Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/r/r-bioc-rhtslib/r-bioc-rhtslib_1.28.0+dfsg-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/r-bioc-rhtslib-1.28.0+dfsg-1qx_8zgyw/r-bioc-rhtslib_1.28.0+dfsg-1_amd64.buildinfo Get source package info: r-bioc-rhtslib=1.28.0+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/r-bioc-rhtslib/1.28.0+dfsg-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6+b1 binutils=2.38-4 binutils-common=2.38-4 binutils-x86-64-linux-gnu=2.38-4 bsdextrautils=2.38-4 bsdutils=1:2.38-4 build-essential=12.9 bzip2=1.0.8-5 ca-certificates=20211016 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.3.0-1 dash=0.5.11+git20210903+057cd650a4ed-8 dctrl-tools=2.24-3+b1 debconf=1.5.79 debhelper=13.7.1 debianutils=5.7-0.2 dh-autoreconf=20 dh-r=20210816 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.7 dpkg-dev=1.21.7 dwz=0.14-1 file=1:5.41-4 findutils=4.9.0-3 fontconfig=2.13.1-4.4 fontconfig-config=2.13.1-4.4 fonts-dejavu-core=2.37-2 g++=4:11.2.0-2 g++-11=11.3.0-1 gcc=4:11.2.0-2 gcc-11=11.3.0-1 gcc-11-base=11.3.0-1 gcc-12-base=12.1.0-1 gettext=0.21-6 gettext-base=0.21-6 gfortran=4:11.2.0-2 gfortran-11=11.3.0-1 grep=3.7-1 groff-base=1.22.4-8 gzip=1.12-1 hostname=3.23 icu-devtools=71.1-3 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libalgorithm-c3-perl=0.11-1 libarchive-zip-perl=1.68-1 libasan6=11.3.0-1 libatomic1=12.1.0-1 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libb-hooks-endofscope-perl=0.26-1 libb-hooks-op-check-perl=0.22-1+b4 libbinutils=2.38-4 libblas-dev=3.10.1-1 libblas3=3.10.1-1 libblkid1=2.38-4 libbrotli1=1.0.9-2+b3 libbsd0=0.11.6-1 libbz2-1.0=1.0.8-5 libbz2-dev=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcairo2=1.16.0-5 libcap-ng0=0.7.9-2.2+b2 libcap2=1:2.44-1 libcc1-0=12.1.0-1 libclass-c3-perl=0.35-1 libclass-load-perl=0.25-1 libclass-load-xs-perl=0.10-1+b6 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-4 libctf0=2.38-4 libcurl3-gnutls=7.83.1-1 libcurl4=7.83.1-1 libcurl4-openssl-dev=7.83.1-1 libdata-optlist-perl=0.112-1 libdatrie1=0.2.13-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.262 libdebhelper-perl=13.7.1 libdeflate0=1.10-2 libdevel-callchecker-perl=0.008-1+b3 libdevel-globaldestruction-perl=0.14-1.1 libdevel-overloadinfo-perl=0.007-1 libdevel-stacktrace-perl=2.0400-1 libdist-checkconflicts-perl=0.11-1.1 libdpkg-perl=1.21.7 libdynaloader-functions-perl=0.003-1.1 libelf1=0.187-1 libencode-locale-perl=1.05-1.1 libeval-closure-perl=0.14-1 libexpat1=2.4.8-1 libffi8=3.4.2-4 libfile-stripnondeterminism-perl=1.13.0-1 libfile-which-perl=1.27-1 libfontconfig1=2.13.1-4.4 libfreetype6=2.12.1+dfsg-1 libfribidi0=1.0.8-2.1 libgcc-11-dev=11.3.0-1 libgcc-s1=12.1.0-1 libgcrypt20=1.10.1-2 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgfortran-11-dev=11.3.0-1 libgfortran5=12.1.0-1 libglib2.0-0=2.72.1-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.4-2 libgomp1=12.1.0-1 libgpg-error0=1.45-2 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.19.2-2+b1 libharfbuzz0b=2.7.4-1+b1 libhogweed6=3.7.3-1 libhttp-date-perl=6.05-1 libhttp-message-perl=6.36-1 libice6=2:1.0.10-1 libicu-dev=71.1-3 libicu71=71.1-3 libidn2-0=2.3.2-2 libio-html-perl=1.004-3 libisl23=0.24-2 libitm1=12.1.0-1 libjbig0=2.1-3.1+b2 libjpeg-dev=1:2.1.2-1 libjpeg62-turbo=1:2.1.2-1 libjpeg62-turbo-dev=1:2.1.2-1 libk5crypto3=1.19.2-2+b1 libkeyutils1=1.6.1-3 libkrb5-3=1.19.2-2+b1 libkrb5support0=1.19.2-2+b1 liblapack-dev=3.10.1-1 liblapack3=3.10.1-1 libldap-2.5-0=2.5.12+dfsg-1 liblsan0=12.1.0-1 liblwp-mediatypes-perl=6.04-1 liblz4-1=1.9.3-2 liblzma-dev=5.2.5-2.1 liblzma5=5.2.5-2.1 libmagic-mgc=1:5.41-4 libmagic1=1:5.41-4 libmd0=1.0.4-1 libmodule-implementation-perl=0.09-1.1 libmodule-runtime-conflicts-perl=0.003-1.1 libmodule-runtime-perl=0.016-1 libmoose-perl=2.2200-1+b1 libmount1=2.38-4 libmpc3=1.2.1-2 libmpfr6=4.1.0-3 libmro-compat-perl=0.15-1 libnamespace-clean-perl=0.27-1 libncurses-dev=6.3+20220423-2 libncurses5-dev=6.3+20220423-2 libncurses6=6.3+20220423-2 libncursesw6=6.3+20220423-2 libnettle8=3.7.3-1 libnghttp2-14=1.47.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.24.1-1 libpackage-deprecationmanager-perl=0.17-1.1 libpackage-stash-perl=0.40-1 libpackage-stash-xs-perl=0.29-1+b3 libpam-modules=1.4.0-13 libpam-modules-bin=1.4.0-13 libpam-runtime=1.4.0-13 libpam0g=1.4.0-13 libpango-1.0-0=1.50.7+ds-1 libpangocairo-1.0-0=1.50.7+ds-1 libpangoft2-1.0-0=1.50.7+ds-1 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libparams-classify-perl=0.015-1+b4 libparams-util-perl=1.102-1+b2 libpcre16-3=2:8.39-14 libpcre2-16-0=10.40-1 libpcre2-32-0=10.40-1 libpcre2-8-0=10.40-1 libpcre2-dev=10.40-1 libpcre2-posix3=10.40-1 libpcre3=2:8.39-14 libpcre3-dev=2:8.39-14 libpcre32-3=2:8.39-14 libpcrecpp0v5=2:8.39-14 libperl5.34=5.34.0-4 libpipeline1=1.5.6-1 libpixman-1-0=0.40.0-1 libpng-dev=1.6.37-5 libpng16-16=1.6.37-5 libpsl5=0.21.0-1.2 libquadmath0=12.1.0-1 libreadline-dev=8.1.2-1.2 libreadline8=8.1.2-1.2 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.28+dfsg-4 libsasl2-modules-db=2.1.28+dfsg-4 libscalar-list-utils-perl=1:1.62-1 libseccomp2=2.5.4-1 libselinux1=3.3-1+b2 libsigsegv2=2.14-1 libsm6=2:1.2.3-1 libsmartcols1=2.38-4 libssh2-1=1.10.0-3 libssl1.1=1.1.1o-1 libstdc++-11-dev=11.3.0-1 libstdc++6=12.1.0-1 libsub-exporter-perl=0.988-1 libsub-exporter-progressive-perl=0.001013-1 libsub-identify-perl=0.14-1+b4 libsub-install-perl=0.928-1.1 libsub-name-perl=0.26-1+b2 libsub-override-perl=0.09-2 libswitch-perl=2.17-2.1 libsystemd0=250.4-1 libtasn1-6=4.18.0-4 libtcl8.6=8.6.12+dfsg-1 libthai-data=0.1.29-1 libthai0=0.1.29-1 libtiff5=4.3.0-7 libtimedate-perl=2.3300-2 libtinfo6=6.3+20220423-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtk8.6=8.6.12-1 libtool=2.4.7-4 libtry-tiny-perl=0.31-1 libtsan0=11.3.0-1 libubsan1=12.1.0-1 libuchardet0=0.0.7-1 libudev1=250.4-1 libunistring2=1.0-1 liburi-perl=5.10-1 libuuid1=2.38-4 libvariable-magic-perl=0.62-1+b4 libwebp7=1.2.2-2+b1 libwww-curl-perl=4.17-7+b2 libwww-curl-simple-perl=0.100191-2 libx11-6=2:1.7.5-1 libx11-data=2:1.7.5-1 libxau6=1:1.0.9-1 libxcb-render0=1.14-3 libxcb-shm0=1.14-3 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxft2=2.3.4-1 libxml2=2.9.14+dfsg-1 libxmuu1=2:1.1.3-3 libxrender1=1:0.9.10-1 libxss1=1:1.2.3-1 libxt6=1:1.2.1-1 libzstd1=1.5.2+dfsg-1 linux-libc-dev=5.17.3-1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 ncurses-base=6.3+20220423-2 ncurses-bin=6.3+20220423-2 openssl=1.1.1o-1 patch=2.7.6-7 perl=5.34.0-4 perl-base=5.34.0-4 perl-modules-5.34=5.34.0-4 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 r-base-core=4.2.0-1+b1 r-base-dev=4.2.0-1 r-bioc-biocgenerics=0.42.0-1 r-bioc-zlibbioc=1.42.0+dfsg-1 readline-common=8.1.2-1.2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.03-1 tar=1.34+dfsg-1 tzdata=2022a-1 ucf=3.0043 unzip=6.0-26 util-linux=2.38-4 util-linux-extra=2.38-4 x11-common=1:7.7+23 xauth=1:1.1.1-1 xdg-utils=1.1.3-4.1 xz-utils=5.2.5-2.1 zip=3.0-12 zlib1g=1:1.2.11.dfsg-4 zlib1g-dev=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/20220524T030904Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220524T030904Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220516T154358Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220511T204932Z/ 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 r-bioc-rhtslib=1.28.0+dfsg-1 && mkdir -p /build/r-bioc-rhtslib-fB7wJ2 && dpkg-source --no-check -x /*.dsc /build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg && chown -R builduser:builduser /build/r-bioc-rhtslib-fB7wJ2" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1652447115" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/r-bioc-rhtslib-fB7wJ2 /tmp/r-bioc-rhtslib-1.28.0+dfsg-1qx_8zgyw bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220511T204932Z unstable 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.I7KoPAodlV 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.I7KoPAodlV 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 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220511T204932Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220511T204932Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (1035 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 ... 4628 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... 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/20220524T030904Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220524T030904Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220516T154358Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220511T204932Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.I7KoPAodlV Get:1 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm InRelease [130 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220516T154358Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20220511T204932Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main Sources [12.0 MB] Get:5 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main amd64 Packages [11.5 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220516T154358Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220516T154358Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220516T154358Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220516T154358Z unstable/main amd64 Packages [12.4 MB] Fetched 36.1 MB in 30s (1219 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.I7KoPAodlV I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d r-bioc-rhtslib=1.28.0+dfsg-1 && mkdir -p /build/r-bioc-rhtslib-fB7wJ2 && dpkg-source --no-check -x /*.dsc /build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg && chown -R builduser:builduser /build/r-bioc-rhtslib-fB7wJ2"' exec /tmp/mmdebstrap.I7KoPAodlV Reading package lists... NOTICE: 'r-bioc-rhtslib' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/r-pkg-team/r-bioc-rhtslib.git Please use: git clone https://salsa.debian.org/r-pkg-team/r-bioc-rhtslib.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 951 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main r-bioc-rhtslib 1.28.0+dfsg-1 (dsc) [2134 B] Get:2 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main r-bioc-rhtslib 1.28.0+dfsg-1 (tar) [945 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main r-bioc-rhtslib 1.28.0+dfsg-1 (diff) [4116 B] Fetched 951 kB in 1s (1216 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'r-bioc-rhtslib_1.28.0+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting r-bioc-rhtslib in /build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg dpkg-source: info: unpacking r-bioc-rhtslib_1.28.0+dfsg.orig.tar.xz dpkg-source: info: unpacking r-bioc-rhtslib_1.28.0+dfsg-1.debian.tar.xz I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1652447115" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.I7KoPAodlV dpkg-buildpackage: info: source package r-bioc-rhtslib dpkg-buildpackage: info: source version 1.28.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem R debian/rules override_dh_auto_clean make[1]: Entering directory '/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg' dh_auto_clean find src -name "*.o" -delete find src -name "*.pico" -delete rm -f src/*/libhts.a src/*/libhts.so* rm -f src/*/version.h make[1]: Leaving directory '/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg' dh_autoreconf_clean -O--buildsystem=R dh_clean -O--buildsystem=R debian/rules binary-arch dh binary-arch --buildsystem R dh_update_autotools_config -a -O--buildsystem=R dh_autoreconf -a -O--buildsystem=R dh_auto_configure -a -O--buildsystem=R dh_auto_build -a -O--buildsystem=R dh: command-omitted: The call to "dh_auto_test -a -O--buildsystem=R" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=R dh_prep -a -O--buildsystem=R dh_auto_install --destdir=debian/r-bioc-rhtslib/ -a -O--buildsystem=R I: R Package: Rhtslib Version: 1.28.0 I: Building using R version 4.2.0-1 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Fri, 13 May 2022 15:05:15 +0200 mkdir -p /build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0\+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library R CMD INSTALL -l /build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0\+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library --clean . "--built-timestamp='Fri, 13 May 2022 15:05:15 +0200'" * installing *source* package ‘Rhtslib’ ... ** using non-staged installation via StagedInstall field ** libs make[1]: Entering directory '/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/src' cd "htslib-1.7" && make -f "/usr/lib/R/etc/Makeconf" -f "Makefile.Rhtslib" make[2]: Entering directory '/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/src/htslib-1.7' Makefile.Rhtslib:131: warning: overriding recipe for target '.c.o' /usr/lib/R/etc/Makeconf:168: warning: ignoring old recipe for target '.c.o' gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.7"' > version.h gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c hts.c: In function ‘hts_idx_init’: hts.c:1366:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ [-Woverflow] 1366 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; | ^~~ gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c realn.c: In function ‘sam_prob_realn’: realn.c:112:23: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 112 | *(bq - 3) = 'Z'; | ~~~~~~~~~~^~~~~ realn.c:96:15: note: at offset -2 into destination object of size [0, 9223372036854775807] allocated by ‘bam_aux_get’ 96 | if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq; | ^~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c In file included from htslib/vcf.h:40, from vcf.c:38: In function ‘kputsn’, inlined from ‘bcf_hdr_subset’ at vcf.c:3044:9: htslib/kstring.h:150:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 150 | s->s[s->l] = 0; | ~~~~~~~~~~~^~~ In file included from /usr/include/string.h:519, from vcf.c:31: In function ‘memcpy’, inlined from ‘kputsn’ at htslib/kstring.h:148:2, inlined from ‘bcf_hdr_subset’ at vcf.c:3044:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:10: warning: ‘__builtin_memcpy’ specified bound 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c In file included from ./textutils_internal.h:32, from ./hts_internal.h:31, from cram/cram_index.c:65: In function ‘kputsn’, inlined from ‘kputs’ at ./htslib/kstring.h:156:9, inlined from ‘cram_index_build’ at cram/cram_index.c:571:9: ./htslib/kstring.h:150:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 150 | s->s[s->l] = 0; | ~~~~~~~~~~~^~~ In file included from /usr/include/string.h:519, from cram/cram_index.c:57: In function ‘memcpy’, inlined from ‘kputsn’ at ./htslib/kstring.h:148:2, inlined from ‘kputs’ at ./htslib/kstring.h:156:9, inlined from ‘cram_index_build’ at cram/cram_index.c:571:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:10: warning: ‘__builtin_memcpy’ specified bound 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c cram/cram_io.c: In function ‘cram_populate_ref’: cram/cram_io.c:2178:34: warning: ‘.tmp_’ directive writing 5 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 2178 | sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t); | ^~~~~ In file included from /usr/include/stdio.h:866, from cram/cram_io.c:49: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 11 and 4134 bytes into a destination of size 4096 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/files.o cram/files.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.o cram/sam_header.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.o hfile_libcurl.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o ranlib libhts.a gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o kfunc.pico kfunc.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o knetfile.pico knetfile.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o kstring.pico kstring.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o bgzf.pico bgzf.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o errmod.pico errmod.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o faidx.pico faidx.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile.pico hfile.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile_net.pico hfile_net.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hts.pico hts.c hts.c: In function ‘hts_idx_init’: hts.c:1366:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ [-Woverflow] 1366 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; | ^~~ gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hts_os.pico hts_os.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o md5.pico md5.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o multipart.pico multipart.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o probaln.pico probaln.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o realn.pico realn.c realn.c: In function ‘sam_prob_realn’: realn.c:112:23: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 112 | *(bq - 3) = 'Z'; | ~~~~~~~~~~^~~~~ realn.c:96:15: note: at offset -2 into destination object of size [0, 9223372036854775807] allocated by ‘bam_aux_get’ 96 | if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq; | ^~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o regidx.pico regidx.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o sam.pico sam.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.pico vcf_sweep.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o tbx.pico tbx.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o textutils.pico textutils.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o thread_pool.pico thread_pool.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcf.pico vcf.c In file included from htslib/vcf.h:40, from vcf.c:38: In function ‘kputsn’, inlined from ‘bcf_hdr_subset’ at vcf.c:3044:9: htslib/kstring.h:150:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 150 | s->s[s->l] = 0; | ~~~~~~~~~~~^~~ In file included from /usr/include/string.h:519, from vcf.c:31: In function ‘memcpy’, inlined from ‘kputsn’ at htslib/kstring.h:148:2, inlined from ‘bcf_hdr_subset’ at vcf.c:3044:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:10: warning: ‘__builtin_memcpy’ specified bound 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcfutils.pico vcfutils.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.pico cram/cram_external.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.pico cram/cram_index.c In file included from ./textutils_internal.h:32, from ./hts_internal.h:31, from cram/cram_index.c:65: In function ‘kputsn’, inlined from ‘kputs’ at ./htslib/kstring.h:156:9, inlined from ‘cram_index_build’ at cram/cram_index.c:571:9: ./htslib/kstring.h:150:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 150 | s->s[s->l] = 0; | ~~~~~~~~~~~^~~ In file included from /usr/include/string.h:519, from cram/cram_index.c:57: In function ‘memcpy’, inlined from ‘kputsn’ at ./htslib/kstring.h:148:2, inlined from ‘kputs’ at ./htslib/kstring.h:156:9, inlined from ‘cram_index_build’ at cram/cram_index.c:571:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:10: warning: ‘__builtin_memcpy’ specified bound 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.pico cram/cram_io.c cram/cram_io.c: In function ‘cram_populate_ref’: cram/cram_io.c:2178:34: warning: ‘.tmp_’ directive writing 5 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 2178 | sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t); | ^~~~~ In file included from /usr/include/stdio.h:866, from cram/cram_io.c:49: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 11 and 4134 bytes into a destination of size 4096 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.pico cram/cram_samtools.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/files.pico cram/files.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.pico cram/mFILE.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.pico cram/rANS_static.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.pico cram/sam_header.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.pico hfile_libcurl.c gcc -shared -Wl,-soname,libhts.so.2 -Wl,-z,relro -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico hfile_libcurl.pico -lz -lm -lbz2 -llzma -lcurl -lpthread ln -sf libhts.so libhts.so.2 make[2]: Leaving directory '/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/src/htslib-1.7' mkdir -p "/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library/Rhtslib/include/htslib" cd "htslib-1.7/htslib" && cp * "/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library/Rhtslib/include" gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library/Rhtslib/include" -I'/usr/lib/R/site-library/zlibbioc/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-eH67wr/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_init_Rhtslib.c -o R_init_Rhtslib.o mkdir -p "/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library/Rhtslib/usrlib" cd "htslib-1.7" && cp libhts.so libhts.a "/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library/Rhtslib/usrlib" cd "/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library/Rhtslib/usrlib" && ln -s libhts.so libhts.so.2 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o Rhtslib.so R_init_Rhtslib.o /build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/usr/lib/R/lib -lR mkdir -p "/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library/Rhtslib/testdata/tabix" cd "htslib-1.7/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library/Rhtslib/testdata/tabix" 2>/dev/null || true) make[1]: Leaving directory '/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/src' make[1]: Entering directory '/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/src' make[1]: Leaving directory '/build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/src' installing to /build/r-bioc-rhtslib-fB7wJ2/r-bioc-rhtslib-1.28.0+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library/Rhtslib/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Rhtslib) Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 300. Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 301. Use of uninitialized value $dep_line in split at /usr/share/perl5/Dpkg/Deps.pm line 304. I: Using r-cran-knitr for Suggests:knitr I: Using r-cran-rmarkdown for Suggests:rmarkdown I: Using r-bioc-biocstyle for Suggests:BiocStyle I: Using r-bioc-zlibbioc for Imports:zlibbioc I: Using r-bioc-zlibbioc for LinkingTo:zlibbioc I: BioConductor API version: r-api-bioc-3.15 I: Use r-bioc-rhtslib as Debian binary package for variables substitution dh_installdocs -a -O--buildsystem=R dh_installchangelogs -a -O--buildsystem=R dh_installsystemduser -a -O--buildsystem=R dh_perl -a -O--buildsystem=R dh_link -a -O--buildsystem=R dh_strip_nondeterminism -a -O--buildsystem=R dh_compress -a -O--buildsystem=R dh_fixperms -a -O--buildsystem=R dh_missing -a -O--buildsystem=R dh_dwz -a -O--buildsystem=R dh_strip -a -O--buildsystem=R dh_makeshlibs -a -O--buildsystem=R dh_shlibdeps -a -O--buildsystem=R dh_installdeb -a -O--buildsystem=R dh_gencontrol -a -O--buildsystem=R dh_md5sums -a -O--buildsystem=R dh_builddeb -a -O--buildsystem=R dpkg-deb: building package 'r-bioc-rhtslib' in '../r-bioc-rhtslib_1.28.0+dfsg-1_amd64.deb'. dpkg-deb: building package 'r-bioc-rhtslib-dbgsym' in '../r-bioc-rhtslib-dbgsym_1.28.0+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=any -O../r-bioc-rhtslib_1.28.0+dfsg-1_amd64.buildinfo dpkg-genchanges --build=any -O../r-bioc-rhtslib_1.28.0+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/r-bioc-rhtslib-fB7wJ2 /tmp/r-bioc-rhtslib-1.28.0+dfsg-1qx_8zgyw I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.I7KoPAodlV... I: success in 463.9485 seconds md5: r-bioc-rhtslib-dbgsym_1.28.0+dfsg-1_amd64.deb: OK md5: r-bioc-rhtslib_1.28.0+dfsg-1_amd64.deb: OK sha1: r-bioc-rhtslib-dbgsym_1.28.0+dfsg-1_amd64.deb: OK sha1: r-bioc-rhtslib_1.28.0+dfsg-1_amd64.deb: OK sha256: r-bioc-rhtslib-dbgsym_1.28.0+dfsg-1_amd64.deb: OK sha256: r-bioc-rhtslib_1.28.0+dfsg-1_amd64.deb: OK Checksums: OK