjax.js;g'
find debian/bedops-doc/usr/share/doc/bedops/html/content -type f | xargs sed -i 's;https://cdn[js]*\..*//MathJax.js;../_static/mathjax.js;g'
find debian/bedops-doc/usr/share/doc/bedops/html -type f | xargs sed -i 's;https://cdn[js]*\..*/MathJax.js;_static/mathjax.js;g'
ln -s /usr/share/javascript/mathjax/MathJax.js debian/bedops-doc/usr/share/doc/bedops/html/_static/mathjax.js
dh_installdocs -i
make[1]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg'
dh_installdocs -Nbedops-doc
dh_sphinxdoc -i
dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/bedops-doc/usr/share/doc/bedops/html/_static/mathjax.js
dh_installchangelogs
debian/rules override_dh_installman-arch
make[1]: Entering directory '/build/reproducible-path/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
dh_installman -a
make[1]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg'
dh_installman -Nbedops
dh_perl
dh_link
dh_strip_nondeterminism
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debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_chop_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172.
debian/bedops-doc/usr/share/doc/bedops/html/_static/starch_specification_metadatachecksum.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172.
debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_bedmap_mapref_ref1.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172.
debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_symmetricdifference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172.
debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_everything.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172.
debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_merge_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172.
debian/bedops-doc/usr/share/doc/bedops/html/_static/overview.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172.
debian/bedops-doc/usr/share/doc/bedops/html/_static/bioinformatics.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172.
debian/bedops-doc/usr/share/doc/bedops/html/_static/other.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172.
debian/bedops-doc/usr/share/doc/bedops/html/_static/BEDOPS_Presentation_starch_efficiency.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172.
debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_bedops_merge_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172.
debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_partition_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172.
debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_bedops_intersect_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172.
debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_elementof_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172.
debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_bedops_merge_unsorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172.
dh_compress
dh_fixperms
dh_missing
debian/rules override_dh_dwz
make[1]: Entering directory '/build/reproducible-path/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 '/build/reproducible-path/bedops-2.4.41+dfsg'
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dpkg-gencontrol: warning: package bedops-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined
dpkg-gencontrol: warning: package bedops-doc: substitution variable ${sphinxdoc:Depends} unused, but is defined
dh_md5sums
dh_builddeb
dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.41+dfsg-3_amd64.deb'.
dpkg-deb: building package 'bedops-doc' in '../bedops-doc_2.4.41+dfsg-3_all.deb'.
dpkg-deb: building package 'bedops' in '../bedops_2.4.41+dfsg-3_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../bedops_2.4.41+dfsg-3_amd64.buildinfo
dpkg-genchanges --build=binary -O../bedops_2.4.41+dfsg-3_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/2776650 and its subdirectories
I: Current time: Thu Apr 9 14:26:57 -12 2026
I: pbuilder-time-stamp: 1775788017