Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/b/bedops/bedops_2.4.41+dfsg-1_all.buildinfo Use metasnap for getting required timestamps Cannot get timestamps from metasnap: 404 (Not Found) Use snapshot for getting required timestamps Get source package info: bedops=2.4.41+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/bedops/2.4.41+dfsg-1/srcfiles?fileinfo=1 Initialize APT cache Get binary package info: autoconf=2.71-2 Binary URL: http://snapshot.notset.fr/mr/binary/autoconf/2.71-2/binfiles?fileinfo=1 Get binary package info: automake=1:1.16.5-1.3 Binary URL: http://snapshot.notset.fr/mr/binary/automake/1:1.16.5-1.3/binfiles?fileinfo=1 Get binary package info: autopoint=0.21-6 Binary URL: http://snapshot.notset.fr/mr/binary/autopoint/0.21-6/binfiles?fileinfo=1 Get binary package info: autotools-dev=20220109.1 Binary URL: http://snapshot.notset.fr/mr/binary/autotools-dev/20220109.1/binfiles?fileinfo=1 Get binary package info: base-files=12.2 Binary URL: http://snapshot.notset.fr/mr/binary/base-files/12.2/binfiles?fileinfo=1 Get binary package info: base-passwd=3.5.52 Binary URL: http://snapshot.notset.fr/mr/binary/base-passwd/3.5.52/binfiles?fileinfo=1 Get binary package info: bash=5.1-6.1 Binary URL: http://snapshot.notset.fr/mr/binary/bash/5.1-6.1/binfiles?fileinfo=1 Get binary package info: binutils=2.38.90.20220713-2 Binary URL: http://snapshot.notset.fr/mr/binary/binutils/2.38.90.20220713-2/binfiles?fileinfo=1 Get binary package info: binutils-common=2.38.90.20220713-2 Binary URL: http://snapshot.notset.fr/mr/binary/binutils-common/2.38.90.20220713-2/binfiles?fileinfo=1 Get binary package info: binutils-x86-64-linux-gnu=2.38.90.20220713-2 Binary URL: http://snapshot.notset.fr/mr/binary/binutils-x86-64-linux-gnu/2.38.90.20220713-2/binfiles?fileinfo=1 Get binary package info: bsdextrautils=2.38-5 Binary URL: http://snapshot.notset.fr/mr/binary/bsdextrautils/2.38-5/binfiles?fileinfo=1 Get binary package info: bsdutils=1:2.38-5 Binary URL: http://snapshot.notset.fr/mr/binary/bsdutils/1:2.38-5/binfiles?fileinfo=1 Get binary package info: build-essential=12.9 Binary URL: http://snapshot.notset.fr/mr/binary/build-essential/12.9/binfiles?fileinfo=1 Get binary package info: bzip2=1.0.8-5 Binary URL: http://snapshot.notset.fr/mr/binary/bzip2/1.0.8-5/binfiles?fileinfo=1 Get binary package info: ca-certificates=20211016 Binary URL: http://snapshot.notset.fr/mr/binary/ca-certificates/20211016/binfiles?fileinfo=1 Get binary package info: coreutils=8.32-4.1 Binary URL: http://snapshot.notset.fr/mr/binary/coreutils/8.32-4.1/binfiles?fileinfo=1 Get binary package info: cpp=4:11.2.0-2 Binary URL: http://snapshot.notset.fr/mr/binary/cpp/4:11.2.0-2/binfiles?fileinfo=1 Get binary package info: cpp-11=11.3.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/cpp-11/11.3.0-4/binfiles?fileinfo=1 Get binary package info: dash=0.5.11+git20210903+057cd650a4ed-8 Binary URL: http://snapshot.notset.fr/mr/binary/dash/0.5.11+git20210903+057cd650a4ed-8/binfiles?fileinfo=1 Get binary package info: debconf=1.5.79 Binary URL: http://snapshot.notset.fr/mr/binary/debconf/1.5.79/binfiles?fileinfo=1 Get binary package info: debhelper=13.8 Binary URL: http://snapshot.notset.fr/mr/binary/debhelper/13.8/binfiles?fileinfo=1 Get binary package info: debianutils=5.7-0.2 Binary URL: http://snapshot.notset.fr/mr/binary/debianutils/5.7-0.2/binfiles?fileinfo=1 Get binary package info: dh-autoreconf=20 Binary URL: http://snapshot.notset.fr/mr/binary/dh-autoreconf/20/binfiles?fileinfo=1 Get binary package info: dh-strip-nondeterminism=1.13.0-1 Binary URL: http://snapshot.notset.fr/mr/binary/dh-strip-nondeterminism/1.13.0-1/binfiles?fileinfo=1 Get binary package info: diffutils=1:3.7-5 Binary URL: http://snapshot.notset.fr/mr/binary/diffutils/1:3.7-5/binfiles?fileinfo=1 Get binary package info: docutils-common=0.17.1+dfsg-2 Binary URL: http://snapshot.notset.fr/mr/binary/docutils-common/0.17.1+dfsg-2/binfiles?fileinfo=1 Get binary package info: dpkg=1.21.9 Binary URL: http://snapshot.notset.fr/mr/binary/dpkg/1.21.9/binfiles?fileinfo=1 Get binary package info: dpkg-dev=1.21.9 Binary URL: http://snapshot.notset.fr/mr/binary/dpkg-dev/1.21.9/binfiles?fileinfo=1 Get binary package info: dwz=0.14-1 Binary URL: http://snapshot.notset.fr/mr/binary/dwz/0.14-1/binfiles?fileinfo=1 Get binary package info: file=1:5.41-4 Binary URL: http://snapshot.notset.fr/mr/binary/file/1:5.41-4/binfiles?fileinfo=1 Get binary package info: findutils=4.9.0-3 Binary URL: http://snapshot.notset.fr/mr/binary/findutils/4.9.0-3/binfiles?fileinfo=1 Get binary package info: fonts-mathjax=2.7.9+dfsg-1 Binary URL: http://snapshot.notset.fr/mr/binary/fonts-mathjax/2.7.9+dfsg-1/binfiles?fileinfo=1 Get binary package info: g++=4:11.2.0-2 Binary URL: http://snapshot.notset.fr/mr/binary/g++/4:11.2.0-2/binfiles?fileinfo=1 Get binary package info: g++-11=11.3.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/g++-11/11.3.0-4/binfiles?fileinfo=1 Get binary package info: gcc=4:11.2.0-2 Binary URL: http://snapshot.notset.fr/mr/binary/gcc/4:11.2.0-2/binfiles?fileinfo=1 Get binary package info: gcc-11=11.3.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/gcc-11/11.3.0-4/binfiles?fileinfo=1 Get binary package info: gcc-11-base=11.3.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/gcc-11-base/11.3.0-4/binfiles?fileinfo=1 Get binary package info: gcc-12-base=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/gcc-12-base/12.1.0-5/binfiles?fileinfo=1 Get binary package info: gettext=0.21-6 Binary URL: http://snapshot.notset.fr/mr/binary/gettext/0.21-6/binfiles?fileinfo=1 Get binary package info: gettext-base=0.21-6 Binary URL: http://snapshot.notset.fr/mr/binary/gettext-base/0.21-6/binfiles?fileinfo=1 Get binary package info: grep=3.7-1 Binary URL: http://snapshot.notset.fr/mr/binary/grep/3.7-1/binfiles?fileinfo=1 Get binary package info: groff-base=1.22.4-8 Binary URL: http://snapshot.notset.fr/mr/binary/groff-base/1.22.4-8/binfiles?fileinfo=1 Get binary package info: gzip=1.12-1 Binary URL: http://snapshot.notset.fr/mr/binary/gzip/1.12-1/binfiles?fileinfo=1 Get binary package info: help2man=1.49.2 Binary URL: http://snapshot.notset.fr/mr/binary/help2man/1.49.2/binfiles?fileinfo=1 Get binary package info: hostname=3.23 Binary URL: http://snapshot.notset.fr/mr/binary/hostname/3.23/binfiles?fileinfo=1 Get binary package info: init-system-helpers=1.64 Binary URL: http://snapshot.notset.fr/mr/binary/init-system-helpers/1.64/binfiles?fileinfo=1 Get binary package info: intltool-debian=0.35.0+20060710.5 Binary URL: http://snapshot.notset.fr/mr/binary/intltool-debian/0.35.0+20060710.5/binfiles?fileinfo=1 Get binary package info: libacl1=2.3.1-1 Binary URL: http://snapshot.notset.fr/mr/binary/libacl1/2.3.1-1/binfiles?fileinfo=1 Get binary package info: libarchive-zip-perl=1.68-1 Binary URL: http://snapshot.notset.fr/mr/binary/libarchive-zip-perl/1.68-1/binfiles?fileinfo=1 Get binary package info: libasan6=11.3.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/libasan6/11.3.0-4/binfiles?fileinfo=1 Get binary package info: libatomic1=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libatomic1/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libattr1=1:2.5.1-1 Binary URL: http://snapshot.notset.fr/mr/binary/libattr1/1:2.5.1-1/binfiles?fileinfo=1 Get binary package info: libaudit-common=1:3.0.7-1 Binary URL: http://snapshot.notset.fr/mr/binary/libaudit-common/1:3.0.7-1/binfiles?fileinfo=1 Get binary package info: libaudit1=1:3.0.7-1+b1 Binary URL: http://snapshot.notset.fr/mr/binary/libaudit1/1:3.0.7-1+b1/binfiles?fileinfo=1 Get binary package info: libbinutils=2.38.90.20220713-2 Binary URL: http://snapshot.notset.fr/mr/binary/libbinutils/2.38.90.20220713-2/binfiles?fileinfo=1 Get binary package info: libblkid1=2.38-5 Binary URL: http://snapshot.notset.fr/mr/binary/libblkid1/2.38-5/binfiles?fileinfo=1 Get binary package info: libbz2-1.0=1.0.8-5 Binary URL: http://snapshot.notset.fr/mr/binary/libbz2-1.0/1.0.8-5/binfiles?fileinfo=1 Get binary package info: libbz2-dev=1.0.8-5 Binary URL: http://snapshot.notset.fr/mr/binary/libbz2-dev/1.0.8-5/binfiles?fileinfo=1 Get binary package info: libc-bin=2.33-8 Binary URL: http://snapshot.notset.fr/mr/binary/libc-bin/2.33-8/binfiles?fileinfo=1 Get binary package info: libc-dev-bin=2.33-8 Binary URL: http://snapshot.notset.fr/mr/binary/libc-dev-bin/2.33-8/binfiles?fileinfo=1 Get binary package info: libc6=2.33-8 Binary URL: http://snapshot.notset.fr/mr/binary/libc6/2.33-8/binfiles?fileinfo=1 Get binary package info: libc6-dev=2.33-8 Binary URL: http://snapshot.notset.fr/mr/binary/libc6-dev/2.33-8/binfiles?fileinfo=1 Get binary package info: libcap-ng0=0.8.3-1 Binary URL: http://snapshot.notset.fr/mr/binary/libcap-ng0/0.8.3-1/binfiles?fileinfo=1 Get binary package info: libcap2=1:2.44-1 Binary URL: http://snapshot.notset.fr/mr/binary/libcap2/1:2.44-1/binfiles?fileinfo=1 Get binary package info: libcc1-0=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libcc1-0/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libcom-err2=1.46.5-2 Binary URL: http://snapshot.notset.fr/mr/binary/libcom-err2/1.46.5-2/binfiles?fileinfo=1 Get binary package info: libcrypt-dev=1:4.4.28-2 Binary URL: http://snapshot.notset.fr/mr/binary/libcrypt-dev/1:4.4.28-2/binfiles?fileinfo=1 Get binary package info: libcrypt1=1:4.4.28-2 Binary URL: http://snapshot.notset.fr/mr/binary/libcrypt1/1:4.4.28-2/binfiles?fileinfo=1 Get binary package info: libctf-nobfd0=2.38.90.20220713-2 Binary URL: http://snapshot.notset.fr/mr/binary/libctf-nobfd0/2.38.90.20220713-2/binfiles?fileinfo=1 Get binary package info: libctf0=2.38.90.20220713-2 Binary URL: http://snapshot.notset.fr/mr/binary/libctf0/2.38.90.20220713-2/binfiles?fileinfo=1 Get binary package info: libdb5.3=5.3.28+dfsg1-0.10 Binary URL: http://snapshot.notset.fr/mr/binary/libdb5.3/5.3.28+dfsg1-0.10/binfiles?fileinfo=1 Get binary package info: libdebconfclient0=0.263 Binary URL: http://snapshot.notset.fr/mr/binary/libdebconfclient0/0.263/binfiles?fileinfo=1 Get binary package info: libdebhelper-perl=13.8 Binary URL: http://snapshot.notset.fr/mr/binary/libdebhelper-perl/13.8/binfiles?fileinfo=1 Get binary package info: libdpkg-perl=1.21.9 Binary URL: http://snapshot.notset.fr/mr/binary/libdpkg-perl/1.21.9/binfiles?fileinfo=1 Get binary package info: libelf1=0.187-1 Binary URL: http://snapshot.notset.fr/mr/binary/libelf1/0.187-1/binfiles?fileinfo=1 Get binary package info: libexpat1=2.4.8-1 Binary URL: http://snapshot.notset.fr/mr/binary/libexpat1/2.4.8-1/binfiles?fileinfo=1 Get binary package info: libffi8=3.4.2-4 Binary URL: http://snapshot.notset.fr/mr/binary/libffi8/3.4.2-4/binfiles?fileinfo=1 Get binary package info: libfile-stripnondeterminism-perl=1.13.0-1 Binary URL: http://snapshot.notset.fr/mr/binary/libfile-stripnondeterminism-perl/1.13.0-1/binfiles?fileinfo=1 Get binary package info: libgcc-11-dev=11.3.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/libgcc-11-dev/11.3.0-4/binfiles?fileinfo=1 Get binary package info: libgcc-s1=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libgcc-s1/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libgcrypt20=1.10.1-2 Binary URL: http://snapshot.notset.fr/mr/binary/libgcrypt20/1.10.1-2/binfiles?fileinfo=1 Get binary package info: libgdbm-compat4=1.23-1 Binary URL: http://snapshot.notset.fr/mr/binary/libgdbm-compat4/1.23-1/binfiles?fileinfo=1 Get binary package info: libgdbm6=1.23-1 Binary URL: http://snapshot.notset.fr/mr/binary/libgdbm6/1.23-1/binfiles?fileinfo=1 Get binary package info: libgmp10=2:6.2.1+dfsg1-1 Binary URL: http://snapshot.notset.fr/mr/binary/libgmp10/2:6.2.1+dfsg1-1/binfiles?fileinfo=1 Get binary package info: libgomp1=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libgomp1/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libgpg-error0=1.45-2 Binary URL: http://snapshot.notset.fr/mr/binary/libgpg-error0/1.45-2/binfiles?fileinfo=1 Get binary package info: libgprofng0=2.38.90.20220713-2 Binary URL: http://snapshot.notset.fr/mr/binary/libgprofng0/2.38.90.20220713-2/binfiles?fileinfo=1 Get binary package info: libgssapi-krb5-2=1.19.2-2+b2 Binary URL: http://snapshot.notset.fr/mr/binary/libgssapi-krb5-2/1.19.2-2+b2/binfiles?fileinfo=1 Get binary package info: libicu71=71.1-3 Binary URL: http://snapshot.notset.fr/mr/binary/libicu71/71.1-3/binfiles?fileinfo=1 Get binary package info: libisl23=0.25-1 Binary URL: http://snapshot.notset.fr/mr/binary/libisl23/0.25-1/binfiles?fileinfo=1 Get binary package info: libitm1=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libitm1/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libjansson-dev=2.14-2 Binary URL: http://snapshot.notset.fr/mr/binary/libjansson-dev/2.14-2/binfiles?fileinfo=1 Get binary package info: libjansson4=2.14-2 Binary URL: http://snapshot.notset.fr/mr/binary/libjansson4/2.14-2/binfiles?fileinfo=1 Get binary package info: libjs-jquery=3.6.0+dfsg+~3.5.13-1 Binary URL: http://snapshot.notset.fr/mr/binary/libjs-jquery/3.6.0+dfsg+~3.5.13-1/binfiles?fileinfo=1 Get binary package info: libjs-mathjax=2.7.9+dfsg-1 Binary URL: http://snapshot.notset.fr/mr/binary/libjs-mathjax/2.7.9+dfsg-1/binfiles?fileinfo=1 Get binary package info: libjs-sphinxdoc=4.5.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/libjs-sphinxdoc/4.5.0-4/binfiles?fileinfo=1 Get binary package info: libjs-underscore=1.13.3~dfsg+~1.11.4-1 Binary URL: http://snapshot.notset.fr/mr/binary/libjs-underscore/1.13.3~dfsg+~1.11.4-1/binfiles?fileinfo=1 Get binary package info: libjson-perl=4.07000-1 Binary URL: http://snapshot.notset.fr/mr/binary/libjson-perl/4.07000-1/binfiles?fileinfo=1 Get binary package info: libk5crypto3=1.19.2-2+b2 Binary URL: http://snapshot.notset.fr/mr/binary/libk5crypto3/1.19.2-2+b2/binfiles?fileinfo=1 Get binary package info: libkeyutils1=1.6.3-1 Binary URL: http://snapshot.notset.fr/mr/binary/libkeyutils1/1.6.3-1/binfiles?fileinfo=1 Get binary package info: libkrb5-3=1.19.2-2+b2 Binary URL: http://snapshot.notset.fr/mr/binary/libkrb5-3/1.19.2-2+b2/binfiles?fileinfo=1 Get binary package info: libkrb5support0=1.19.2-2+b2 Binary URL: http://snapshot.notset.fr/mr/binary/libkrb5support0/1.19.2-2+b2/binfiles?fileinfo=1 Get binary package info: liblocale-gettext-perl=1.07-4+b2 Binary URL: http://snapshot.notset.fr/mr/binary/liblocale-gettext-perl/1.07-4+b2/binfiles?fileinfo=1 Get binary package info: liblsan0=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/liblsan0/12.1.0-5/binfiles?fileinfo=1 Get binary package info: liblz4-1=1.9.3-2 Binary URL: http://snapshot.notset.fr/mr/binary/liblz4-1/1.9.3-2/binfiles?fileinfo=1 Get binary package info: liblzma5=5.2.5-2.1 Binary URL: http://snapshot.notset.fr/mr/binary/liblzma5/5.2.5-2.1/binfiles?fileinfo=1 Get binary package info: libmagic-mgc=1:5.41-4 Binary URL: http://snapshot.notset.fr/mr/binary/libmagic-mgc/1:5.41-4/binfiles?fileinfo=1 Get binary package info: libmagic1=1:5.41-4 Binary URL: http://snapshot.notset.fr/mr/binary/libmagic1/1:5.41-4/binfiles?fileinfo=1 Get binary package info: libmount1=2.38-5 Binary URL: http://snapshot.notset.fr/mr/binary/libmount1/2.38-5/binfiles?fileinfo=1 Get binary package info: libmpc3=1.2.1-2 Binary URL: http://snapshot.notset.fr/mr/binary/libmpc3/1.2.1-2/binfiles?fileinfo=1 Get binary package info: libmpdec3=2.5.1-2 Binary URL: http://snapshot.notset.fr/mr/binary/libmpdec3/2.5.1-2/binfiles?fileinfo=1 Get binary package info: libmpfr6=4.1.0-3 Binary URL: http://snapshot.notset.fr/mr/binary/libmpfr6/4.1.0-3/binfiles?fileinfo=1 Get binary package info: libncursesw6=6.3+20220423-2 Binary URL: http://snapshot.notset.fr/mr/binary/libncursesw6/6.3+20220423-2/binfiles?fileinfo=1 Get binary package info: libnsl-dev=1.3.0-2 Binary URL: http://snapshot.notset.fr/mr/binary/libnsl-dev/1.3.0-2/binfiles?fileinfo=1 Get binary package info: libnsl2=1.3.0-2 Binary URL: http://snapshot.notset.fr/mr/binary/libnsl2/1.3.0-2/binfiles?fileinfo=1 Get binary package info: libpam-modules=1.4.0-13 Binary URL: http://snapshot.notset.fr/mr/binary/libpam-modules/1.4.0-13/binfiles?fileinfo=1 Get binary package info: libpam-modules-bin=1.4.0-13 Binary URL: http://snapshot.notset.fr/mr/binary/libpam-modules-bin/1.4.0-13/binfiles?fileinfo=1 Get binary package info: libpam-runtime=1.4.0-13 Binary URL: http://snapshot.notset.fr/mr/binary/libpam-runtime/1.4.0-13/binfiles?fileinfo=1 Get binary package info: libpam0g=1.4.0-13 Binary URL: http://snapshot.notset.fr/mr/binary/libpam0g/1.4.0-13/binfiles?fileinfo=1 Get binary package info: libpcre2-8-0=10.40-1 Binary URL: http://snapshot.notset.fr/mr/binary/libpcre2-8-0/10.40-1/binfiles?fileinfo=1 Get binary package info: libpcre3=2:8.39-14 Binary URL: http://snapshot.notset.fr/mr/binary/libpcre3/2:8.39-14/binfiles?fileinfo=1 Get binary package info: libperl5.34=5.34.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libperl5.34/5.34.0-5/binfiles?fileinfo=1 Get binary package info: libpipeline1=1.5.6-1 Binary URL: http://snapshot.notset.fr/mr/binary/libpipeline1/1.5.6-1/binfiles?fileinfo=1 Get binary package info: libpython3-stdlib=3.10.5-1 Binary URL: http://snapshot.notset.fr/mr/binary/libpython3-stdlib/3.10.5-1/binfiles?fileinfo=1 Get binary package info: libpython3.10-minimal=3.10.5-1 Binary URL: http://snapshot.notset.fr/mr/binary/libpython3.10-minimal/3.10.5-1/binfiles?fileinfo=1 Get binary package info: libpython3.10-stdlib=3.10.5-1 Binary URL: http://snapshot.notset.fr/mr/binary/libpython3.10-stdlib/3.10.5-1/binfiles?fileinfo=1 Get binary package info: libquadmath0=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libquadmath0/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libreadline8=8.1.2-1.2 Binary URL: http://snapshot.notset.fr/mr/binary/libreadline8/8.1.2-1.2/binfiles?fileinfo=1 Get binary package info: libseccomp2=2.5.4-1 Binary URL: http://snapshot.notset.fr/mr/binary/libseccomp2/2.5.4-1/binfiles?fileinfo=1 Get binary package info: libselinux1=3.4-1 Binary URL: http://snapshot.notset.fr/mr/binary/libselinux1/3.4-1/binfiles?fileinfo=1 Get binary package info: libsigsegv2=2.14-1 Binary URL: http://snapshot.notset.fr/mr/binary/libsigsegv2/2.14-1/binfiles?fileinfo=1 Get binary package info: libsmartcols1=2.38-5 Binary URL: http://snapshot.notset.fr/mr/binary/libsmartcols1/2.38-5/binfiles?fileinfo=1 Get binary package info: libsqlite3-0=3.39.1-1 Binary URL: http://snapshot.notset.fr/mr/binary/libsqlite3-0/3.39.1-1/binfiles?fileinfo=1 Get binary package info: libssl3=3.0.4-2 Binary URL: http://snapshot.notset.fr/mr/binary/libssl3/3.0.4-2/binfiles?fileinfo=1 Get binary package info: libstdc++-11-dev=11.3.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/libstdc++-11-dev/11.3.0-4/binfiles?fileinfo=1 Get binary package info: libstdc++6=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libstdc++6/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libsub-override-perl=0.09-3 Binary URL: http://snapshot.notset.fr/mr/binary/libsub-override-perl/0.09-3/binfiles?fileinfo=1 Get binary package info: libsystemd0=251.3-1 Binary URL: http://snapshot.notset.fr/mr/binary/libsystemd0/251.3-1/binfiles?fileinfo=1 Get binary package info: libtinfo6=6.3+20220423-2 Binary URL: http://snapshot.notset.fr/mr/binary/libtinfo6/6.3+20220423-2/binfiles?fileinfo=1 Get binary package info: libtirpc-common=1.3.2-2 Binary URL: http://snapshot.notset.fr/mr/binary/libtirpc-common/1.3.2-2/binfiles?fileinfo=1 Get binary package info: libtirpc-dev=1.3.2-2 Binary URL: http://snapshot.notset.fr/mr/binary/libtirpc-dev/1.3.2-2/binfiles?fileinfo=1 Get binary package info: libtirpc3=1.3.2-2 Binary URL: http://snapshot.notset.fr/mr/binary/libtirpc3/1.3.2-2/binfiles?fileinfo=1 Get binary package info: libtool=2.4.7-4 Binary URL: http://snapshot.notset.fr/mr/binary/libtool/2.4.7-4/binfiles?fileinfo=1 Get binary package info: libtsan0=11.3.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/libtsan0/11.3.0-4/binfiles?fileinfo=1 Get binary package info: libubsan1=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libubsan1/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libuchardet0=0.0.7-1 Binary URL: http://snapshot.notset.fr/mr/binary/libuchardet0/0.0.7-1/binfiles?fileinfo=1 Get binary package info: libudev1=251.3-1 Binary URL: http://snapshot.notset.fr/mr/binary/libudev1/251.3-1/binfiles?fileinfo=1 Get binary package info: libunistring2=1.0-1 Binary URL: http://snapshot.notset.fr/mr/binary/libunistring2/1.0-1/binfiles?fileinfo=1 Get binary package info: libuuid1=2.38-5 Binary URL: http://snapshot.notset.fr/mr/binary/libuuid1/2.38-5/binfiles?fileinfo=1 Get binary package info: libxml2=2.9.14+dfsg-1 Binary URL: http://snapshot.notset.fr/mr/binary/libxml2/2.9.14+dfsg-1/binfiles?fileinfo=1 Get binary package info: libzstd1=1.5.2+dfsg-1 Binary URL: http://snapshot.notset.fr/mr/binary/libzstd1/1.5.2+dfsg-1/binfiles?fileinfo=1 Get binary package info: linux-libc-dev=5.18.5-1 Binary URL: http://snapshot.notset.fr/mr/binary/linux-libc-dev/5.18.5-1/binfiles?fileinfo=1 Get binary package info: login=1:4.11.1+dfsg1-2 Binary URL: http://snapshot.notset.fr/mr/binary/login/1:4.11.1+dfsg1-2/binfiles?fileinfo=1 Get binary package info: lsb-base=11.2 Binary URL: http://snapshot.notset.fr/mr/binary/lsb-base/11.2/binfiles?fileinfo=1 Get binary package info: m4=1.4.18-5 Binary URL: http://snapshot.notset.fr/mr/binary/m4/1.4.18-5/binfiles?fileinfo=1 Get binary package info: make=4.3-4.1 Binary URL: http://snapshot.notset.fr/mr/binary/make/4.3-4.1/binfiles?fileinfo=1 Get binary package info: man-db=2.10.2-1 Binary URL: http://snapshot.notset.fr/mr/binary/man-db/2.10.2-1/binfiles?fileinfo=1 Get binary package info: mawk=1.3.4.20200120-3.1 Binary URL: http://snapshot.notset.fr/mr/binary/mawk/1.3.4.20200120-3.1/binfiles?fileinfo=1 Get binary package info: media-types=8.0.0 Binary URL: http://snapshot.notset.fr/mr/binary/media-types/8.0.0/binfiles?fileinfo=1 Get binary package info: ncurses-base=6.3+20220423-2 Binary URL: http://snapshot.notset.fr/mr/binary/ncurses-base/6.3+20220423-2/binfiles?fileinfo=1 Get binary package info: ncurses-bin=6.3+20220423-2 Binary URL: http://snapshot.notset.fr/mr/binary/ncurses-bin/6.3+20220423-2/binfiles?fileinfo=1 Get binary package info: openssl=3.0.4-2 Binary URL: http://snapshot.notset.fr/mr/binary/openssl/3.0.4-2/binfiles?fileinfo=1 Get binary package info: patch=2.7.6-7 Binary URL: http://snapshot.notset.fr/mr/binary/patch/2.7.6-7/binfiles?fileinfo=1 Get binary package info: perl=5.34.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/perl/5.34.0-5/binfiles?fileinfo=1 Get binary package info: perl-base=5.34.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/perl-base/5.34.0-5/binfiles?fileinfo=1 Get binary package info: perl-modules-5.34=5.34.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/perl-modules-5.34/5.34.0-5/binfiles?fileinfo=1 Get binary package info: po-debconf=1.0.21+nmu1 Binary URL: http://snapshot.notset.fr/mr/binary/po-debconf/1.0.21+nmu1/binfiles?fileinfo=1 Get binary package info: python-babel-localedata=2.8.0+dfsg.1-7 Binary URL: http://snapshot.notset.fr/mr/binary/python-babel-localedata/2.8.0+dfsg.1-7/binfiles?fileinfo=1 Get binary package info: python3=3.10.5-1 Binary URL: http://snapshot.notset.fr/mr/binary/python3/3.10.5-1/binfiles?fileinfo=1 Get binary package info: python3-alabaster=0.7.12-1 Binary URL: http://snapshot.notset.fr/mr/binary/python3-alabaster/0.7.12-1/binfiles?fileinfo=1 Get binary package info: python3-babel=2.8.0+dfsg.1-7 Binary URL: http://snapshot.notset.fr/mr/binary/python3-babel/2.8.0+dfsg.1-7/binfiles?fileinfo=1 Get binary package info: python3-certifi=2020.6.20-1 Binary URL: http://snapshot.notset.fr/mr/binary/python3-certifi/2020.6.20-1/binfiles?fileinfo=1 Get binary package info: python3-chardet=4.0.0-2 Binary URL: http://snapshot.notset.fr/mr/binary/python3-chardet/4.0.0-2/binfiles?fileinfo=1 Get binary package info: python3-charset-normalizer=2.0.6-2 Binary URL: http://snapshot.notset.fr/mr/binary/python3-charset-normalizer/2.0.6-2/binfiles?fileinfo=1 Get binary package info: python3-distutils=3.10.5-2 Binary URL: http://snapshot.notset.fr/mr/binary/python3-distutils/3.10.5-2/binfiles?fileinfo=1 Get binary package info: python3-docutils=0.17.1+dfsg-2 Binary URL: http://snapshot.notset.fr/mr/binary/python3-docutils/0.17.1+dfsg-2/binfiles?fileinfo=1 Get binary package info: python3-idna=3.3-1 Binary URL: http://snapshot.notset.fr/mr/binary/python3-idna/3.3-1/binfiles?fileinfo=1 Get binary package info: python3-imagesize=1.4.1-1 Binary URL: http://snapshot.notset.fr/mr/binary/python3-imagesize/1.4.1-1/binfiles?fileinfo=1 Get binary package info: python3-importlib-metadata=4.6.4-1 Binary URL: http://snapshot.notset.fr/mr/binary/python3-importlib-metadata/4.6.4-1/binfiles?fileinfo=1 Get binary package info: python3-jinja2=3.0.3-1 Binary URL: http://snapshot.notset.fr/mr/binary/python3-jinja2/3.0.3-1/binfiles?fileinfo=1 Get binary package info: python3-lib2to3=3.10.5-2 Binary URL: http://snapshot.notset.fr/mr/binary/python3-lib2to3/3.10.5-2/binfiles?fileinfo=1 Get binary package info: python3-markupsafe=2.0.1-2+b1 Binary URL: http://snapshot.notset.fr/mr/binary/python3-markupsafe/2.0.1-2+b1/binfiles?fileinfo=1 Get binary package info: python3-minimal=3.10.5-1 Binary URL: http://snapshot.notset.fr/mr/binary/python3-minimal/3.10.5-1/binfiles?fileinfo=1 Get binary package info: python3-more-itertools=8.10.0-2 Binary URL: http://snapshot.notset.fr/mr/binary/python3-more-itertools/8.10.0-2/binfiles?fileinfo=1 Get binary package info: python3-packaging=21.3-1 Binary URL: http://snapshot.notset.fr/mr/binary/python3-packaging/21.3-1/binfiles?fileinfo=1 Get binary package info: python3-pkg-resources=59.6.0-1.2 Binary URL: http://snapshot.notset.fr/mr/binary/python3-pkg-resources/59.6.0-1.2/binfiles?fileinfo=1 Get binary package info: python3-pygments=2.12.0+dfsg-2 Binary URL: http://snapshot.notset.fr/mr/binary/python3-pygments/2.12.0+dfsg-2/binfiles?fileinfo=1 Get binary package info: python3-pyparsing=3.0.7-2 Binary URL: http://snapshot.notset.fr/mr/binary/python3-pyparsing/3.0.7-2/binfiles?fileinfo=1 Get binary package info: python3-requests=2.27.1+dfsg-1 Binary URL: http://snapshot.notset.fr/mr/binary/python3-requests/2.27.1+dfsg-1/binfiles?fileinfo=1 Get binary package info: python3-roman=3.3-1 Binary URL: http://snapshot.notset.fr/mr/binary/python3-roman/3.3-1/binfiles?fileinfo=1 Get binary package info: python3-six=1.16.0-3 Binary URL: http://snapshot.notset.fr/mr/binary/python3-six/1.16.0-3/binfiles?fileinfo=1 Get binary package info: python3-snowballstemmer=2.2.0-1 Binary URL: http://snapshot.notset.fr/mr/binary/python3-snowballstemmer/2.2.0-1/binfiles?fileinfo=1 Get binary package info: python3-sphinx=4.5.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/python3-sphinx/4.5.0-4/binfiles?fileinfo=1 Get binary package info: python3-tz=2022.1-1 Binary URL: http://snapshot.notset.fr/mr/binary/python3-tz/2022.1-1/binfiles?fileinfo=1 Get binary package info: python3-urllib3=1.26.9-1 Binary URL: http://snapshot.notset.fr/mr/binary/python3-urllib3/1.26.9-1/binfiles?fileinfo=1 Get binary package info: python3-zipp=1.0.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/python3-zipp/1.0.0-4/binfiles?fileinfo=1 Get binary package info: python3.10=3.10.5-1 Binary URL: http://snapshot.notset.fr/mr/binary/python3.10/3.10.5-1/binfiles?fileinfo=1 Get binary package info: python3.10-minimal=3.10.5-1 Binary URL: http://snapshot.notset.fr/mr/binary/python3.10-minimal/3.10.5-1/binfiles?fileinfo=1 Get binary package info: readline-common=8.1.2-1.2 Binary URL: http://snapshot.notset.fr/mr/binary/readline-common/8.1.2-1.2/binfiles?fileinfo=1 Get binary package info: rpcsvc-proto=1.4.2-4 Binary URL: http://snapshot.notset.fr/mr/binary/rpcsvc-proto/1.4.2-4/binfiles?fileinfo=1 Get binary package info: sed=4.8-1 Binary URL: http://snapshot.notset.fr/mr/binary/sed/4.8-1/binfiles?fileinfo=1 Get binary package info: sensible-utils=0.0.17 Binary URL: http://snapshot.notset.fr/mr/binary/sensible-utils/0.0.17/binfiles?fileinfo=1 Get binary package info: sgml-base=1.30 Binary URL: http://snapshot.notset.fr/mr/binary/sgml-base/1.30/binfiles?fileinfo=1 Get binary package info: sphinx-common=4.5.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/sphinx-common/4.5.0-4/binfiles?fileinfo=1 Get binary package info: sysvinit-utils=3.03-1 Binary URL: http://snapshot.notset.fr/mr/binary/sysvinit-utils/3.03-1/binfiles?fileinfo=1 Get binary package info: tar=1.34+dfsg-1 Binary URL: http://snapshot.notset.fr/mr/binary/tar/1.34+dfsg-1/binfiles?fileinfo=1 Get binary package info: tzdata=2022a-1 Binary URL: http://snapshot.notset.fr/mr/binary/tzdata/2022a-1/binfiles?fileinfo=1 Get binary package info: util-linux=2.38-5 Binary URL: http://snapshot.notset.fr/mr/binary/util-linux/2.38-5/binfiles?fileinfo=1 Get binary package info: util-linux-extra=2.38-5 Binary URL: http://snapshot.notset.fr/mr/binary/util-linux-extra/2.38-5/binfiles?fileinfo=1 Get binary package info: xml-core=0.18+nmu1 Binary URL: http://snapshot.notset.fr/mr/binary/xml-core/0.18+nmu1/binfiles?fileinfo=1 Get binary package info: xz-utils=5.2.5-2.1 Binary URL: http://snapshot.notset.fr/mr/binary/xz-utils/5.2.5-2.1/binfiles?fileinfo=1 Get binary package info: zlib1g=1:1.2.11.dfsg-4 Binary URL: http://snapshot.notset.fr/mr/binary/zlib1g/1:1.2.11.dfsg-4/binfiles?fileinfo=1 Get binary package info: zlib1g-dev=1:1.2.11.dfsg-4 Binary URL: http://snapshot.notset.fr/mr/binary/zlib1g-dev/1:1.2.11.dfsg-4/binfiles?fileinfo=1 Remaining packages to be found: 213 Timestamp source (24 packages): deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220713T145608Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220720T032429Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220714T210818Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220611T030612Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220501T085721Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211103T025035Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220426T025843Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220720T211439Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220419T024549Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220511T030041Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220707T212059Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220405T031327Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211205T025806Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220703T032011Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210816T024705Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220416T025423Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220625T210921Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210823T024636Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220705T030342Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211223T031038Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211016T210235Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220706T025631Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210901T090918Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220216T030243Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220714T091738Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220509T030319Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220414T030009Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220208T091208Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220623T092901Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220329T030734Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220620T031814Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220707T030959Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211128T033921Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210824T024320Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220331T030648Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210911T144836Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220321T040007Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220211T025424Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220125T033125Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210930T025245Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220602T030029Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220209T093507Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211108T025858Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220317T031134Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220507T034236Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220430T025357Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210909T025907Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220101T024315Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220412T025122Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210903T030245Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220318T025831Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220628T032327Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220106T025822Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220619T155342Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220404T152929Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220122T031231Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220616T214802Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220502T032918Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220513T034642Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220722T030020Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220226T025804Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220713T030737Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220212T154028Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220413T150025Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220427T031445Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220202T030237Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220619T030107Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220212T031344Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220510T155316Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220310T035035Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220528T035722Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220323T030602Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220520T032818Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220425T032014Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220219T032615Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220712T090125Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211118T205424Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211109T030457Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220123T025342Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220715T090257Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220420T025302Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220330T152746Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211028T024824Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211231T092922Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211115T024854Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220321T153231Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220610T025651Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210902T030735Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220421T030943Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220325T035240Z/ bookworm main Remaining packages to be found: 15 Timestamp source (8 packages): deb http://snapshot.notset.fr/archive/debian/20220716T031917Z/ unstable main Remaining packages to be found: 5 Timestamp source (3 packages): deb http://snapshot.notset.fr/archive/debian/20220717T214311Z/ unstable main New buildinfo file: /tmp/bedops-2.4.41+dfsg-1pbztv_o9/bedops_2.4.41+dfsg-1_all.buildinfo env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf:all=2.71-2 automake:all=1:1.16.5-1.3 autopoint:all=0.21-6 autotools-dev:all=20220109.1 base-files:amd64=12.2 base-passwd:amd64=3.5.52 bash:amd64=5.1-6.1 binutils:amd64=2.38.90.20220713-2 binutils-common:amd64=2.38.90.20220713-2 binutils-x86-64-linux-gnu:amd64=2.38.90.20220713-2 bsdextrautils:amd64=2.38-5 bsdutils:amd64=1:2.38-5 build-essential:amd64=12.9 bzip2:amd64=1.0.8-5 ca-certificates:all=20211016 coreutils:amd64=8.32-4.1 cpp:amd64=4:11.2.0-2 cpp-11:amd64=11.3.0-4 dash:amd64=0.5.11+git20210903+057cd650a4ed-8 debconf:all=1.5.79 debhelper:all=13.8 debianutils:amd64=5.7-0.2 dh-autoreconf:all=20 dh-strip-nondeterminism:all=1.13.0-1 diffutils:amd64=1:3.7-5 docutils-common:all=0.17.1+dfsg-2 dpkg:amd64=1.21.9 dpkg-dev:all=1.21.9 dwz:amd64=0.14-1 file:amd64=1:5.41-4 findutils:amd64=4.9.0-3 fonts-mathjax:all=2.7.9+dfsg-1 g++:amd64=4:11.2.0-2 g++-11:amd64=11.3.0-4 gcc:amd64=4:11.2.0-2 gcc-11:amd64=11.3.0-4 gcc-11-base:amd64=11.3.0-4 gcc-12-base:amd64=12.1.0-5 gettext:amd64=0.21-6 gettext-base:amd64=0.21-6 grep:amd64=3.7-1 groff-base:amd64=1.22.4-8 gzip:amd64=1.12-1 help2man:amd64=1.49.2 hostname:amd64=3.23 init-system-helpers:all=1.64 intltool-debian:all=0.35.0+20060710.5 libacl1:amd64=2.3.1-1 libarchive-zip-perl:all=1.68-1 libasan6:amd64=11.3.0-4 libatomic1:amd64=12.1.0-5 libattr1:amd64=1:2.5.1-1 libaudit-common:all=1:3.0.7-1 libaudit1:amd64=1:3.0.7-1+b1 libbinutils:amd64=2.38.90.20220713-2 libblkid1:amd64=2.38-5 libbz2-1.0:amd64=1.0.8-5 libbz2-dev:amd64=1.0.8-5 libc-bin:amd64=2.33-8 libc-dev-bin:amd64=2.33-8 libc6:amd64=2.33-8 libc6-dev:amd64=2.33-8 libcap-ng0:amd64=0.8.3-1 libcap2:amd64=1:2.44-1 libcc1-0:amd64=12.1.0-5 libcom-err2:amd64=1.46.5-2 libcrypt-dev:amd64=1:4.4.28-2 libcrypt1:amd64=1:4.4.28-2 libctf-nobfd0:amd64=2.38.90.20220713-2 libctf0:amd64=2.38.90.20220713-2 libdb5.3:amd64=5.3.28+dfsg1-0.10 libdebconfclient0:amd64=0.263 libdebhelper-perl:all=13.8 libdpkg-perl:all=1.21.9 libelf1:amd64=0.187-1 libexpat1:amd64=2.4.8-1 libffi8:amd64=3.4.2-4 libfile-stripnondeterminism-perl:all=1.13.0-1 libgcc-11-dev:amd64=11.3.0-4 libgcc-s1:amd64=12.1.0-5 libgcrypt20:amd64=1.10.1-2 libgdbm-compat4:amd64=1.23-1 libgdbm6:amd64=1.23-1 libgmp10:amd64=2:6.2.1+dfsg1-1 libgomp1:amd64=12.1.0-5 libgpg-error0:amd64=1.45-2 libgprofng0:amd64=2.38.90.20220713-2 libgssapi-krb5-2:amd64=1.19.2-2+b2 libicu71:amd64=71.1-3 libisl23:amd64=0.25-1 libitm1:amd64=12.1.0-5 libjansson-dev:amd64=2.14-2 libjansson4:amd64=2.14-2 libjs-jquery:all=3.6.0+dfsg+~3.5.13-1 libjs-mathjax:all=2.7.9+dfsg-1 libjs-sphinxdoc:all=4.5.0-4 libjs-underscore:all=1.13.3~dfsg+~1.11.4-1 libjson-perl:all=4.07000-1 libk5crypto3:amd64=1.19.2-2+b2 libkeyutils1:amd64=1.6.3-1 libkrb5-3:amd64=1.19.2-2+b2 libkrb5support0:amd64=1.19.2-2+b2 liblocale-gettext-perl:amd64=1.07-4+b2 liblsan0:amd64=12.1.0-5 liblz4-1:amd64=1.9.3-2 liblzma5:amd64=5.2.5-2.1 libmagic-mgc:amd64=1:5.41-4 libmagic1:amd64=1:5.41-4 libmount1:amd64=2.38-5 libmpc3:amd64=1.2.1-2 libmpdec3:amd64=2.5.1-2 libmpfr6:amd64=4.1.0-3 libncursesw6:amd64=6.3+20220423-2 libnsl-dev:amd64=1.3.0-2 libnsl2:amd64=1.3.0-2 libpam-modules:amd64=1.4.0-13 libpam-modules-bin:amd64=1.4.0-13 libpam-runtime:all=1.4.0-13 libpam0g:amd64=1.4.0-13 libpcre2-8-0:amd64=10.40-1 libpcre3:amd64=2:8.39-14 libperl5.34:amd64=5.34.0-5 libpipeline1:amd64=1.5.6-1 libpython3-stdlib:amd64=3.10.5-1 libpython3.10-minimal:amd64=3.10.5-1 libpython3.10-stdlib:amd64=3.10.5-1 libquadmath0:amd64=12.1.0-5 libreadline8:amd64=8.1.2-1.2 libseccomp2:amd64=2.5.4-1 libselinux1:amd64=3.4-1 libsigsegv2:amd64=2.14-1 libsmartcols1:amd64=2.38-5 libsqlite3-0:amd64=3.39.1-1 libssl3:amd64=3.0.4-2 libstdc++-11-dev:amd64=11.3.0-4 libstdc++6:amd64=12.1.0-5 libsub-override-perl:all=0.09-3 libsystemd0:amd64=251.3-1 libtinfo6:amd64=6.3+20220423-2 libtirpc-common:all=1.3.2-2 libtirpc-dev:amd64=1.3.2-2 libtirpc3:amd64=1.3.2-2 libtool:all=2.4.7-4 libtsan0:amd64=11.3.0-4 libubsan1:amd64=12.1.0-5 libuchardet0:amd64=0.0.7-1 libudev1:amd64=251.3-1 libunistring2:amd64=1.0-1 libuuid1:amd64=2.38-5 libxml2:amd64=2.9.14+dfsg-1 libzstd1:amd64=1.5.2+dfsg-1 linux-libc-dev:amd64=5.18.5-1 login:amd64=1:4.11.1+dfsg1-2 lsb-base:all=11.2 m4:amd64=1.4.18-5 make:amd64=4.3-4.1 man-db:amd64=2.10.2-1 mawk:amd64=1.3.4.20200120-3.1 media-types:all=8.0.0 ncurses-base:all=6.3+20220423-2 ncurses-bin:amd64=6.3+20220423-2 openssl:amd64=3.0.4-2 patch:amd64=2.7.6-7 perl:amd64=5.34.0-5 perl-base:amd64=5.34.0-5 perl-modules-5.34:all=5.34.0-5 po-debconf:all=1.0.21+nmu1 python-babel-localedata:all=2.8.0+dfsg.1-7 python3:amd64=3.10.5-1 python3-alabaster:all=0.7.12-1 python3-babel:all=2.8.0+dfsg.1-7 python3-certifi:all=2020.6.20-1 python3-chardet:all=4.0.0-2 python3-charset-normalizer:all=2.0.6-2 python3-distutils:all=3.10.5-2 python3-docutils:all=0.17.1+dfsg-2 python3-idna:all=3.3-1 python3-imagesize:all=1.4.1-1 python3-importlib-metadata:all=4.6.4-1 python3-jinja2:all=3.0.3-1 python3-lib2to3:all=3.10.5-2 python3-markupsafe:amd64=2.0.1-2+b1 python3-minimal:amd64=3.10.5-1 python3-more-itertools:all=8.10.0-2 python3-packaging:all=21.3-1 python3-pkg-resources:all=59.6.0-1.2 python3-pygments:all=2.12.0+dfsg-2 python3-pyparsing:all=3.0.7-2 python3-requests:all=2.27.1+dfsg-1 python3-roman:all=3.3-1 python3-six:all=1.16.0-3 python3-snowballstemmer:all=2.2.0-1 python3-sphinx:all=4.5.0-4 python3-tz:all=2022.1-1 python3-urllib3:all=1.26.9-1 python3-zipp:all=1.0.0-4 python3.10:amd64=3.10.5-1 python3.10-minimal:amd64=3.10.5-1 readline-common:all=8.1.2-1.2 rpcsvc-proto:amd64=1.4.2-4 sed:amd64=4.8-1 sensible-utils:all=0.0.17 sgml-base:all=1.30 sphinx-common:all=4.5.0-4 sysvinit-utils:amd64=3.03-1 tar:amd64=1.34+dfsg-1 tzdata:all=2022a-1 util-linux:amd64=2.38-5 util-linux-extra:amd64=2.38-5 xml-core:all=0.18+nmu1 xz-utils:amd64=5.2.5-2.1 zlib1g:amd64=1:1.2.11.dfsg-4 zlib1g-dev:amd64=1:1.2.11.dfsg-4 --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/20220723T030313Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220723T030313Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220716T031917Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220717T214311Z/ 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=2.4.41+dfsg-1 && mkdir -p /build/bedops-FdcueA && dpkg-source --no-check -x /*.dsc /build/bedops-FdcueA/bedops-2.4.41+dfsg && chown -R builduser:builduser /build/bedops-FdcueA" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bedops-FdcueA/bedops-2.4.41+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1658132971" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/bedops-FdcueA /tmp/bedops-2.4.41+dfsg-1pbztv_o9 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220720T211439Z bookworm main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.SP4NZLJ8Un 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.SP4NZLJ8Un Reading package lists... Building dependency tree... util-linux is already the newest version (2.38-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 136 kB of archives. After this operation, 401 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220720T211439Z bookworm/main amd64 libfakeroot amd64 1.29-1 [48.5 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220720T211439Z bookworm/main amd64 fakeroot amd64 1.29-1 [87.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 136 kB in 0s (1041 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 ... 4656 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.29-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.29-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.29-1_amd64.deb ... Unpacking fakeroot (1.29-1) ... Setting up libfakeroot:amd64 (1.29-1) ... Setting up fakeroot (1.29-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-8) ... 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/20220723T030313Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220723T030313Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220716T031917Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220717T214311Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.SP4NZLJ8Un Get:1 http://snapshot.notset.fr/archive/debian/20220723T030313Z bookworm InRelease [157 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220716T031917Z unstable InRelease [165 kB] Ign:4 http://snapshot.notset.fr/archive/debian/20220723T030313Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220723T030313Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220723T030313Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220723T030313Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220723T030313Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220723T030313Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20220723T030313Z bookworm/main Sources [12.1 MB] Get:6 http://snapshot.notset.fr/archive/debian/20220717T214311Z unstable InRelease [165 kB] Get:5 http://snapshot.notset.fr/archive/debian/20220723T030313Z bookworm/main amd64 Packages [11.5 MB] Ign:7 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:8 http://snapshot.notset.fr/archive/debian/20220716T031917Z unstable/main amd64 Packages Ign:9 http://snapshot.notset.fr/archive/debian/20220717T214311Z unstable/main amd64 Packages Ign:7 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:8 http://snapshot.notset.fr/archive/debian/20220716T031917Z unstable/main amd64 Packages Ign:9 http://snapshot.notset.fr/archive/debian/20220717T214311Z unstable/main amd64 Packages Ign:7 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:8 http://snapshot.notset.fr/archive/debian/20220716T031917Z unstable/main amd64 Packages Ign:9 http://snapshot.notset.fr/archive/debian/20220717T214311Z unstable/main amd64 Packages Get:7 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Get:8 http://snapshot.notset.fr/archive/debian/20220716T031917Z unstable/main amd64 Packages [12.5 MB] Get:9 http://snapshot.notset.fr/archive/debian/20220717T214311Z unstable/main amd64 Packages [12.5 MB] Fetched 60.4 MB in 48s (1253 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.SP4NZLJ8Un I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d bedops=2.4.41+dfsg-1 && mkdir -p /build/bedops-FdcueA && dpkg-source --no-check -x /*.dsc /build/bedops-FdcueA/bedops-2.4.41+dfsg && chown -R builduser:builduser /build/bedops-FdcueA"' exec /tmp/mmdebstrap.SP4NZLJ8Un 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/20220723T030313Z bookworm/main bedops 2.4.41+dfsg-1 (dsc) [2178 B] Get:2 http://snapshot.notset.fr/archive/debian/20220723T030313Z bookworm/main bedops 2.4.41+dfsg-1 (tar) [13.5 MB] Get:3 http://snapshot.notset.fr/archive/debian/20220723T030313Z bookworm/main bedops 2.4.41+dfsg-1 (diff) [10.4 kB] Fetched 13.5 MB in 11s (1270 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'bedops_2.4.41+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting bedops in /build/bedops-FdcueA/bedops-2.4.41+dfsg dpkg-source: info: unpacking bedops_2.4.41+dfsg.orig.tar.xz dpkg-source: info: unpacking bedops_2.4.41+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests_use_installed_binaries.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying use_debian_libs dpkg-source: info: applying parallel.patch dpkg-source: info: applying adapt_to_new_sphinx.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bedops-FdcueA/bedops-2.4.41+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1658132971" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.SP4NZLJ8Un dpkg-buildpackage: info: source package bedops dpkg-buildpackage: info: source version 2.4.41+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg' dh_auto_clean make -j10 clean make[2]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg' make clean -f system.mk/Makefile.linux make[3]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg' rm -rf bin rm -rf bin rm -rf bin make -C applications/bed/bedextract/src -f Makefile clean make -C applications/bed/bedmap/src -f Makefile clean make -C applications/bed/bedops/src -f Makefile clean rm -rf modules make -C applications/bed/closestfeats/src -f Makefile clean make -C applications/bed/conversion/src -f Makefile clean make -C applications/bed/sort-bed/src -f Makefile clean make -C applications/bed/starch/src -f Makefile clean make[4]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/bedmap/src' rm -rf objects_typical make[4]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/bedextract/src' rm -rf objects_typical make[4]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/bedops/src' rm -rf objects_typical make[4]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/sort-bed/src' rm -rf ../bin make[4]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/closestfeats/src' rm -rf objects_typical rm -rf ../bin rm -rf ../bin make[4]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/starch/src' rm -rf ../lib make[4]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/bedmap/src' rm -rf ../bin make[4]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/conversion/src' rm -rf ../bin rm -rf objects-typical make[4]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/bedops/src' rm -f ../lib/libstarch_debug.a make[4]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/bedextract/src' make[4]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/closestfeats/src' rm -rf objects rm -f ../lib/libstarch_gprof.a rm -rf ../bin rm -rf objects rm -rf *.so *~ make[4]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/sort-bed/src' rm -rf ../bin make[4]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/starch/src' make[4]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/conversion/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-FdcueA/bedops-2.4.41+dfsg' make[2]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg' rm -rf docs/_build/ make[1]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg' dh_clean debian/rules binary-indep dh binary-indep dh_update_autotools_config -i dh_autoreconf -i dh_auto_configure -i dh_auto_build -i make -j10 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg' make -f system.mk/Makefile.linux make[2]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg' #bzcat | tar -x -C third-party #cd third-party/jansson-2.6 && ./configure --prefix=/build/bedops-FdcueA/bedops-2.4.41+dfsg/third-party/jansson-2.6 && make && make install && cd /build/bedops-FdcueA/bedops-2.4.41+dfsg && rm -f jansson && ln -sf jansson-2.6 third-party/jansson #bzcat | tar -x -C third-party #cd third-party/bzip2-1.0.6 && make libbz2.a && cd /build/bedops-FdcueA/bedops-2.4.41+dfsg && rm -f bzip2 && ln -sf bzip2-1.0.6 third-party/bzip2 #bzcat | tar -x -C third-party #cd third-party/zlib-1.2.7 && ./configure --static && make && cd /build/bedops-FdcueA/bedops-2.4.41+dfsg && rm -f zlib && ln -sf zlib-1.2.7 third-party/zlib make build -f /build/bedops-FdcueA/bedops-2.4.41+dfsg/system.mk/Makefile.linux make[3]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg' make -C applications/bed/bedextract/src -f Makefile build make -C applications/bed/bedmap/src -f Makefile build make -C applications/bed/bedops/src -f Makefile build make -C applications/bed/closestfeats/src -f Makefile build make -C applications/bed/conversion/src -f Makefile build make -C applications/bed/sort-bed/src -f Makefile build make[4]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/bedmap/src' mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers make -C applications/bed/starch/src -f Makefile build make[4]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/bedextract/src' mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/bedops/src' mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/sort-bed/src' make[4]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/closestfeats/src' make[4]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/conversion/src' mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p ../bin && cc -Wall -Wextra -pedantic -std=c99 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -iquote"/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/conversion/src" -iquote"../../../../interfaces/general-headers" convert2bed.c -o ../bin/convert2bed-typical -lpthread make[4]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/starch/src' mkdir -p objects mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects-typical/starchConstants.o -iquote../../../../interfaces/general-headers g++ -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchConstants.c -o objects/starchConstants.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects-typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects g++ -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects/unstarchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects-typical/starchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects g++ -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchHelpers.c -o objects/starchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects g++ -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/src/data/starch/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 )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ convert2bed.c: In function ‘c2b_line_convert_rmsk_to_bed_unsorted’: convert2bed.c:3780:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 3780 | fprintf(stderr, "Error: Invalid query coordinates at line [%llu]\n", c2b_globals.rmsk->line); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects-typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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 -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, 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:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, 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:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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 g++ -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects/starchFileHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects g++ -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects/starchSha1Digest.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects-typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects g++ -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects/starchBase64Coding.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../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 )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects-typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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 -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p ../bin cp starchcluster_gnuParallel.tcsh ../bin/starchcluster_gnuParallel-typical mkdir -p ../bin cp starchcluster_sge.tcsh ../bin/starchcluster_sge-typical mkdir -p ../bin cp starchcluster_slurm.tcsh ../bin/starchcluster_slurm-typical mkdir -p ../bin cp starch-diff.py ../bin/starch-diff-typical mkdir -p ../lib ar rcs ../lib/libstarch.a objects/starchConstants.o objects/unstarchHelpers.o objects/starchHelpers.o objects/starchMetadataHelpers.o objects/starchFileHelpers.o objects/starchSha1Digest.o objects/starchBase64Coding.o mkdir -p ../bin g++ -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starch.c -o objects/starch.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 SortDetails.cpp -o objects-typical/SortDetails.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers g++ -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starch.o -o ../bin/starch-typical ../lib/libstarch.a -ljansson -lz -lbz2 mkdir -p ../bin g++ -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c unstarch.c -o objects/unstarch.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers 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 )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/unstarch.o -o ../bin/unstarch-typical ../lib/libstarch.a -ljansson -lz -lbz2 ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p ../bin g++ -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starchcat.c -o objects/starchcat.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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/c++/11/cassert:44, from starchcat.c:33: starchcat.c: In function ‘int main(int, char**)’: starchcat.c:136:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 136 | assert( STARCHCAT_allocMetadataRecords ( &mdRecords, static_cast( 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++/11/cassert:44, from starchcat.c:33: starchcat.c: In function ‘int starch::STARCHCAT_mergeChromosomeStreams(const ChromosomeSummaries*, starch::CompressionType, const char*)’: starchcat.c:4402:60: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4402 | static_cast( 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 )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/include/c++/11/cassert:44, from starchcat.c:33: starchcat.c: In function ‘int starch::STARCHCAT2_mergeChromosomeStreams(const ChromosomeSummaries*, starch::CompressionType, const char*, size_t*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: starchcat.c:5902:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 5902 | static_cast( 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 )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p ../bin && g++ -o ../bin/bedops-typical -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 Bedops.cpp 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 ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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 -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p ../bin && g++ -o ../bin/bedextract-typical -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 ExtractRows.cpp ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp: In function ‘ChromBedData* initializeChromBedData(char*, double*)’: SortDetails.cpp:250:12: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 250 | strncpy(chrom->chromName, chromBuf, chromBufLen); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp:249:25: note: length computed here 249 | chromBufLen = strlen(chromBuf); // we know >= 1 | ~~~~~~^~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers convert2bed.c: In function ‘c2b_line_convert_sam_to_bed_unsorted_with_split_operation’: convert2bed.c:5017:25: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict] 5017 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ convert2bed.c:5043:21: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict] 5043 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ convert2bed.c:5061:21: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict] 5061 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ convert2bed.c:4950:25: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict] 4950 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ convert2bed.c:4974:21: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict] 4974 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p ../bin && cp update-sort-bed-slurm.py ../bin/update-sort-bed-slurm-typical mkdir -p ../bin mkdir -p ../bin && g++ -o ../bin/closest-features-typical -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 ClosestFeature.cpp mkdir -p ../bin && cp update-sort-bed-starch-slurm.py ../bin/update-sort-bed-starch-slurm-typical g++ -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starchstrip.c -o objects/starchstrip.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p ../bin && cp update-sort-bed-migrate-candidates.py ../bin/update-sort-bed-migrate-candidates-typical ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp: In function ‘void lexSortBedData(BedData*)’: SortDetails.cpp:1343:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1343 | strncpy(chromBuf, beds->chroms[i]->chromName, chromBufLen); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp:1342:33: note: length computed here 1342 | chromBufLen = strlen(beds->chroms[i]->chromName); // we know >= 1 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p ../bin && g++ -o ../bin/bedmap-typical -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 Bedmap.cpp In function ‘ChromBedData* initializeChromBedData(char*, double*)’, inlined from ‘int processData(const char**, unsigned int, double, char*, bool, bool)’ at SortDetails.cpp:909:59: SortDetails.cpp:250:12: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 250 | strncpy(chrom->chromName, chromBuf, chromBufLen); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp: In function ‘int processData(const char**, unsigned int, double, char*, bool, bool)’: SortDetails.cpp:249:25: note: length computed here 249 | chromBufLen = strlen(chromBuf); // we know >= 1 | ~~~~~~^~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starchstrip.o -o ../bin/starchstrip-typical ../lib/libstarch.a -ljansson -lz -lbz2 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); | ^~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)’: starchcat.c:3123:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 3123 | strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:3123:78: note: length computed here 3123 | strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); | ~~~~~~^~~~~~~ rm -rf objects make[4]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/conversion/src' g++ -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starchcat.o -o ../bin/starchcat-typical ../lib/libstarch.a -ljansson -lz -lbz2 rm -rf objects make[4]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/starch/src' In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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 ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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 ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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 ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:634:52, inlined from ‘static bool starch::Starch::isStarch(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:698:56, inlined from ‘static bool starch::Starch::isStarch(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:678:25, inlined from ‘Bed::bed_check_iterator::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:92:90: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::bed_check_iterator::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:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: In member function ‘void starch::Starch::setCurrentChromosome(char*)’, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::bed_check_iterator::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: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::bed_check_iterator::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 member function ‘void starch::Starch::setCurrentChromosome(char*)’, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::bed_check_iterator::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: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::bed_check_iterator::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 member function ‘void starch::Starch::setCurrentChromosome(char*)’, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::bed_check_iterator 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 ‘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:267:24, inlined from ‘int checkSort(const char**, unsigned int)’ at CheckSort.cpp:51:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: 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 ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p ../bin && g++ -o ../bin/sort-bed-typical -g -O2 -ffile-prefix-map=/build/bedops-FdcueA/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -iquote../../../../interfaces/general-headers objects-typical/starchConstants.o objects-typical/starchFileHelpers.o objects-typical/starchHelpers.o objects-typical/starchMetadataHelpers.o objects-typical/unstarchHelpers.o objects-typical/starchSha1Digest.o objects-typical/starchBase64Coding.o objects-typical/SortDetails.o objects-typical/Sort.o objects-typical/CheckSort.o -ljansson -lz -lbz2 rm -rf objects-typical make[4]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/sort-bed/src' rm -rf objects_typical make[4]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/bedextract/src' rm -rf objects_typical make[4]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/closestfeats/src' In member function ‘void starch::Starch::setCurrentChromosome(char*)’, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::bed_check_iterator& Bed::bed_check_iterator::operator++() [with BedType = Bed::BasicCoords; long unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:261:36, inlined from ‘BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::bed_check_iterator*, 512>]’ at BedPadReader.hpp:140:11, inlined from ‘void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector*, 512> >*, std::allocator*, 512> >*> >; PQueue = std::priority_queue*, std::vector*>, Bed::InvertGenomicAddressCompare, Bed::BasicCoords > >]’ at Bedops.cpp:1411:39: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function ‘void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector*, 512> >*, std::allocator*, 512> >*> >; PQueue = std::priority_queue*, std::vector*>, Bed::InvertGenomicAddressCompare, Bed::BasicCoords > >]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In member function ‘void starch::Starch::setCurrentChromosome(char*)’, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::bed_check_iterator& Bed::bed_check_iterator::operator++() [with BedType = Bed::BasicCoords; long unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:261:36, inlined from ‘BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::bed_check_iterator*, 512>]’ at BedPadReader.hpp:140:11, inlined from ‘void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector*, 512> >*, std::allocator*, 512> >*> >; PQueue = std::priority_queue*, std::vector*, std::allocator*> >, Bed::InvertGenomicAddressCompare, Bed::BasicCoords > >]’ at Bedops.cpp:1411:39: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function ‘void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector*, 512> >*, std::allocator*, 512> >*> >; PQueue = std::priority_queue*, std::vector*, std::allocator*> >, Bed::InvertGenomicAddressCompare, Bed::BasicCoords > >]’: ../../../../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-FdcueA/bedops-2.4.41+dfsg/applications/bed/bedops/src' In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rm -rf objects_typical make[4]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg/applications/bed/bedmap/src' make[3]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg' make[2]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg' make[1]: Leaving directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg' dh: command-omitted: The call to "dh_auto_test -i" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -i dh_auto_install -i make -j10 install DESTDIR=/build/bedops-FdcueA/bedops-2.4.41\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bedops-FdcueA/bedops-2.4.41+dfsg' mkdir -p bin cp applications/bed/conversion/src/wrappers/bam2bed applications/bed/conversion/src/wrappers/bam2bed_gnuParallel applications/bed/conversion/src/wrappers/bam2bed_sge applications/bed/conversion/src/wrappers/bam2bed_slurm applications/bed/conversion/src/wrappers/bam2starch applications/bed/conversion/src/wrappers/bam2starch_gnuParallel applications/bed/conversion/src/wrappers/bam2starch_sge applications/bed/conversion/src/wrappers/bam2starch_slurm applications/bed/conversion/src/wrappers/gff2bed applications/bed/conversion/src/wrappers/gff2starch applications/bed/conversion/src/wrappers/gtf2bed applications/bed/conversion/src/wrappers/gtf2starch applications/bed/conversion/src/wrappers/gvf2bed applications/bed/conversion/src/wrappers/gvf2starch applications/bed/conversion/src/wrappers/psl2bed applications/bed/conversion/src/wrappers/psl2starch applications/bed/conversion/src/wrappers/rmsk2bed applications/bed/conversion/src/wrappers/rmsk2starch applications/bed/conversion/src/wrappers/sam2bed applications/bed/conversion/src/wrappers/sam2starch applications/bed/conversion/src/wrappers/vcf2bed applications/bed/conversion/src/wrappers/vcf2starch applications/bed/conversion/src/wrappers/wig2bed applications/bed/conversion/src/wrappers/wig2starch bin cp applications/bed/starch/bin/starchcluster_sge-typical bin/starchcluster_sge cp applications/bed/starch/bin/starchcluster_gnuParallel-typical bin/starchcluster_gnuParallel cp applications/bed/starch/bin/starchcluster_slurm-typical bin/starchcluster_slurm cp applications/bed/starch/bin/starch-diff-typical bin/starch-diff cp applications/bed/sort-bed/bin/sort-bed-typical bin/sort-bed cp applications/bed/sort-bed/bin/update-sort-bed-slurm-typical bin/update-sort-bed-slurm cp applications/bed/sort-bed/bin/update-sort-bed-starch-slurm-typical bin/update-sort-bed-starch-slurm cp applications/bed/sort-bed/bin/update-sort-bed-migrate-candidates-typical bin/update-sort-bed-migrate-candidates cp applications/bed/bedops/bin/bedops-typical bin/bedops cp applications/bed/closestfeats/bin/closest-features-typical bin/closest-features cp applications/bed/bedmap/bin/bedmap-typical bin/bedmap cp applications/bed/bedextract/bin/bedextract-typical bin/bedextract cp applications/bed/starch/bin/starch-typical bin/starch cp applications/bed/starch/bin/unstarch-typical bin/unstarch cp applications/bed/starch/bin/starchcat-typical bin/starchcat cp 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debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_mapref_ref3_padded.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/_images/performance_bedops_intersect_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_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/_images/performance_bedops_merge_unsorted.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_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/_images/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/_images/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/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/reference_setops_bedops_inputs@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/_images/performance_independent_grok.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/quick_start.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/downloads_v3.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/linux_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/macosx_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/source_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/reference_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/set_operations_v2.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_2.4.41+dfsg-1_all.deb'. dpkg-genbuildinfo --build=all -O../bedops_2.4.41+dfsg-1_all.buildinfo dpkg-genchanges --build=all -O../bedops_2.4.41+dfsg-1_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-FdcueA /tmp/bedops-2.4.41+dfsg-1pbztv_o9 I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.SP4NZLJ8Un... I: success in 904.5979 seconds md5: bedops-doc_2.4.41+dfsg-1_all.deb: OK sha1: bedops-doc_2.4.41+dfsg-1_all.deb: OK sha256: bedops-doc_2.4.41+dfsg-1_all.deb: OK Checksums: OK