Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/r/r-bioc-rhtslib/r-bioc-rhtslib_1.22.0+dfsg-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/r-bioc-rhtslib-1.22.0+dfsg-1vwod3piu/r-bioc-rhtslib_1.22.0+dfsg-1_amd64.buildinfo Get source package info: r-bioc-rhtslib=1.22.0+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/r-bioc-rhtslib/1.22.0+dfsg-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.2-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1~rc1-2 binutils=2.35.1-2 binutils-common=2.35.1-2 binutils-x86-64-linux-gnu=2.35.1-2 bsdextrautils=2.36-3+b2 bsdutils=1:2.36-3+b1 build-essential=12.8 bzip2=1.0.8-4 ca-certificates=20200601 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-16 dash=0.5.10.2-7 dctrl-tools=2.24-3+b1 debconf=1.5.74 debhelper=13.2.1 debianutils=4.11.2 dh-autoreconf=19 dh-r=20200923 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.38-5 findutils=4.7.0+git20201010-2 fontconfig=2.13.1-4.2 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:10.2.0-1 g++-10=10.2.0-16 gcc=4:10.2.0-1 gcc-10=10.2.0-16 gcc-10-base=10.2.0-16 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 gfortran=4:10.2.0-1 gfortran-10=10.2.0-16 grep=3.4-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 icu-devtools=67.1-4 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan6=10.2.0-16 libatomic1=10.2.0-16 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1 libbinutils=2.35.1-2 libblas-dev=3.9.0-3 libblas3=3.9.0-3 libblkid1=2.36-3+b1 libbrotli1=1.0.9-2+b1 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-4 libbz2-dev=1.0.8-4 libc-bin=2.31-4 libc-dev-bin=2.31-4 libc6=2.31-4 libc6-dev=2.31-4 libcairo2=1.16.0-4 libcap-ng0=0.7.9-2.2 libcc1-0=10.2.0-16 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-2 libctf0=2.35.1-2 libcurl4=7.72.0-1 libcurl4-openssl-dev=7.72.0-1 libdatrie1=0.2.12-3 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.2.1 libdpkg-perl=1.20.5 libelf1=0.181-1 libexpat1=2.2.10-1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.9.0-1 libfile-which-perl=1.23-1 libfontconfig1=2.13.1-4.2 libfreetype6=2.10.2+dfsg-4 libfribidi0=1.0.8-2 libgcc-10-dev=10.2.0-16 libgcc-s1=10.2.0-16 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libgfortran-10-dev=10.2.0-16 libgfortran5=10.2.0-16 libglib2.0-0=2.66.2-1 libgmp10=2:6.2.0+dfsg-6 libgnutls30=3.6.15-4 libgomp1=10.2.0-16 libgpg-error0=1.38-2 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.17-10 libharfbuzz0b=2.6.7-1 libhogweed6=3.6-2 libice6=2:1.0.10-1 libicu-dev=67.1-4 libicu67=67.1-4 libidn2-0=2.3.0-1 libisl22=0.22.1-1 libitm1=10.2.0-16 libjbig0=2.1-3.1+b2 libjpeg-dev=1:2.0.5-1.1 libjpeg62-turbo=1:2.0.5-1.1 libjpeg62-turbo-dev=1:2.0.5-1.1 libk5crypto3=1.17-10 libkeyutils1=1.6.1-2 libkrb5-3=1.17-10 libkrb5support0=1.17-10 liblapack-dev=3.9.0-3 liblapack3=3.9.0-3 libldap-2.4-2=2.4.55+dfsg-1 liblsan0=10.2.0-16 liblz4-1=1.9.2-2 liblzma-dev=5.2.4-1+b1 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmount1=2.36-3+b1 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncurses-dev=6.2+20200918-1 libncurses5-dev=6.2+20200918-1 libncurses6=6.2+20200918-1 libncursesw6=6.2+20200918-1 libnettle8=3.6-2 libnghttp2-14=1.41.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnss-nis=3.1-4 libnss-nisplus=1.3-4 libp11-kit0=0.23.21-2 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpango-1.0-0=1.46.2-1 libpangocairo-1.0-0=1.46.2-1 libpangoft2-1.0-0=1.46.2-1 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libpcre16-3=2:8.39-13 libpcre2-16-0=10.34-7 libpcre2-32-0=10.34-7 libpcre2-8-0=10.34-7 libpcre2-dev=10.34-7 libpcre2-posix2=10.34-7 libpcre3=2:8.39-13 libpcre3-dev=2:8.39-13 libpcre32-3=2:8.39-13 libpcrecpp0v5=2:8.39-13 libperl5.30=5.30.3-4 libpipeline1=1.5.3-1 libpixman-1-0=0.36.0-1 libpng-dev=1.6.37-3 libpng16-16=1.6.37-3 libpsl5=0.21.0-1.1 libquadmath0=10.2.0-16 libreadline-dev=8.0-4 libreadline8=8.0-4 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.4.4-1+b1 libselinux1=3.1-2+b1 libsigsegv2=2.12-2 libsm6=2:1.2.3-1 libsmartcols1=2.36-3+b1 libssh2-1=1.8.0-2.1 libssl1.1=1.1.1h-1 libstdc++-10-dev=10.2.0-16 libstdc++6=10.2.0-16 libsub-override-perl=0.09-2 libswitch-perl=2.17-2 libsystemd0=246.6-2 libtasn1-6=4.16.0-2 libtcl8.6=8.6.10+dfsg-1 libthai-data=0.1.28-3 libthai0=0.1.28-3 libtiff5=4.1.0+git191117-2 libtinfo6=6.2+20200918-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtk8.6=8.6.10-1 libtool=2.4.6-14 libtsan0=10.2.0-16 libubsan1=10.2.0-16 libuchardet0=0.0.7-1 libudev1=246.6-2 libunistring2=0.9.10-4 libuuid1=2.36-3+b1 libwebp6=0.6.1-2+b1 libx11-6=2:1.6.12-1 libx11-data=2:1.6.12-1 libxau6=1:1.0.8-1+b2 libxcb-render0=1.14-2 libxcb-shm0=1.14-2 libxcb1=1.14-2 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1+b2 libxft2=2.3.2-2 libxml2=2.9.10+dfsg-6.2 libxmuu1=2:1.1.2-2+b3 libxrender1=1:0.9.10-1 libxss1=1:1.2.3-1 libxt6=1:1.2.0-1 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.1-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20200918-1 ncurses-bin=6.2+20200918-1 openssl=1.1.1h-1 patch=2.7.6-6 perl=5.30.3-4 perl-base=5.30.3-4 perl-modules-5.30=5.30.3-4 pkg-config=0.29.2-1 po-debconf=1.0.21 r-base-core=4.0.3-1 r-base-dev=4.0.3-1 r-bioc-biocgenerics=0.36.0-1 r-bioc-zlibbioc=1.36.0+dfsg-1 readline-common=8.0-4 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.30+dfsg-7 tzdata=2020d-1 ucf=3.0043 unzip=6.0-25 util-linux=2.36-3+b1 x11-common=1:7.7+21 xauth=1:1.0.10-1 xdg-utils=1.1.3-2 xz-utils=5.2.4-1+b1 zip=3.0-11+b1 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201116T092020Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201101T210343Z/ 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=1.22.0+dfsg-1 && mkdir -p /build/r-bioc-rhtslib-C64dCU && dpkg-source --no-check -x /*.dsc /build/r-bioc-rhtslib-C64dCU/r-bioc-rhtslib-1.22.0+dfsg && chown -R builduser:builduser /build/r-bioc-rhtslib-C64dCU" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/r-bioc-rhtslib-C64dCU/r-bioc-rhtslib-1.22.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1604321244" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/r-bioc-rhtslib-C64dCU /tmp/r-bioc-rhtslib-1.22.0+dfsg-1vwod3piu bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201101T210343Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.JJxQZbEOFb 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.JJxQZbEOFb Reading package lists... Building dependency tree... util-linux is already the newest version (2.36-3+b1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201101T210343Z unstable/main amd64 libfakeroot amd64 1.25.3-1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201101T210343Z unstable/main amd64 fakeroot amd64 1.25.3-1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (840 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 ... 4664 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1_amd64.deb ... Unpacking fakeroot (1.25.3-1) ... Setting up libfakeroot:amd64 (1.25.3-1) ... Setting up fakeroot (1.25.3-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201116T092020Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201101T210343Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.JJxQZbEOFb Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201116T092020Z unstable InRelease [146 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201101T210343Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20201116T092020Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201116T092020Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201116T092020Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20201116T092020Z unstable/main amd64 Packages [11.5 MB] Fetched 34.3 MB in 28s (1204 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.JJxQZbEOFb I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d r-bioc-rhtslib=1.22.0+dfsg-1 && mkdir -p /build/r-bioc-rhtslib-C64dCU && dpkg-source --no-check -x /*.dsc /build/r-bioc-rhtslib-C64dCU/r-bioc-rhtslib-1.22.0+dfsg && chown -R builduser:builduser /build/r-bioc-rhtslib-C64dCU"' exec /tmp/mmdebstrap.JJxQZbEOFb 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/20210814T212851Z bookworm/main r-bioc-rhtslib 1.22.0+dfsg-1 (dsc) [2134 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main r-bioc-rhtslib 1.22.0+dfsg-1 (tar) [945 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main r-bioc-rhtslib 1.22.0+dfsg-1 (diff) [3712 B] Fetched 951 kB in 1s (1143 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'r-bioc-rhtslib_1.22.0+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-C64dCU/r-bioc-rhtslib-1.22.0+dfsg dpkg-source: info: unpacking r-bioc-rhtslib_1.22.0+dfsg.orig.tar.xz dpkg-source: info: unpacking r-bioc-rhtslib_1.22.0+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-C64dCU/r-bioc-rhtslib-1.22.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1604321244" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.JJxQZbEOFb dpkg-buildpackage: info: source package r-bioc-rhtslib dpkg-buildpackage: info: source version 1.22.0+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 dh_auto_clean -O--buildsystem=R 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_auto_test -a -O--buildsystem=R create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=R dh_prep -a -O--buildsystem=R dh_auto_install -a -O--buildsystem=R I: R Package: Rhtslib Version: 1.22.0 I: Building using R version 4.0.3-1 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Mon, 02 Nov 2020 13:47:24 +0100 mkdir -p /build/r-bioc-rhtslib-C64dCU/r-bioc-rhtslib-1.22.0\+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library R CMD INSTALL -l /build/r-bioc-rhtslib-C64dCU/r-bioc-rhtslib-1.22.0\+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 02 Nov 2020 13:47:24 +0100'" * installing *source* package ‘Rhtslib’ ... ** using non-staged installation via StagedInstall field ** libs make[1]: Entering directory '/build/r-bioc-rhtslib-C64dCU/r-bioc-rhtslib-1.22.0+dfsg/src' cd "htslib-1.7" && make -f "/usr/lib/R/etc/Makeconf" -f "Makefile.Rhtslib" make[2]: Entering directory '/build/r-bioc-rhtslib-C64dCU/r-bioc-rhtslib-1.22.0+dfsg/src/htslib-1.7' Makefile.Rhtslib:128: warning: overriding recipe for target '.c.o' /usr/lib/R/etc/Makeconf:172: warning: ignoring old recipe for target '.c.o' gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.7"' > version.h gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c In file included from /usr/include/string.h:495, 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:34:10: warning: ‘__builtin_memcpy’ specified bound 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 34 | return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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:2178:27: 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:867, from cram/cram_io.c:49: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 11 and 4134 bytes into a destination of size 4096 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/files.o cram/files.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.o cram/rANS_static.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.o cram/sam_header.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o kfunc.pico kfunc.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o knetfile.pico knetfile.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o kstring.pico kstring.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o bgzf.pico bgzf.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o errmod.pico errmod.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o faidx.pico faidx.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile.pico hfile.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile_net.pico hfile_net.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hts_os.pico hts_os.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o md5.pico md5.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o multipart.pico multipart.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o probaln.pico probaln.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o realn.pico realn.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o regidx.pico regidx.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o sam.pico sam.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.pico vcf_sweep.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o tbx.pico tbx.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o textutils.pico textutils.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o thread_pool.pico thread_pool.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcf.pico vcf.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcfutils.pico vcfutils.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.pico cram/cram_decode.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.pico cram/cram_encode.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.pico cram/cram_external.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.pico cram/cram_index.c In file included from /usr/include/string.h:495, 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:34:10: warning: ‘__builtin_memcpy’ specified bound 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 34 | return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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:2178:27: 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:867, from cram/cram_io.c:49: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 11 and 4134 bytes into a destination of size 4096 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.pico cram/cram_samtools.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.pico cram/cram_stats.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/files.pico cram/files.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.pico cram/mFILE.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.pico cram/rANS_static.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.pico cram/sam_header.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.pico cram/string_alloc.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.pico hfile_libcurl.c gcc -std=gnu99 -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-C64dCU/r-bioc-rhtslib-1.22.0+dfsg/src/htslib-1.7' mkdir -p "/build/r-bioc-rhtslib-C64dCU/r-bioc-rhtslib-1.22.0+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library/Rhtslib/include/htslib" cd "htslib-1.7/htslib" && cp * "/build/r-bioc-rhtslib-C64dCU/r-bioc-rhtslib-1.22.0+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-C64dCU/r-bioc-rhtslib-1.22.0+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library/Rhtslib/include" gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/build/r-bioc-rhtslib-C64dCU/r-bioc-rhtslib-1.22.0+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library/Rhtslib/include" -I'/usr/lib/R/site-library/zlibbioc/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_Rhtslib.c -o R_init_Rhtslib.o mkdir -p "/build/r-bioc-rhtslib-C64dCU/r-bioc-rhtslib-1.22.0+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-C64dCU/r-bioc-rhtslib-1.22.0+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library/Rhtslib/usrlib" cd "/build/r-bioc-rhtslib-C64dCU/r-bioc-rhtslib-1.22.0+dfsg/debian/r-bioc-rhtslib/usr/lib/R/site-library/Rhtslib/usrlib" && ln -s libhts.so libhts.so.2 gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o Rhtslib.so R_init_Rhtslib.o /build/r-bioc-rhtslib-C64dCU/r-bioc-rhtslib-1.22.0+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-C64dCU/r-bioc-rhtslib-1.22.0+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-C64dCU/r-bioc-rhtslib-1.22.0+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-C64dCU/r-bioc-rhtslib-1.22.0+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-C64dCU/r-bioc-rhtslib-1.22.0+dfsg/src' make[1]: Entering directory '/build/r-bioc-rhtslib-C64dCU/r-bioc-rhtslib-1.22.0+dfsg/src' make[1]: Leaving directory '/build/r-bioc-rhtslib-C64dCU/r-bioc-rhtslib-1.22.0+dfsg/src' installing to /build/r-bioc-rhtslib-C64dCU/r-bioc-rhtslib-1.22.0+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 299. 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 split at /usr/share/perl5/Dpkg/Deps.pm line 303. I: Using r-bioc-biocstyle for Suggests:BiocStyle I: Using r-cran-knitr for Suggests:knitr I: Using r-bioc-zlibbioc for Imports:zlibbioc I: Using r-bioc-zlibbioc for LinkingTo:zlibbioc I: BioConductor API version: r-api-bioc-3.12 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 -a -O--buildsystem=R dh_strip -a -a -O--buildsystem=R dh_makeshlibs -a -a -O--buildsystem=R dh_shlibdeps -a -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_1.22.0+dfsg-1_amd64.deb'. dpkg-deb: building package 'r-bioc-rhtslib-dbgsym' in '../r-bioc-rhtslib-dbgsym_1.22.0+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../r-bioc-rhtslib_1.22.0+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-C64dCU /tmp/r-bioc-rhtslib-1.22.0+dfsg-1vwod3piu I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.JJxQZbEOFb... I: success in 838.6242 seconds md5: r-bioc-rhtslib-dbgsym_1.22.0+dfsg-1_amd64.deb: OK md5: r-bioc-rhtslib_1.22.0+dfsg-1_amd64.deb: OK sha1: r-bioc-rhtslib-dbgsym_1.22.0+dfsg-1_amd64.deb: OK sha1: r-bioc-rhtslib_1.22.0+dfsg-1_amd64.deb: OK sha256: r-bioc-rhtslib-dbgsym_1.22.0+dfsg-1_amd64.deb: OK sha256: r-bioc-rhtslib_1.22.0+dfsg-1_amd64.deb: OK Checksums: OK