Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/b/bedops/bedops_2.4.39+dfsg1-2_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/bedops-2.4.39+dfsg1-2s_ibss1b/bedops_2.4.39+dfsg1-2_all.buildinfo Get source package info: bedops=2.4.39+dfsg1-2 Source URL: http://snapshot.notset.fr/mr/package/bedops/2.4.39+dfsg1-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.49 bash=5.1-2 binutils=2.35.1-7 binutils-common=2.35.1-7 binutils-x86-64-linux-gnu=2.35.1-7 bsdextrautils=2.36.1-7 bsdutils=1:2.36.1-7 build-essential=12.9 bzip2=1.0.8-4 ca-certificates=20210119 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20200708+dd9ef66-5 debconf=1.5.74 debhelper=13.3.3 debianutils=4.11.2 dh-autoreconf=20 dh-strip-nondeterminism=1.11.0-1 diffutils=1:3.7-5 docutils-common=0.16+dfsg-3 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.13+20210201-1 file=1:5.39-3 findutils=4.8.0-1 fonts-mathjax=2.7.9+dfsg-1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-2 help2man=1.48.1 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-10 libarchive-zip-perl=1.68-1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.1-7 libblkid1=2.36.1-7 libbz2-1.0=1.0.8-4 libbz2-dev=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcom-err2=1.46.1-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-7 libctf0=2.35.1-7 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.256 libdebhelper-perl=13.3.3 libdpkg-perl=1.20.7.1 libelf1=0.183-1 libexpat1=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.11.0-1 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-3 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libicu67=67.1-6 libisl23=0.23-1 libitm1=10.2.1-6 libjansson-dev=2.13.1-1.1 libjansson4=2.13.1-1.1 libjs-jquery=3.5.1+dfsg+~3.5.5-7 libjs-mathjax=2.7.9+dfsg-1 libjs-sphinxdoc=3.4.3-1 libjs-underscore=1.9.1~dfsg-1 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblocale-gettext-perl=1.07-4+b1 liblsan0=10.2.1-6 liblz4-1=1.9.3-1 liblzma5=5.2.5-1.0 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-7 libmpc3=1.2.0-1 libmpdec3=2.5.1-1 libmpfr6=4.1.0-3 libncursesw6=6.2+20201114-2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-4 libpam-modules-bin=1.4.0-4 libpam-runtime=1.4.0-4 libpam0g=1.4.0-4 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-2 libpipeline1=1.5.3-1 libpython3-stdlib=3.9.1-1 libpython3.9-minimal=3.9.1-4 libpython3.9-stdlib=3.9.1-4 libquadmath0=10.2.1-6 libreadline8=8.1-1 libseccomp2=2.5.1-1 libselinux1=3.1-3 libsigsegv2=2.13-1 libsmartcols1=2.36.1-7 libsqlite3-0=3.34.1-2 libssl1.1=1.1.1j-1 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.3-1 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.3-1 libunistring2=0.9.10-4 libuuid1=2.36.1-7 libxml2=2.9.10+dfsg-6.3+b1 libzstd1=1.4.8+dfsg-1 linux-libc-dev=5.10.13-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 openssl=1.1.1j-1 patch=2.7.6-7 perl=5.32.1-2 perl-base=5.32.1-2 perl-modules-5.32=5.32.1-2 po-debconf=1.0.21+nmu1 python-babel-localedata=2.8.0+dfsg.1-6 python3=3.9.1-1 python3-alabaster=0.7.8-1.1 python3-babel=2.8.0+dfsg.1-6 python3-certifi=2020.6.20-1 python3-chardet=4.0.0-1 python3-distutils=3.9.1-2 python3-docutils=0.16+dfsg-3 python3-idna=2.10-1 python3-imagesize=1.2.0-2 python3-jinja2=2.11.2-1 python3-lib2to3=3.9.1-2 python3-markupsafe=1.1.1-1+b3 python3-minimal=3.9.1-1 python3-packaging=20.9-2 python3-pkg-resources=52.0.0-1 python3-pygments=2.7.1+dfsg-1 python3-pyparsing=2.4.7-1 python3-requests=2.25.1+dfsg-2 python3-roman=2.0.0-5 python3-six=1.15.0-2 python3-snowballstemmer=2.1.0-1 python3-sphinx=3.4.3-1 python3-tz=2021.1-1 python3-urllib3=1.26.2-1 python3.9=3.9.1-4 python3.9-minimal=3.9.1-4 readline-common=8.1-1 sed=4.7-1 sensible-utils=0.0.14 sgml-base=1.30 sphinx-common=3.4.3-1 sysvinit-utils=2.96-5 tar=1.34+dfsg-1 tzdata=2021a-1 util-linux=2.36.1-7 xml-core=0.18+nmu1 xz-utils=5.2.5-1.0 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211009T024746Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210218T111050Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d bedops=2.4.39+dfsg1-2 && mkdir -p /build/bedops-jA2UgM && dpkg-source --no-check -x /*.dsc /build/bedops-jA2UgM/bedops-2.4.39+dfsg1 && chown -R builduser:builduser /build/bedops-jA2UgM" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bedops-jA2UgM/bedops-2.4.39+dfsg1 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1613728232" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/bedops-jA2UgM /tmp/bedops-2.4.39+dfsg1-2s_ibss1b bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210218T111050Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.zxbGfu2rUI as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.zxbGfu2rUI Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-7). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210218T111050Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210218T111050Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (742 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4662 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-9) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211009T024746Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210218T111050Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.zxbGfu2rUI Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20210218T111050Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable/main amd64 Packages [11.9 MB] Fetched 34.6 MB in 31s (1108 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.zxbGfu2rUI I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d bedops=2.4.39+dfsg1-2 && mkdir -p /build/bedops-jA2UgM && dpkg-source --no-check -x /*.dsc /build/bedops-jA2UgM/bedops-2.4.39+dfsg1 && chown -R builduser:builduser /build/bedops-jA2UgM"' exec /tmp/mmdebstrap.zxbGfu2rUI Reading package lists... NOTICE: 'bedops' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bedops.git Please use: git clone https://salsa.debian.org/med-team/bedops.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 13.5 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main bedops 2.4.39+dfsg1-2 (dsc) [2185 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main bedops 2.4.39+dfsg1-2 (tar) [13.4 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main bedops 2.4.39+dfsg1-2 (diff) [11.1 kB] Fetched 13.5 MB in 11s (1280 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'bedops_2.4.39+dfsg1-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting bedops in /build/bedops-jA2UgM/bedops-2.4.39+dfsg1 dpkg-source: info: unpacking bedops_2.4.39+dfsg1.orig.tar.xz dpkg-source: info: unpacking bedops_2.4.39+dfsg1-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests_use_installed_binaries.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying use_debian_libs dpkg-source: info: applying hardening.patch dpkg-source: info: applying parallel.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bedops-jA2UgM/bedops-2.4.39+dfsg1 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1613728232" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.zxbGfu2rUI dpkg-buildpackage: info: source package bedops dpkg-buildpackage: info: source version 2.4.39+dfsg1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Juhani Numminen dpkg-source --before-build . fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1' dh_auto_clean make -j4 clean make[2]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1' make clean -f system.mk/Makefile.linux make[3]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1' rm -rf bin rm -rf bin rm -rf bin make -C applications/bed/bedmap/src -f Makefile clean make -C applications/bed/sort-bed/src -f Makefile clean make -C applications/bed/bedops/src -f Makefile clean rm -rf modules make[4]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/sort-bed/src' make[4]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/bedmap/src' rm -rf objects_typical make -C applications/bed/closestfeats/src -f Makefile clean make[4]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/bedops/src' rm -rf objects_typical rm -rf objects-typical rm -rf ../bin rm -rf ../bin rm -rf ../bin make[4]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/bedmap/src' make[4]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/closestfeats/src' rm -rf objects_typical make -C applications/bed/bedextract/src -f Makefile clean make[4]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/bedops/src' make -C applications/bed/starch/src -f Makefile clean make[4]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/sort-bed/src' make -C applications/bed/conversion/src -f Makefile clean rm -rf ../bin make[4]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/bedextract/src' rm -rf objects_typical make[4]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/starch/src' rm -rf ../lib make[4]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/closestfeats/src' make[4]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/conversion/src' rm -rf ../bin rm -rf ../bin rm -f ../lib/libstarch_debug.a rm -rf objects make[4]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/bedextract/src' rm -f ../lib/libstarch_gprof.a rm -rf *.so *~ rm -rf objects rm -rf ../bin make[4]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/conversion/src' make[4]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/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/bedops-jA2UgM/bedops-2.4.39+dfsg1' make[2]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1' rm -rf docs/_build/ make[1]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1' dh_clean debian/rules build-indep dh build-indep dh_update_autotools_config -i dh_autoreconf -i dh_auto_configure -i dh_auto_build -i make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1' make -f system.mk/Makefile.linux make[2]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1' #bzcat | tar -x -C third-party #cd third-party/jansson-2.6 && ./configure --prefix=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/third-party/jansson-2.6 && make && make install && cd /build/bedops-jA2UgM/bedops-2.4.39+dfsg1 && 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/bedops-jA2UgM/bedops-2.4.39+dfsg1 && 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/bedops-jA2UgM/bedops-2.4.39+dfsg1 && rm -f zlib && ln -sf zlib-1.2.7 third-party/zlib make build -f /build/bedops-jA2UgM/bedops-2.4.39+dfsg1/system.mk/Makefile.linux make[3]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1' make -C applications/bed/bedmap/src -f Makefile build make -C applications/bed/sort-bed/src -f Makefile build make -C applications/bed/bedops/src -f Makefile build make -C applications/bed/closestfeats/src -f Makefile build make[4]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/sort-bed/src' make[4]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/bedmap/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/bedops/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/closestfeats/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchConstants.c -o objects-typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects-typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchHelpers.c -o objects-typical/starchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here 359 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here 383 | strncpy(*chr, s, strlen(s) + 1); | ~~~~~~^~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here 485 | strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here 923 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here 1411 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here 2416 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here 359 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here 383 | strncpy(*chr, s, strlen(s) + 1); | ~~~~~~^~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here 485 | strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here 923 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here 359 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here 383 | strncpy(*chr, s, strlen(s) + 1); | ~~~~~~^~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here 485 | strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here 359 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here 383 | strncpy(*chr, s, strlen(s) + 1); | ~~~~~~^~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here 485 | strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here 1411 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here 923 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here 923 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here 2416 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here 1411 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here 1411 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here 3695 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here 2416 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here 2416 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here 3695 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects-typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here 3695 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here 3695 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here 2228 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here 2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here 2256 | strncpy(recFilename, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here 1684 | strncpy(*note, streamNote, strlen(streamNote) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here 1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); | ~~~~~~^~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects-typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here 2228 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here 2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here 2256 | strncpy(recFilename, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here 1684 | strncpy(*note, streamNote, strlen(streamNote) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here 1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); | ~~~~~~^~~~~~~~~~~~~ ../../../../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( 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( mdSha1BufferLength )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2640:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2640 | static_cast( 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( STARCH2_MD_FOOTER_SHA1_LENGTH )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here 2228 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here 2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here 2256 | strncpy(recFilename, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here 2228 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here 2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here 2256 | strncpy(recFilename, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here 1684 | strncpy(*note, streamNote, strlen(streamNote) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here 1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); | ~~~~~~^~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here 1684 | strncpy(*note, streamNote, strlen(streamNote) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here 1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); | ~~~~~~^~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects-typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security SortDetails.cpp -o objects-typical/SortDetails.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p ../bin && g++ -o ../bin/bedops-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 Bedops.cpp mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p ../bin && g++ -o ../bin/closest-features-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 ClosestFeature.cpp mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p ../bin && g++ -o ../bin/bedmap-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 Bedmap.cpp In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from SortDetails.cpp:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘ChromBedData* initializeChromBedData(char*, double*)’ at SortDetails.cpp:250:12: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp: In function ‘ChromBedData* initializeChromBedData(char*, double*)’: SortDetails.cpp:249:25: note: length computed here 249 | chromBufLen = strlen(chromBuf); // we know >= 1 | ~~~~~~^~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from SortDetails.cpp:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void lexSortBedData(BedData*)’ at SortDetails.cpp:1343:20: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp: In function ‘void lexSortBedData(BedData*)’: SortDetails.cpp:1342:33: note: length computed here 1342 | chromBufLen = strlen(beds->chroms[i]->chromName); // we know >= 1 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::listJSONMetadata(FILE*, FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1226:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1226 | static_cast( getArchiveType() ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1230:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1230 | static_cast( getArchiveHeaderFlag() ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1231:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1231 | static_cast( getArchiveShowNewlineFlag() )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractAllData(const string&, FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:2003:51: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2003 | static_cast( getArchiveHeaderFlag() )) != 0 ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:2014:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2014 | static_cast( getArchiveHeaderFlag() )) != 0 ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp: In instantiation of ‘Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’: CheckSort.cpp:51:28: required from here ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:268:12: warning: implicitly-declared ‘Bed::bed_check_iterator*, 16>::bed_check_iterator(const Bed::bed_check_iterator*, 16>&)’ is deprecated [-Wdeprecated-copy] 268 | auto __tmp = *this; | ^~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:308:10: note: because ‘Bed::bed_check_iterator*, 16>’ has user-provided ‘bool Bed::bed_check_iterator::operator=(const Bed::bed_check_iterator&) [with BedType = Bed::BasicCoords; 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*, 16>::bed_check_iterator(const Bed::bed_check_iterator*, 16>&)’ is deprecated [-Wdeprecated-copy] 295 | return __tmp; | ^~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:308:10: note: because ‘Bed::bed_check_iterator*, 16>’ has user-provided ‘bool Bed::bed_check_iterator::operator=(const Bed::bed_check_iterator&) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’ 308 | bool operator=(const bed_check_iterator& b); | ^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here 551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); | ~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here 556 | std::strncpy(_recFilename, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::Starch::zReadLine()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1521:82: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1712:86: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1758:40: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1769:45: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1576:86: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1620:40: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1628:45: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentRemainder(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here 899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here 551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); | ~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here 556 | std::strncpy(_recFilename, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::Starch::zReadLine()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1521:82: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1712:86: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1758:40: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1769:45: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1576:86: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1620:40: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1628:45: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentRemainder(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here 899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, 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::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, 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 Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36, inlined from ‘int checkSort(const char**, unsigned int)’ at CheckSort.cpp:51:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function ‘int checkSort(const char**, unsigned int)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:551:89: note: length computed here 551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); | ~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:556:78: note: length computed here 556 | std::strncpy(_recFilename, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘const char* starch::Starch::getCurrentChromosome()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::Starch::zReadLine()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1769:45: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1628:45: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentRemainder(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here 899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ mkdir -p ../bin && cp update-sort-bed-slurm.py ../bin/update-sort-bed-slurm-typical mkdir -p ../bin && cp update-sort-bed-starch-slurm.py ../bin/update-sort-bed-starch-slurm-typical mkdir -p ../bin && cp update-sort-bed-migrate-candidates.py ../bin/update-sort-bed-migrate-candidates-typical mkdir -p ../bin && g++ -o ../bin/sort-bed-typical -s -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now objects-typical/starchConstants.o objects-typical/starchFileHelpers.o objects-typical/starchHelpers.o objects-typical/starchMetadataHelpers.o objects-typical/unstarchHelpers.o objects-typical/starchSha1Digest.o objects-typical/starchBase64Coding.o objects-typical/SortDetails.o objects-typical/Sort.o objects-typical/CheckSort.o -ljansson -lz -lbz2 rm -rf objects-typical make[4]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/sort-bed/src' make -C applications/bed/bedextract/src -f Makefile build make[4]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/bedextract/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here 359 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here 383 | strncpy(*chr, s, strlen(s) + 1); | ~~~~~~^~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here 485 | strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here 923 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here 1411 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::allocate_iterator_starch_bed Bed::allocate_iterator_starch_bed::operator++(int) [with BedType = Bed::BasicCoords; long unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:207:36, inlined from ‘FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]’ at BedReader.hpp:78:19: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here 2416 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, 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::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 512]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here 3695 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::allocate_iterator_starch_bed::allocate_iterator_starch_bed(Ext::FPWrap&, Ext::PooledMemory&, const string&) [with ErrorType = Ext::Exception, 0>; BedType = Bed::BasicCoords; long unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:117:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::allocate_iterator_starch_bed::allocate_iterator_starch_bed(Ext::FPWrap&, Ext::PooledMemory&, const string&) [with ErrorType = Ext::Exception, 0>; BedType = Bed::BasicCoords; long unsigned int SZ = 512]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, 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 Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; long unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36, inlined from ‘FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::bed_check_iterator*, 512>]’ at BedReader.hpp:78:19: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::bed_check_iterator*, 512>]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here 2228 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here 2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here 2256 | strncpy(recFilename, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here 1684 | strncpy(*note, streamNote, strlen(streamNote) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here 1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); | ~~~~~~^~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p ../bin && g++ -o ../bin/bedextract-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 ExtractRows.cpp rm -rf objects_typical make[4]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/closestfeats/src' make -C applications/bed/starch/src -f Makefile build make[4]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/starch/src' mkdir -p objects g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchConstants.c -o objects/starchConstants.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects/unstarchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘void starch::UNSTARCH_printMetadataSignature(const unsigned char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2276:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2276 | static_cast( 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( mdSha1BufferLength )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2640:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2640 | static_cast( 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( STARCH2_MD_FOOTER_SHA1_LENGTH )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchHelpers.c -o objects/starchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here 359 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here 383 | strncpy(*chr, s, strlen(s) + 1); | ~~~~~~^~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here 485 | strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here 923 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here 1411 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here 2416 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here 3695 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:551:89: note: length computed here 551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); | ~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:556:78: note: length computed here 556 | std::strncpy(_recFilename, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::Starch::zReadLine()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1521:82: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1712:86: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1758:40: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1769:45: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1576:86: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1620:40: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1628:45: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentRemainder(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here 899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ mkdir -p objects g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here 2228 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here 2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here 2256 | strncpy(recFilename, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here 1684 | strncpy(*note, streamNote, strlen(streamNote) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here 1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); | ~~~~~~^~~~~~~~~~~~~ mkdir -p objects g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects/starchFileHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects/starchSha1Digest.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects/starchBase64Coding.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p ../bin cp starchcluster_gnuParallel.tcsh ../bin/starchcluster_gnuParallel-typical mkdir -p ../bin cp starchcluster_sge.tcsh ../bin/starchcluster_sge-typical mkdir -p ../bin cp starchcluster_slurm.tcsh ../bin/starchcluster_slurm-typical mkdir -p ../bin cp starch-diff.py ../bin/starch-diff-typical mkdir -p ../lib ar rcs ../lib/libstarch.a objects/starchConstants.o objects/unstarchHelpers.o objects/starchHelpers.o objects/starchMetadataHelpers.o objects/starchFileHelpers.o objects/starchSha1Digest.o objects/starchBase64Coding.o mkdir -p ../bin g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c starch.c -o objects/starch.o -iquote../../../../interfaces/general-headers -iquote../../../.. starch.c: In function ‘int main(int, char**)’: starch.c:106:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 106 | static_cast( type ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:121:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 121 | static_cast( type ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:123:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 123 | static_cast( kStarchFinalizeTransformTrue ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:146:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 146 | static_cast( type ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:161:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 161 | static_cast( type ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:163:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 163 | static_cast( kStarchFinalizeTransformTrue ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:191:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 191 | static_cast( type ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:194:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 194 | static_cast( bedGeneratePerChrSignatureFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:195:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 195 | static_cast( bedHeaderFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:196:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 196 | static_cast( bedReportProgressFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:197:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 197 | static_cast( bedReportProgressN )) != STARCH_EXIT_SUCCESS) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security objects/starch.o -o ../bin/starch-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, 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::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ mkdir -p ../bin g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c unstarch.c -o objects/unstarch.o -iquote../../../../interfaces/general-headers -iquote../../../.. unstarch.c: In function ‘int main(int, char**)’: unstarch.c:401:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 401 | static_cast( metadataOffset ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:402:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 402 | static_cast( headerFlag )) != 0) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:422:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 422 | static_cast( metadataOffset ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:423:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 423 | static_cast( headerFlag )) != 0) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:452:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 452 | static_cast( sizeof(starchRevision2HeaderBytes) ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:453:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 453 | static_cast( headerFlag )) != 0) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:473:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 473 | static_cast( sizeof(starchRevision2HeaderBytes) ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:474:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 474 | static_cast( headerFlag )) != 0) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:567:39: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 567 | UNSTARCH_printCompressionType(static_cast( type )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:798:78: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 798 | static_cast( sizeof(starchRevision2HeaderBytes) ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:809:82: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 809 | static_cast( sizeof(starchRevision2HeaderBytes) ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c: In function ‘void starch::UNSTARCH_printMetadataSha1Signature(unsigned char*)’: unstarch.c:1334:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1334 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:1336:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1336 | static_cast( sha1BufferLength )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, 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 Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36, inlined from ‘std::pair Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = Bed::bed_check_iterator*, 16>; Op = Visitors::BedHelpers::Println]’ at ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:102:64: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function ‘std::pair Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = Bed::bed_check_iterator*, 16>; Op = Visitors::BedHelpers::Println]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security objects/unstarch.o -o ../bin/unstarch-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now mkdir -p ../bin g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c starchcat.c -o objects/starchcat.o -iquote../../../../interfaces/general-headers -iquote../../../.. In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; long unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 function ‘Bed::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; long unsigned int SZ = 512]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/c++/10/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( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:137:75: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 137 | assert( STARCHCAT_allocMetadataJSONObjects ( &metadataJSONs, static_cast( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:138:87: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 138 | assert( STARCHCAT_buildMetadataRecords ( &metadataJSONs, &mdRecords, static_cast( firstArgc ), static_cast( argc ), const_cast( argv ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:138:133: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 138 | assert( STARCHCAT_buildMetadataRecords ( &metadataJSONs, &mdRecords, static_cast( firstArgc ), static_cast( argc ), const_cast( argv ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:139:75: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 139 | assert( STARCHCAT_checkMetadataJSONVersions ( &metadataJSONs, static_cast( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:140:145: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 140 | assert( STARCHCAT_buildUniqueChromosomeList ( &chromosomes, &numChromosomes, reinterpret_cast( mdRecords ), static_cast( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:141:69: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 141 | assert( STARCHCAT_allocChromosomeSummary ( &summary, static_cast( numChromosomes ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:142:124: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 142 | assert( STARCHCAT_buildChromosomeSummary ( &summary, reinterpret_cast( mdRecords ), static_cast( numRecords ), const_cast( chromosomes ), static_cast( numChromosomes ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:142:213: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 142 | assert( STARCHCAT_buildChromosomeSummary ( &summary, reinterpret_cast( mdRecords ), static_cast( numRecords ), const_cast( chromosomes ), static_cast( numChromosomes ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:143:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 143 | assert( STARCHCAT_allocChromosomeSummaries ( &summaries, static_cast( numChromosomes ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:144:127: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 144 | assert( STARCHCAT_buildChromosomeSummaries ( &summaries, reinterpret_cast( summary ), static_cast( numChromosomes ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:164:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 164 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:178:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 178 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:223:60: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 223 | assert( STARCHCAT_freeMetadataRecords( &mdRecords, static_cast( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:233:68: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 233 | assert (STARCHCAT_freeMetadataJSONObjects( &metadataJSONs, static_cast( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT2_rewriteInputRecordToOutput(starch::Metadata**, const char*, starch::CompressionType, const char*, const MetadataRecord*, size_t*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: starchcat.c:1338:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1338 | UNSTARCH_reverseTransformCoordinates( static_cast( t_lineIdx ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:1806:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1806 | UNSTARCH_reverseTransformCoordinates( static_cast( t_lineIdx ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT_rewriteInputRecordToOutput(starch::Metadata**, const char*, starch::CompressionType, const char*, const MetadataRecord*)’: starchcat.c:2450:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2450 | static_cast( inRec->mdOffset ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:2451:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2451 | static_cast( inRec->hFlag )) != 0 ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:2471:28: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2471 | static_cast( inRec->mdOffset ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:2472:28: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2472 | static_cast( inRec->hFlag )) != 0 ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:2509:23: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2509 | static_cast( outType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:2511:23: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2511 | static_cast( kStarchFinalizeTransformFalse ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)’: starchcat.c:3152:54: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 3152 | if (STARCHCAT2_setupBzip2InputStream(static_cast( inRecIdx ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:3316:69: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 3316 | static_cast( summary->numRecords ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:3455:77: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 3455 | static_cast( flushZStreamFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT_mergeInputRecordsToOutput(starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*)’: starchcat.c:4265:43: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4265 | static_cast( outType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:4267:43: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4267 | static_cast( kStarchFinalizeTransformFalse ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/cassert:44, from starchcat.c:33: starchcat.c: In function ‘int starch::STARCHCAT_mergeChromosomeStreams(const ChromosomeSummaries*, starch::CompressionType, const char*)’: starchcat.c:4402:60: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4402 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:4420:63: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4420 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:4447:57: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4447 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:4479:39: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4479 | static_cast( hFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT_freeChromosomeSummaries(starch::ChromosomeSummaries**)’: starchcat.c:4541:62: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4541 | STARCHCAT_freeChromosomeSummary( &((*chrSums)->summary), static_cast( (*chrSums)->numChromosomes )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/cassert:44, from starchcat.c:33: starchcat.c: In function ‘int starch::STARCHCAT2_mergeChromosomeStreams(const ChromosomeSummaries*, starch::CompressionType, const char*, size_t*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: starchcat.c:5902:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 5902 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:5929:64: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 5929 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:5952:64: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 5952 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:5990:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 5990 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:6025:38: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 6025 | static_cast( hFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:6053:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 6053 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:6055:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 6055 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT2_fillExtractionBufferFromBzip2Stream(starch::Boolean*, char*, char*, size_t*, BZFILE**, size_t*, char*, size_t*, starch::TransformState*)’: starchcat.c:6719:55: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 6719 | UNSTARCH_reverseTransformCoordinates( static_cast( *t_lineIdxPtr ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT2_fillExtractionBufferFromGzipStream(starch::Boolean*, FILE**, char*, char*, size_t*, z_stream*, size_t*, char**, size_t*, starch::TransformState*)’: starchcat.c:7060:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 7060 | UNSTARCH_reverseTransformCoordinates( static_cast( *t_lineIdxPtr ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; long unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 function ‘Bed::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; long unsigned int SZ = 512]’: ../../../../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/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/bedextract/src' make -C applications/bed/conversion/src -f Makefile build make[4]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/conversion/src' mkdir -p ../bin && gcc -Wall -Wextra -pedantic -std=c99 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -iquote"/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/conversion/src" -iquote"../../../../interfaces/general-headers" -Wl,-z,relro -Wl,-z,now convert2bed.c -o ../bin/convert2bed-typical -lpthread convert2bed.c: In function ‘c2b_line_convert_rmsk_to_bed_unsorted’: convert2bed.c:3540:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 3540 | 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 In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from starchcat.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCHCAT_buildMetadataRecords(json_t***, starch::MetadataRecord**, unsigned int, int, const char**)’ at starchcat.c:5368:20: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT_buildMetadataRecords(json_t***, starch::MetadataRecord**, unsigned int, int, const char**)’: starchcat.c:5368:53: note: length computed here 5368 | strncpy(cTime, creationTimestamp, strlen(creationTimestamp) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from starchcat.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)’ at starchcat.c:3123:16: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)’: starchcat.c:3123:78: note: length computed here 3123 | strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); | ~~~~~~^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security objects/starchcat.o -o ../bin/starchcat-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now mkdir -p ../bin g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c starchstrip.c -o objects/starchstrip.o -iquote../../../../interfaces/general-headers -iquote../../../.. starchstrip.c: In function ‘void starch::STARCHSTRIP_write_updated_metadata(FILE*)’: starchstrip.c:124:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 124 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchstrip.c:126:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 126 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -ffile-prefix-map=/build/bedops-jA2UgM/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security objects/starchstrip.o -o ../bin/starchstrip-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now rm -rf objects make[4]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/starch/src' In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; long unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36, inlined from ‘BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]’ at BedPadReader.hpp:140:11: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ rm -rf objects make[4]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/conversion/src' In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; long unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36, inlined from ‘BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]’ at BedPadReader.hpp:140:11: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]’: ../../../../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/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/bedops/src' In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here 551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); | ~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here 556 | std::strncpy(_recFilename, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘const char* starch::Starch::getCurrentChromosome()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘void starch::Starch::iterateArchiveMdIter()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::Starch::zReadLine()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentRemainder(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here 899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ rm -rf objects_typical make[4]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/applications/bed/bedmap/src' make[3]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1' make[2]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1' make[1]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1' dh_auto_test -i create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-indep dh binary-indep dh_testroot -i dh_prep -i dh_auto_install -i make -j4 install DESTDIR=/build/bedops-jA2UgM/bedops-2.4.39\+dfsg1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1' mkdir -p bin cp applications/bed/conversion/src/wrappers/bam2bed applications/bed/conversion/src/wrappers/bam2bed_gnuParallel applications/bed/conversion/src/wrappers/bam2bed_sge applications/bed/conversion/src/wrappers/bam2bed_slurm applications/bed/conversion/src/wrappers/bam2starch applications/bed/conversion/src/wrappers/bam2starch_gnuParallel applications/bed/conversion/src/wrappers/bam2starch_sge applications/bed/conversion/src/wrappers/bam2starch_slurm applications/bed/conversion/src/wrappers/gff2bed applications/bed/conversion/src/wrappers/gff2starch applications/bed/conversion/src/wrappers/gtf2bed applications/bed/conversion/src/wrappers/gtf2starch applications/bed/conversion/src/wrappers/gvf2bed applications/bed/conversion/src/wrappers/gvf2starch applications/bed/conversion/src/wrappers/psl2bed applications/bed/conversion/src/wrappers/psl2starch applications/bed/conversion/src/wrappers/rmsk2bed applications/bed/conversion/src/wrappers/rmsk2starch applications/bed/conversion/src/wrappers/sam2bed applications/bed/conversion/src/wrappers/sam2starch applications/bed/conversion/src/wrappers/vcf2bed applications/bed/conversion/src/wrappers/vcf2starch applications/bed/conversion/src/wrappers/wig2bed applications/bed/conversion/src/wrappers/wig2starch bin cp applications/bed/starch/bin/starchcluster_sge-typical bin/starchcluster_sge cp applications/bed/starch/bin/starchcluster_gnuParallel-typical bin/starchcluster_gnuParallel cp applications/bed/starch/bin/starchcluster_slurm-typical bin/starchcluster_slurm cp applications/bed/starch/bin/starch-diff-typical bin/starch-diff cp applications/bed/sort-bed/bin/sort-bed-typical bin/sort-bed cp applications/bed/sort-bed/bin/update-sort-bed-slurm-typical bin/update-sort-bed-slurm cp applications/bed/sort-bed/bin/update-sort-bed-starch-slurm-typical bin/update-sort-bed-starch-slurm cp applications/bed/sort-bed/bin/update-sort-bed-migrate-candidates-typical bin/update-sort-bed-migrate-candidates cp applications/bed/bedops/bin/bedops-typical bin/bedops cp applications/bed/closestfeats/bin/closest-features-typical bin/closest-features cp applications/bed/bedmap/bin/bedmap-typical bin/bedmap cp applications/bed/bedextract/bin/bedextract-typical bin/bedextract cp applications/bed/starch/bin/starch-typical bin/starch cp applications/bed/starch/bin/unstarch-typical bin/unstarch cp applications/bed/starch/bin/starchcat-typical bin/starchcat cp applications/bed/starch/bin/starchstrip-typical bin/starchstrip cp applications/bed/conversion/bin/convert2bed-typical bin/convert2bed make[1]: Leaving directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1' dh_install -i debian/rules override_dh_installdocs-indep make[1]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1' cd docs && make html make[2]: Entering directory '/build/bedops-jA2UgM/bedops-2.4.39+dfsg1/docs' sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v3.4.3 making output directory... done /build/bedops-jA2UgM/bedops-2.4.39+dfsg1/docs/conf.py:329: RemovedInSphinx40Warning: The app.add_stylesheet() is deprecated. 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[ 85%] assets/usage-examples/Frequencies-SNPs.bed.starch copying downloadable files... [ 90%] assets/usage-examples/Frequencies-DHSs.bed.starch copying downloadable files... [ 95%] assets/usage-examples/SNP_DHS_heatmap.tcsh copying downloadable files... [100%] assets/usage-examples/SNP_DHS_data.tgz copying static files... done copying extra files... done 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/bedops-jA2UgM/bedops-2.4.39+dfsg1/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/bedops-jA2UgM/bedops-2.4.39+dfsg1' dh_installchangelogs -i dh_installman -i dh_perl -i dh_link -i dh_strip_nondeterminism -i 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/usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_inputs.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/index/support_v2.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/_images/bedops_cygwin_installer_git_screen.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/set-operations/reference_setops_bedops_everything@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_unstarch_extractiontime.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/index/linux.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/_images/reference_setops_bedops_everything@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/set-operations/reference_setops_bedops_elementof_ba.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_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/usage-examples/SNP_DHS_matrix_diseaseSorted.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/_images/SNP_DHS_matrix.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/set-operations/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/starch_specification_magicbytes.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/_images/starch_specification_padding.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/usage-examples/SNP_DHS_matrix.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/_images/bedops_macosx_installer_icon.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/installation/bedops_cygwin_installer_screen.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/installation/bedops_cygwin_installer_gcc_screen.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/downloads_v2.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/installation/bedops_macosx_installer_screen.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_inputs.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/installation/bedops_macosx_installer_screen_v2.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/installation/bedops_cygwin_installer_git_screen.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/installation/bedops_macosx_installer_icon.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. dh_compress -i dh_fixperms -i dh_missing -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'bedops-doc' in '../bedops-doc_2.4.39+dfsg1-2_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../bedops_2.4.39+dfsg1-2_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/bedops-jA2UgM /tmp/bedops-2.4.39+dfsg1-2s_ibss1b I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.zxbGfu2rUI... I: success in 1513.2308 seconds md5: bedops-doc_2.4.39+dfsg1-2_all.deb: OK sha1: bedops-doc_2.4.39+dfsg1-2_all.deb: OK sha256: bedops-doc_2.4.39+dfsg1-2_all.deb: OK Checksums: OK