I: pbuilder: network access will be disabled during build I: Current time: Sun Jul 18 02:47:59 +14 2021 I: pbuilder-time-stamp: 1626526079 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [r-bioc-rsamtools_1.34.1-1.dsc] I: copying [./r-bioc-rsamtools_1.34.1.orig.tar.gz] I: copying [./r-bioc-rsamtools_1.34.1-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Feb 6 00:06:15 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./r-bioc-rsamtools_1.34.1-1.dsc dpkg-source: info: extracting r-bioc-rsamtools in r-bioc-rsamtools-1.34.1 dpkg-source: info: unpacking r-bioc-rsamtools_1.34.1.orig.tar.gz dpkg-source: info: unpacking r-bioc-rsamtools_1.34.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_test_requiring_network.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/15452/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/15452/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/15452/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=53c4c066699e43dabdff968efe1904ff LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=15452 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.wbOZAfJATn/pbuilderrc_cq9Z --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.wbOZAfJATn/b2 --logfile b2/build.log r-bioc-rsamtools_1.34.1-1.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash -rwxr-xr-x 1 root root 109408 Mar 1 2019 date -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd -rwxr-xr-x 1 root root 93744 Mar 1 2019 df -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 35424 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln -rwxr-xr-x 1 root root 56760 Jul 27 2018 login -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 10 2019 more -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 18 02:48 sh -> bash lrwxrwxrwx 1 root root 4 Jul 7 22:24 sh.distrib -> dash -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty -rwsr-xr-x 1 root root 63568 Jan 10 2019 su -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch -rwxr-xr-x 1 root root 35424 Mar 1 2019 true -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/15452/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 12~), dh-r, r-base-dev, r-bioc-genomeinfodb (>= 1.1.3), r-bioc-genomicranges (>= 1.31.8), r-bioc-biostrings (>= 2.47.6), r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-xvector (>= 0.19.7), r-bioc-zlibbioc, r-cran-bitops, r-bioc-biocparallel dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 12~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-r; however: Package dh-r is not installed. pbuilder-satisfydepends-dummy depends on r-base-dev; however: Package r-base-dev is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-genomeinfodb (>= 1.1.3); however: Package r-bioc-genomeinfodb is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-genomicranges (>= 1.31.8); however: Package r-bioc-genomicranges is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biostrings (>= 2.47.6); however: Package r-bioc-biostrings is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biocgenerics (>= 0.25.1); however: Package r-bioc-biocgenerics is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-s4vectors (>= 0.17.25); however: Package r-bioc-s4vectors is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-iranges (>= 2.13.12); however: Package r-bioc-iranges is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-xvector (>= 0.19.7); however: Package r-bioc-xvector is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-zlibbioc; however: Package r-bioc-zlibbioc is not installed. pbuilder-satisfydepends-dummy depends on r-cran-bitops; however: Package r-cran-bitops is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biocparallel; however: Package r-bioc-biocparallel is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} ca-certificates{a} dctrl-tools{a} debhelper{a} dh-autoreconf{a} dh-r{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} gfortran{a} gfortran-8{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libbsd0{a} libbz2-dev{a} libcairo2{a} libcroco3{a} libcurl4{a} libdatrie1{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran-8-dev{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libice6{a} libicu-dev{a} libicu63{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.4-2{a} libldap-common{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses-dev{a} libncurses5-dev{a} libncurses6{a} libnghttp2-14{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpcre16-3{a} libpcre3-dev{a} libpcre32-3{a} libpcrecpp0v5{a} libpipeline1{a} libpixman-1-0{a} libpng-dev{a} libpng16-16{a} libpsl5{a} libreadline-dev{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsm6{a} libssh2-1{a} libssl1.1{a} libswitch-perl{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff5{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp6{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxmuu1{a} libxrender1{a} libxss1{a} libxt6{a} lsb-base{a} m4{a} man-db{a} openssl{a} pkg-config{a} po-debconf{a} r-base-core{a} r-base-dev{a} r-bioc-biocgenerics{a} r-bioc-biocparallel{a} r-bioc-biostrings{a} r-bioc-genomeinfodb{a} r-bioc-genomeinfodbdata{a} r-bioc-genomicranges{a} r-bioc-iranges{a} r-bioc-s4vectors{a} r-bioc-xvector{a} r-bioc-zlibbioc{a} r-cran-bitops{a} r-cran-formatr{a} r-cran-futile.logger{a} r-cran-futile.options{a} r-cran-lambda.r{a} r-cran-rcurl{a} r-cran-snow{a} readline-common{a} sensible-utils{a} ucf{a} unzip{a} x11-common{a} xauth{a} xdg-utils{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl devscripts krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libnet-dbus-perl libpng-tools libsasl2-modules libx11-protocol-perl lynx publicsuffix r-bioc-annotate r-bioc-rsamtools r-bioc-summarizedexperiment r-cran-batchjobs r-cran-batchtools r-cran-codetools r-cran-digest r-cran-doparallel r-cran-rmpi r-cran-runit r-cran-survival r-cran-testit r-cran-testthat r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 147 newly installed, 0 to remove and 0 not upgraded. Need to get 123 MB of archives. After unpacking 301 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u6 [1539 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u6 [844 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 dctrl-tools amd64 2.24-3 [103 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 zip amd64 3.0-11+b1 [234 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 unzip amd64 6.0-23+deb10u2 [172 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libpaper1 amd64 1.1.28 [21.3 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libpaper-utils amd64 1.1.28 [18.0 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 xdg-utils all 1.1.3-1+deb10u1 [73.7 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u2 [380 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u2 [299 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u2 [757 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 libxcb-render0 amd64 1.13.1-2 [109 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 libxcb-shm0 amd64 1.13.1-2 [99.2 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libcairo2 amd64 1.16.0-4+deb10u1 [688 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u1 [65.8 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u1 [122 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u1 [369 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u1 [158 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libcurl4 amd64 7.64.0-4+deb10u2 [332 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 x11-common all 1:7.7+19 [251 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 fontconfig amd64 2.13.1-2 [405 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libfribidi0 amd64 1.0.5-3.1+deb10u1 [63.7 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libthai-data all 0.1.28-2 [170 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libdatrie1 amd64 0.2.12-2 [39.3 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 libthai0 amd64 0.1.28-2 [54.1 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libpango-1.0-0 amd64 1.42.4-8~deb10u1 [186 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 libgraphite2-3 amd64 1.3.13-7 [80.7 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libharfbuzz0b amd64 2.3.1-1 [1187 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libpangoft2-1.0-0 amd64 1.42.4-8~deb10u1 [68.3 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 libpangocairo-1.0-0 amd64 1.42.4-8~deb10u1 [55.7 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 libtcl8.6 amd64 8.6.9+dfsg-2 [1005 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 libwebp6 amd64 0.6.1-2+deb10u1 [261 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u2 [271 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 libtk8.6 amd64 8.6.9-2 [768 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 libxt6 amd64 1:1.1.5-1+b3 [190 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 r-base-core amd64 3.5.2-1 [23.9 MB] Get: 104 http://deb.debian.org/debian buster/main amd64 libgfortran-8-dev amd64 8.3.0-6 [616 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 gfortran-8 amd64 8.3.0-6 [9375 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 gfortran amd64 4:8.3.0-1 [1432 B] Get: 107 http://deb.debian.org/debian buster/main amd64 libblas-dev amd64 3.8.0-2 [154 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 liblapack-dev amd64 3.8.0-2 [2140 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 libncurses-dev amd64 6.1+20181013-2+deb10u2 [333 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 libncurses5-dev amd64 6.1+20181013-2+deb10u2 [948 B] Get: 111 http://deb.debian.org/debian buster/main amd64 libreadline-dev amd64 7.0-5 [133 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo-dev amd64 1:1.5.2-2+deb10u1 [208 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 libjpeg-dev all 1:1.5.2-2+deb10u1 [57.7 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 libpcre16-3 amd64 2:8.39-12 [259 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 libpcre32-3 amd64 2:8.39-12 [250 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 libpcrecpp0v5 amd64 2:8.39-12 [152 kB] Get: 117 http://deb.debian.org/debian buster/main amd64 libpcre3-dev amd64 2:8.39-12 [650 kB] Get: 118 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Get: 119 http://deb.debian.org/debian buster/main amd64 libpng-dev amd64 1.6.36-6 [300 kB] Get: 120 http://deb.debian.org/debian buster/main amd64 libbz2-dev amd64 1.0.6-9.2~deb10u1 [30.2 kB] Get: 121 http://deb.debian.org/debian buster/main amd64 liblzma-dev amd64 5.2.4-1 [210 kB] Get: 122 http://deb.debian.org/debian buster/main amd64 icu-devtools amd64 63.1-6+deb10u1 [189 kB] Get: 123 http://deb.debian.org/debian buster/main amd64 libicu-dev amd64 63.1-6+deb10u1 [9186 kB] Get: 124 http://deb.debian.org/debian buster/main amd64 libxmuu1 amd64 2:1.1.2-2+b3 [23.9 kB] Get: 125 http://deb.debian.org/debian buster/main amd64 xauth amd64 1:1.0.10-1 [40.3 kB] Get: 126 http://deb.debian.org/debian buster/main amd64 pkg-config amd64 0.29-6 [63.5 kB] Get: 127 http://deb.debian.org/debian buster/main amd64 r-base-dev all 3.5.2-1 [4480 B] Get: 128 http://deb.debian.org/debian buster/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get: 129 http://deb.debian.org/debian buster/main amd64 libswitch-perl all 2.17-2 [20.5 kB] Get: 130 http://deb.debian.org/debian buster/main amd64 dh-r all 20190121 [35.1 kB] Get: 131 http://deb.debian.org/debian buster/main amd64 r-bioc-biocgenerics all 0.28.0-2 [644 kB] Get: 132 http://deb.debian.org/debian buster/main amd64 r-cran-formatr all 1.5-3 [149 kB] Get: 133 http://deb.debian.org/debian buster/main amd64 r-cran-lambda.r all 1.2.3-2 [117 kB] Get: 134 http://deb.debian.org/debian buster/main amd64 r-cran-futile.options all 1.0.1-2 [19.8 kB] Get: 135 http://deb.debian.org/debian buster/main amd64 r-cran-futile.logger all 1.4.3-3 [102 kB] Get: 136 http://deb.debian.org/debian buster/main amd64 r-cran-snow all 1:0.4.3-1 [108 kB] Get: 137 http://deb.debian.org/debian buster/main amd64 r-bioc-biocparallel amd64 1.16.6-1 [1063 kB] Get: 138 http://deb.debian.org/debian buster/main amd64 r-bioc-s4vectors amd64 0.20.1-2 [1815 kB] Get: 139 http://deb.debian.org/debian buster/main amd64 r-bioc-iranges amd64 2.16.0-1 [2130 kB] Get: 140 http://deb.debian.org/debian buster/main amd64 r-bioc-xvector amd64 0.22.0-1 [603 kB] Get: 141 http://deb.debian.org/debian buster/main amd64 r-bioc-biostrings amd64 2.50.2-1 [14.1 MB] Get: 142 http://deb.debian.org/debian buster/main amd64 r-cran-bitops amd64 1.0-6-4 [24.3 kB] Get: 143 http://deb.debian.org/debian buster/main amd64 r-cran-rcurl amd64 1.95-4.11-1 [715 kB] Get: 144 http://deb.debian.org/debian buster/main amd64 r-bioc-genomeinfodbdata all 1.2.0-1 [9196 kB] Get: 145 http://deb.debian.org/debian buster/main amd64 r-bioc-genomeinfodb all 1.18.1-1 [3692 kB] Get: 146 http://deb.debian.org/debian buster/main amd64 r-bioc-genomicranges amd64 1.34.0+dfsg-1 [1769 kB] Get: 147 http://deb.debian.org/debian buster/main amd64 r-bioc-zlibbioc all 1.28.0+dfsg-1 [8540 B] Fetched 123 MB in 2s (58.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0: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 ... 19195 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. 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Unpacking openssl (1.1.1d-0+deb10u6) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../021-ca-certificates_20200601~deb10u2_all.deb ... Unpacking ca-certificates (20200601~deb10u2) ... Selecting previously unselected package dctrl-tools. Preparing to unpack .../022-dctrl-tools_2.24-3_amd64.deb ... Unpacking dctrl-tools (2.24-3) ... Selecting previously unselected package libtool. Preparing to unpack .../023-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../024-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../025-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../026-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../027-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../028-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../029-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../030-libglib2.0-0_2.58.3-2+deb10u3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../031-libicu63_63.1-6+deb10u1_amd64.deb ... Unpacking libicu63:amd64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../032-libxml2_2.9.4+dfsg1-7+deb10u2_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../033-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../034-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../035-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../036-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../037-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. 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Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/r-bioc-rsamtools-1.34.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package r-bioc-rsamtools dpkg-buildpackage: info: source version 1.34.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot 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 build make: 'build' is up to date. fakeroot debian/rules binary dh binary --buildsystem R dh_update_autotools_config -O--buildsystem=R dh_autoreconf -O--buildsystem=R dh_auto_configure -O--buildsystem=R dh_auto_build -O--buildsystem=R dh_auto_test -O--buildsystem=R create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=R dh_prep -O--buildsystem=R dh_auto_install -O--buildsystem=R I: R packages needed for DEP8: runit, shortread I: R Package: Rsamtools Version: 1.34.1 I: Building using R version 3.5.2-1 I: R API version: r-api-3.5 I: Using built-time from d/changelog: Tue, 05 Feb 2019 10:58:48 +0100 mkdir -p /build/r-bioc-rsamtools-1.34.1/debian/r-bioc-rsamtools/usr/lib/R/site-library R CMD INSTALL -l /build/r-bioc-rsamtools-1.34.1/debian/r-bioc-rsamtools/usr/lib/R/site-library --clean . "--built-timestamp='Tue, 05 Feb 2019 10:58:48 +0100'" * installing *source* package 'Rsamtools' ... ** libs make[1]: Entering directory '/build/r-bioc-rsamtools-1.34.1/src' gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o g++ -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PileupBuffer.cpp -o PileupBuffer.o g++ -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PosCacheColl.cpp -o PosCacheColl.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_Rsamtools.c -o R_init_Rsamtools.o g++ -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ResultManager.cpp -o ResultManager.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XVector_stubs.c -o XVector_stubs.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c as_bam.c -o as_bam.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bam_data.c -o bam_data.o g++ -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bam_mate_iter.cpp -o bam_mate_iter.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bambuffer.c -o bambuffer.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bamfile.c -o bamfile.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bcffile.c -o bcffile.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c encode.c -o encode.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fafile.c -o fafile.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c idxstats.c -o idxstats.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io_sam.c -o io_sam.o g++ -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o g++ -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pileup.cpp -o pileup.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pileupbam.c -o pileupbam.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools_patch.c -o samtools_patch.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c scan_bam_data.c -o scan_bam_data.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tabixfile.c -o tabixfile.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tagfilter.c -o tagfilter.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utilities.c -o utilities.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c zip_compression.c -o zip_compression.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bgzf.c -o samtools/bgzf.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/kstring.c -o samtools/kstring.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_aux.c -o samtools/bam_aux.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam.c -o samtools/bam.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_import.c -o samtools/bam_import.o In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/limits.h:26, from /usr/lib/gcc/x86_64-linux-gnu/8/include-fixed/limits.h:194, from /usr/lib/gcc/x86_64-linux-gnu/8/include-fixed/syslimits.h:7, from /usr/lib/gcc/x86_64-linux-gnu/8/include-fixed/limits.h:34, from /usr/include/zconf.h:418, from /usr/include/zlib.h:34, from samtools/bam_import.c:3: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/sam.c -o samtools/sam.o In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/string.h:26, from samtools/sam.c:3: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_index.c -o samtools/bam_index.o samtools/bam_index.c: In function 'bam_index_load_core': samtools/bam_index.c:335:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(magic, 1, 4, fp); ^~~~~~~~~~~~~~~~~~~~~~ samtools/bam_index.c:342:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&idx->n, 4, 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_pileup.c -o samtools/bam_pileup.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_md.c -o samtools/bam_md.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/razf.c -o samtools/razf.o samtools/razf.c: In function 'razf_flush': samtools/razf.c:221:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:234:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c: In function '_razf_write': samtools/razf.c:201:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c: In function 'razf_close': samtools/razf.c:810:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &rz->in, sizeof(int64_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:811:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &rz->out, sizeof(int64_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:814:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &v64, sizeof(int64_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:816:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &v64, sizeof(int64_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c: In function 'razf_end_flush': samtools/razf.c:258:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c: In function 'save_zindex': samtools/razf.c:96:12: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] if(is_be) write(fd, &rz->index->size, sizeof(int)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:99:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd, &v32, sizeof(uint32_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:106:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:107:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/faidx.c -o samtools/faidx.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/knetfile.c -o samtools/knetfile.o In file included from /usr/include/time.h:25, from samtools/knetfile.c:33: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from samtools/knetfile.c:49: samtools/knetfile.c: In function 'kftp_send_cmd': samtools/knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] #define netwrite(fd, ptr, len) write(fd, ptr, len) ^~~~~~~~~~~~~~~~~~~ samtools/knetfile.c:239:2: note: in expansion of macro 'netwrite' netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); ^~~~~~~~ samtools/knetfile.c: In function 'khttp_connect_file': samtools/knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] #define netwrite(fd, ptr, len) write(fd, ptr, len) ^~~~~~~~~~~~~~~~~~~ samtools/knetfile.c:418:2: note: in expansion of macro 'netwrite' netwrite(fp->fd, buf, l); ^~~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_sort.c -o samtools/bam_sort.o In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdlib.h:25, from samtools/bam_sort.c:3: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/sam_header.c -o samtools/sam_header.o In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/sam_header.c:3: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_reheader.c -o samtools/bam_reheader.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/kprobaln.c -o samtools/kprobaln.o ar -crus libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o ar: `u' modifier ignored since `D' is the default (see `U') gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/limits.h:26, from /usr/lib/gcc/x86_64-linux-gnu/8/include-fixed/limits.h:194, from /usr/lib/gcc/x86_64-linux-gnu/8/include-fixed/syslimits.h:7, from /usr/lib/gcc/x86_64-linux-gnu/8/include-fixed/limits.h:34, from /usr/include/zconf.h:418, from /usr/include/zlib.h:34, from samtools/bcftools/vcf.c:3: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o In file included from /usr/include/alloca.h:21, from samtools/bcftools/bcfutils.c:3: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/index.c -o samtools/bcftools/index.o In file included from /usr/include/assert.h:35, from samtools/bcftools/index.c:2: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o ar -crus libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o ar: `u' modifier ignored since `D' is the default (see `U') gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tabix/index.c -o tabix/index.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tabix/bedidx.c -o tabix/bedidx.o ar -crus libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o ar: `u' modifier ignored since `D' is the default (see `U') mkdir -p "/build/r-bioc-rsamtools-1.34.1/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/bcftools" mkdir -p "/build/r-bioc-rsamtools-1.34.1/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix" cp samtools/*.h "/build/r-bioc-rsamtools-1.34.1/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/" cp samtools/bcftools/*h "/build/r-bioc-rsamtools-1.34.1/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/bcftools/" cp tabix/*h "/build/r-bioc-rsamtools-1.34.1/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix/" cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \ "/build/r-bioc-rsamtools-1.34.1/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix/" mkdir -p "/build/r-bioc-rsamtools-1.34.1/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib" cp libbam.a libbcf.a libtabix.a "/build/r-bioc-rsamtools-1.34.1/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib" g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -pthread -fopenmp /build/r-bioc-rsamtools-1.34.1/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libbam.a /build/r-bioc-rsamtools-1.34.1/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libbcf.a /build/r-bioc-rsamtools-1.34.1/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libtabix.a -lz -L/usr/lib/R/lib -lR make[1]: Leaving directory '/build/r-bioc-rsamtools-1.34.1/src' make[1]: Entering directory '/build/r-bioc-rsamtools-1.34.1/src' make[1]: Leaving directory '/build/r-bioc-rsamtools-1.34.1/src' installing to /build/r-bioc-rsamtools-1.34.1/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/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 (Rsamtools) rm -f /build/r-bioc-rsamtools-1.34.1/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/LICENSE I: Using r-bioc-genomeinfodb for Depends:GenomeInfoDb (>= 1.1.3) I: Using r-bioc-genomicranges for Depends:GenomicRanges (>= 1.31.8) I: Using r-bioc-biostrings for Depends:Biostrings (>= 2.47.6) I: Using r-cran-runit for Recommends:runit I: Using r-bioc-shortread for Recommends:shortread I: Using r-bioc-genomicalignments for Suggests:GenomicAlignments I: Using r-bioc-genomicfeatures for Suggests:GenomicFeatures W: Cannot find a debian package for Suggests:TxDb.Dmelanogaster.UCSC.dm3.ensGene W: Cannot find a debian package for Suggests:KEGG.db W: Cannot find a debian package for Suggests:TxDb.Hsapiens.UCSC.hg18.knownGene W: Cannot find a debian package for Suggests:RNAseqData.HNRNPC.bam.chr14 W: Cannot find a debian package for Suggests:BSgenome.Hsapiens.UCSC.hg19 W: Cannot find a debian package for Suggests:BiocStyle I: Using r-bioc-biocgenerics for Imports:BiocGenerics (>= 0.25.1) I: Using r-bioc-s4vectors for Imports:S4Vectors (>= 0.17.25) I: Using r-bioc-iranges for Imports:IRanges (>= 2.13.12) I: Using r-bioc-xvector for Imports:XVector (>= 0.19.7) I: Using r-bioc-zlibbioc for Imports:zlibbioc I: Using r-cran-bitops for Imports:bitops I: Using r-bioc-biocparallel for Imports:BiocParallel I: BioConductor API version: r-api-bioc-3.8 Create lintian-override for package-contains-documentation-outside-usr-share-doc due to debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/extdata/tophat/README dh_installdocs -O--buildsystem=R dh_installchangelogs -O--buildsystem=R dh_installinit -O--buildsystem=R dh_installsystemduser -O--buildsystem=R dh_lintian -O--buildsystem=R dh_perl -O--buildsystem=R dh_link -O--buildsystem=R dh_strip_nondeterminism -O--buildsystem=R dh_compress -O--buildsystem=R dh_fixperms -O--buildsystem=R dh_missing -O--buildsystem=R dh_dwz -O--buildsystem=R dh_strip -O--buildsystem=R dh_makeshlibs -O--buildsystem=R dh_shlibdeps -O--buildsystem=R dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/libs/Rsamtools.so was not linked against libgomp.so.1 (it uses none of the library's symbols) dh_installdeb -O--buildsystem=R dh_gencontrol -O--buildsystem=R dh_md5sums -O--buildsystem=R dh_builddeb -O--buildsystem=R dpkg-deb: building package 'r-bioc-rsamtools-dbgsym' in '../r-bioc-rsamtools-dbgsym_1.34.1-1_amd64.deb'. dpkg-deb: building package 'r-bioc-rsamtools' in '../r-bioc-rsamtools_1.34.1-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../r-bioc-rsamtools_1.34.1-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/15452/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/15452/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/15452 and its subdirectories I: Current time: Sun Jul 18 02:50:09 +14 2021 I: pbuilder-time-stamp: 1626526209