I: pbuilder: network access will be disabled during build I: Current time: Sat Apr 6 02:46:43 +14 2024 I: pbuilder-time-stamp: 1712321203 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. 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 [reapr_1.0.18+dfsg-6.dsc] I: copying [./reapr_1.0.18+dfsg.orig.tar.gz] I: copying [./reapr_1.0.18+dfsg-6.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Apr 5 06:59:25 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./reapr_1.0.18+dfsg-6.dsc: no acceptable signature found dpkg-source: info: extracting reapr in reapr-1.0.18+dfsg dpkg-source: info: unpacking reapr_1.0.18+dfsg.orig.tar.gz dpkg-source: info: unpacking reapr_1.0.18+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling dpkg-source: info: applying use_shared_libs dpkg-source: info: applying hardening dpkg-source: info: applying fix_sort_samtools13 dpkg-source: info: applying ld_as_needed I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/8061/tmp/hooks/D01_modify_environment starting debug: Running on virt64z. 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 '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Apr 5 12:46 /bin/sh -> /bin/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/8061/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/8061/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=1a2bd815c5af4085a3263f9724ad89bc LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf 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=8061 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/r-b-build.bwPamMOD/pbuilderrc_TcuN --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bwPamMOD/b2 --logfile b2/build.log reapr_1.0.18+dfsg-6.dsc' SUDO_GID=110 SUDO_UID=103 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-18-arm64 #1 SMP Debian 6.1.76-1 (2024-02-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 5 07:43 /bin -> usr/bin I: user script /srv/workspace/pbuilder/8061/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: armhf 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-compat (= 13), libbamtools-dev, libtabixpp-dev, libhts-dev, zlib1g-dev, asciidoctor, samtools, bamtools, smalt, r-base, snpomatic, tabix, libfile-copy-link-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19466 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-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libtabixpp-dev; however: Package libtabixpp-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on bamtools; however: Package bamtools is not installed. pbuilder-satisfydepends-dummy depends on smalt; however: Package smalt is not installed. pbuilder-satisfydepends-dummy depends on r-base; however: Package r-base is not installed. pbuilder-satisfydepends-dummy depends on snpomatic; however: Package snpomatic is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on libfile-copy-link-perl; however: Package libfile-copy-link-perl 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: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bamtools{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbambamc0{a} libbamtools-dev{a} libbamtools2.5.2{a} libblas3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdatrie1{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libedit2{a} libelf1t64{a} libexpat1{a} libfile-copy-link-perl{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libice6{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblerc4{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{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} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpsl5t64{a} libreadline8t64{a} librtmp1{a} libruby{a} libruby3.1t64{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libsub-override-perl{a} libtabixpp-dev{a} libtabixpp0t64{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{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} libxrender1{a} libxss1{a} libxt6t64{a} libyaml-0-2{a} m4{a} man-db{a} openssl{a} po-debconf{a} r-base{a} r-base-core{a} r-cran-boot{a} r-cran-class{a} r-cran-cluster{a} r-cran-codetools{a} r-cran-foreign{a} r-cran-kernsmooth{a} r-cran-lattice{a} r-cran-mass{a} r-cran-matrix{a} r-cran-mgcv{a} r-cran-nlme{a} r-cran-nnet{a} r-cran-rpart{a} r-cran-spatial{a} r-cran-survival{a} r-recommended{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} samtools{a} sensible-utils{a} smalt{a} snpomatic{a} tabix{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl libnet-dbus-perl libx11-protocol-perl lynx publicsuffix r-base-dev r-base-html r-doc-html shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 157 newly installed, 0 to remove and 0 not upgraded. Need to get 97.2 MB of archives. After unpacking 223 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf tzdata all 2024a-1 [255 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf readline-common all 8.2-4 [69.3 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf openssl armhf 3.2.1-3 [1326 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf ca-certificates all 20240203 [158 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-3+b1 [1091 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.39.3-11 [82.5 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.12.0-4 [1373 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf ucf all 3.0043+nmu1 [55.2 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf rubygems-integration all 1.18 [6704 B] Get: 17 http://deb.debian.org/debian unstable/main armhf rake all 13.2.0-1 [65.1 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf ruby-webrick all 1.8.1-1 [51.4 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf ruby-sdbm armhf 1.0.0-5+b3 [13.3 kB] Get: 22 http://deb.debian.org/debian unstable/main armhf libbsd0 armhf 0.12.2-1 [127 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf libedit2 armhf 3.1-20230828-1 [76.8 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf libncurses6 armhf 6.4+20240113-1 [81.8 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf libyaml-0-2 armhf 0.2.5-1 [46.8 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf libruby3.1t64 armhf 3.1.2-8.3 [5068 kB] Get: 27 http://deb.debian.org/debian unstable/main armhf ruby3.1 armhf 3.1.2-8.3 [663 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf libruby armhf 1:3.1+nmu1 [4664 B] Get: 29 http://deb.debian.org/debian unstable/main armhf ruby-rubygems all 3.4.20-1 [309 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf ruby armhf 1:3.1+nmu1 [5584 B] Get: 31 http://deb.debian.org/debian unstable/main armhf ruby-asciidoctor all 2.0.20-1 [212 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf asciidoctor all 2.0.20-1 [87.7 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf autoconf all 2.71-3 [332 kB] Get: 35 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf autopoint all 0.21-14 [496 kB] Get: 38 http://deb.debian.org/debian unstable/main armhf libbamtools2.5.2 armhf 2.5.2+dfsg-5 [139 kB] Get: 39 http://deb.debian.org/debian unstable/main armhf libjsoncpp25 armhf 1.9.5-6+b2 [69.9 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf bamtools armhf 2.5.2+dfsg-5 [175 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-7 [517 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 44 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 48 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.191-1 [183 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b1 [106 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 54 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 55 http://deb.debian.org/debian unstable/main armhf debhelper all 13.15.3 [901 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.2-1 [83.5 kB] Get: 57 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 58 http://deb.debian.org/debian unstable/main armhf libpng16-16t64 armhf 1.6.43-5 [262 kB] Get: 59 http://deb.debian.org/debian unstable/main armhf libfreetype6 armhf 2.13.2+dfsg-1+b2 [372 kB] Get: 60 http://deb.debian.org/debian unstable/main armhf fonts-dejavu-mono all 2.37-8 [489 kB] Get: 61 http://deb.debian.org/debian unstable/main armhf fonts-dejavu-core all 2.37-8 [840 kB] Get: 62 http://deb.debian.org/debian unstable/main armhf fontconfig-config armhf 2.15.0-1.1 [317 kB] Get: 63 http://deb.debian.org/debian unstable/main armhf libfontconfig1 armhf 2.15.0-1.1 [370 kB] Get: 64 http://deb.debian.org/debian unstable/main armhf fontconfig armhf 2.15.0-1.1 [461 kB] Get: 65 http://deb.debian.org/debian unstable/main armhf libbambamc0 armhf 0.0.50-6+b1 [32.7 kB] Get: 66 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg-3.1 [904 kB] Get: 67 http://deb.debian.org/debian unstable/main armhf libbamtools-dev armhf 2.5.2+dfsg-5 [206 kB] Get: 68 http://deb.debian.org/debian unstable/main armhf libblas3 armhf 3.12.0-3 [108 kB] Get: 69 http://deb.debian.org/debian unstable/main armhf libpixman-1-0 armhf 0.42.2-1+b1 [476 kB] Get: 70 http://deb.debian.org/debian unstable/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 71 http://deb.debian.org/debian unstable/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 72 http://deb.debian.org/debian unstable/main armhf libxcb1 armhf 1.15-1 [140 kB] Get: 73 http://deb.debian.org/debian unstable/main armhf libx11-data all 2:1.8.7-1 [328 kB] Get: 74 http://deb.debian.org/debian unstable/main armhf libx11-6 armhf 2:1.8.7-1 [735 kB] Get: 75 http://deb.debian.org/debian unstable/main armhf libxcb-render0 armhf 1.15-1 [114 kB] Get: 76 http://deb.debian.org/debian unstable/main armhf libxcb-shm0 armhf 1.15-1 [106 kB] Get: 77 http://deb.debian.org/debian unstable/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB] Get: 78 http://deb.debian.org/debian unstable/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.1 kB] Get: 79 http://deb.debian.org/debian unstable/main armhf libcairo2 armhf 1.18.0-3 [441 kB] Get: 80 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.0-2.4 [19.5 kB] Get: 81 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.20.1-6+b1 [30.6 kB] Get: 82 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.20.1-6+b1 [75.5 kB] Get: 83 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-3 [7908 B] Get: 84 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.20.1-6+b1 [290 kB] Get: 85 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.20.1-6+b1 [112 kB] Get: 86 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.61.0-1 [63.0 kB] Get: 87 http://deb.debian.org/debian unstable/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.6 kB] Get: 88 http://deb.debian.org/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b3 [53.2 kB] Get: 89 http://deb.debian.org/debian unstable/main armhf libssh2-1t64 armhf 1.11.0-4.1+b1 [198 kB] Get: 90 http://deb.debian.org/debian unstable/main armhf libcurl3t64-gnutls armhf 8.7.1-2 [383 kB] Get: 91 http://deb.debian.org/debian unstable/main armhf libcurl4-gnutls-dev armhf 8.7.1-2 [498 kB] Get: 92 http://deb.debian.org/debian unstable/main armhf libcurl4t64 armhf 8.7.1-2 [391 kB] Get: 93 http://deb.debian.org/debian unstable/main armhf libdatrie1 armhf 0.2.13-3 [34.4 kB] Get: 94 http://deb.debian.org/debian unstable/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 95 http://deb.debian.org/debian unstable/main armhf libdeflate-dev armhf 1.20-1 [44.0 kB] Get: 96 http://deb.debian.org/debian unstable/main armhf libfile-copy-link-perl all 0.140-5 [13.2 kB] Get: 97 http://deb.debian.org/debian unstable/main armhf libfribidi0 armhf 1.0.13-3+b1 [69.4 kB] Get: 98 http://deb.debian.org/debian unstable/main armhf libgfortran5 armhf 14-20240330-1 [264 kB] Get: 99 http://deb.debian.org/debian unstable/main armhf libglib2.0-0t64 armhf 2.78.4-6 [1053 kB] Get: 100 http://deb.debian.org/debian unstable/main armhf libgraphite2-3 armhf 1.3.14-2 [63.2 kB] Get: 101 http://deb.debian.org/debian unstable/main armhf libharfbuzz0b armhf 8.3.0-2+b1 [2156 kB] Get: 102 http://deb.debian.org/debian unstable/main armhf libhtscodecs2 armhf 1.6.0-1+b1 [61.3 kB] Get: 103 http://deb.debian.org/debian unstable/main armhf libhts3t64 armhf 1.19+ds-1.1+b1 [395 kB] Get: 104 http://deb.debian.org/debian unstable/main armhf liblzma-dev armhf 5.6.1+really5.4.5-1 [281 kB] Get: 105 http://deb.debian.org/debian unstable/main armhf libhts-dev armhf 1.19+ds-1.1+b1 [1598 kB] Get: 106 http://deb.debian.org/debian unstable/main armhf x11-common all 1:7.7+23 [252 kB] Get: 107 http://deb.debian.org/debian unstable/main armhf libice6 armhf 2:1.0.10-1 [51.9 kB] Get: 108 http://deb.debian.org/debian unstable/main armhf libjbig0 armhf 2.1-6.1+b1 [27.3 kB] Get: 109 http://deb.debian.org/debian unstable/main armhf libjpeg62-turbo armhf 1:2.1.5-2+b2 [143 kB] Get: 110 http://deb.debian.org/debian unstable/main armhf liblapack3 armhf 3.12.0-3 [1803 kB] Get: 111 http://deb.debian.org/debian unstable/main armhf liblerc4 armhf 4.0.0+ds-4+b1 [137 kB] Get: 112 http://deb.debian.org/debian unstable/main armhf libthai-data all 0.1.29-2 [168 kB] Get: 113 http://deb.debian.org/debian unstable/main armhf libthai0 armhf 0.1.29-2 [45.8 kB] Get: 114 http://deb.debian.org/debian unstable/main armhf libpango-1.0-0 armhf 1.52.1+ds-1 [192 kB] Get: 115 http://deb.debian.org/debian unstable/main armhf libpangoft2-1.0-0 armhf 1.52.1+ds-1 [41.8 kB] Get: 116 http://deb.debian.org/debian unstable/main armhf libpangocairo-1.0-0 armhf 1.52.1+ds-1 [31.2 kB] Get: 117 http://deb.debian.org/debian unstable/main armhf libpaper1 armhf 1.1.29 [11.9 kB] Get: 118 http://deb.debian.org/debian unstable/main armhf libpaper-utils armhf 1.1.29 [8400 B] Get: 119 http://deb.debian.org/debian unstable/main armhf libreadline8t64 armhf 8.2-4 [145 kB] Get: 120 http://deb.debian.org/debian unstable/main armhf libsharpyuv0 armhf 1.3.2-0.4+b1 [106 kB] Get: 121 http://deb.debian.org/debian unstable/main armhf libsm6 armhf 2:1.2.3-1 [33.0 kB] Get: 122 http://deb.debian.org/debian unstable/main armhf libtabixpp0t64 armhf 1.1.2-2.1 [8956 B] Get: 123 http://deb.debian.org/debian unstable/main armhf libtabixpp-dev armhf 1.1.2-2.1 [8648 B] Get: 124 http://deb.debian.org/debian unstable/main armhf libtcl8.6 armhf 8.6.14+dfsg-1 [928 kB] Get: 125 http://deb.debian.org/debian unstable/main armhf libwebp7 armhf 1.3.2-0.4+b1 [262 kB] Get: 126 http://deb.debian.org/debian unstable/main armhf libtiff6 armhf 4.5.1+git230720-4 [301 kB] Get: 127 http://deb.debian.org/debian unstable/main armhf libtirpc-common all 1.3.4+ds-1.2 [10.9 kB] Get: 128 http://deb.debian.org/debian unstable/main armhf libtirpc3t64 armhf 1.3.4+ds-1.2 [71.0 kB] Get: 129 http://deb.debian.org/debian unstable/main armhf libxft2 armhf 2.3.6-1+b1 [46.4 kB] Get: 130 http://deb.debian.org/debian unstable/main armhf libxss1 armhf 1:1.2.3-1 [17.2 kB] Get: 131 http://deb.debian.org/debian unstable/main armhf libtk8.6 armhf 8.6.14-1 [693 kB] Get: 132 http://deb.debian.org/debian unstable/main armhf libxt6t64 armhf 1:1.2.1-1.2 [159 kB] Get: 133 http://deb.debian.org/debian unstable/main armhf zip armhf 3.0-13 [218 kB] Get: 134 http://deb.debian.org/debian unstable/main armhf unzip armhf 6.0-28 [152 kB] Get: 135 http://deb.debian.org/debian unstable/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 136 http://deb.debian.org/debian unstable/main armhf r-base-core armhf 4.3.3-3 [26.5 MB] Get: 137 http://deb.debian.org/debian unstable/main armhf r-cran-boot all 1.3-30-1 [622 kB] Get: 138 http://deb.debian.org/debian unstable/main armhf r-cran-cluster armhf 2.1.6-1 [562 kB] Get: 139 http://deb.debian.org/debian unstable/main armhf r-cran-foreign armhf 0.8.86-1 [244 kB] Get: 140 http://deb.debian.org/debian unstable/main armhf r-cran-mass armhf 7.3-60.0.1-1 [1116 kB] Get: 141 http://deb.debian.org/debian unstable/main armhf r-cran-kernsmooth armhf 2.23-22-1 [89.3 kB] Get: 142 http://deb.debian.org/debian unstable/main armhf r-cran-lattice armhf 0.22-6-1 [1391 kB] Get: 143 http://deb.debian.org/debian unstable/main armhf r-cran-nlme armhf 3.1.164-1 [2270 kB] Get: 144 http://deb.debian.org/debian unstable/main armhf r-cran-matrix armhf 1.6-5-1 [3707 kB] Get: 145 http://deb.debian.org/debian unstable/main armhf r-cran-mgcv armhf 1.9-1-1 [3191 kB] Get: 146 http://deb.debian.org/debian unstable/main armhf r-cran-survival armhf 3.5-8-1 [6129 kB] Get: 147 http://deb.debian.org/debian unstable/main armhf r-cran-rpart armhf 4.1.23-1 [680 kB] Get: 148 http://deb.debian.org/debian unstable/main armhf r-cran-class armhf 7.3-22-2 [86.2 kB] Get: 149 http://deb.debian.org/debian unstable/main armhf r-cran-nnet armhf 7.3-19-2 [110 kB] Get: 150 http://deb.debian.org/debian unstable/main armhf r-cran-spatial armhf 7.3-17-1 [126 kB] Get: 151 http://deb.debian.org/debian unstable/main armhf r-cran-codetools all 0.2-20-1 [91.1 kB] Get: 152 http://deb.debian.org/debian unstable/main armhf r-recommended all 4.3.3-3 [2572 B] Get: 153 http://deb.debian.org/debian unstable/main armhf r-base all 4.3.3-3 [14.1 kB] Get: 154 http://deb.debian.org/debian unstable/main armhf samtools armhf 1.19.2-1+b1 [614 kB] Get: 155 http://deb.debian.org/debian unstable/main armhf smalt armhf 0.7.6-13 [98.2 kB] Get: 156 http://deb.debian.org/debian unstable/main armhf snpomatic armhf 1.0-7 [69.1 kB] Get: 157 http://deb.debian.org/debian unstable/main armhf tabix armhf 1.19+ds-1.1+b1 [410 kB] Fetched 97.2 MB in 4s (27.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package tzdata. (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 ... 19466 files and directories currently installed.) Preparing to unpack .../000-tzdata_2024a-1_all.deb ... Unpacking tzdata (2024a-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../001-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.22_all.deb ... 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Preparing to unpack .../027-libruby_1%3a3.1+nmu1_armhf.deb ... Unpacking libruby:armhf (1:3.1+nmu1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../028-ruby-rubygems_3.4.20-1_all.deb ... Unpacking ruby-rubygems (3.4.20-1) ... Selecting previously unselected package ruby. Preparing to unpack .../029-ruby_1%3a3.1+nmu1_armhf.deb ... Unpacking ruby (1:3.1+nmu1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../030-ruby-asciidoctor_2.0.20-1_all.deb ... Unpacking ruby-asciidoctor (2.0.20-1) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../031-asciidoctor_2.0.20-1_all.deb ... Unpacking asciidoctor (2.0.20-1) ... Selecting previously unselected package m4. Preparing to unpack .../032-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../033-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../034-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../035-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../036-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libbamtools2.5.2:armhf. Preparing to unpack .../037-libbamtools2.5.2_2.5.2+dfsg-5_armhf.deb ... Unpacking libbamtools2.5.2:armhf (2.5.2+dfsg-5) ... Selecting previously unselected package libjsoncpp25:armhf. Preparing to unpack .../038-libjsoncpp25_1.9.5-6+b2_armhf.deb ... Unpacking libjsoncpp25:armhf (1.9.5-6+b2) ... Selecting previously unselected package bamtools. Preparing to unpack .../039-bamtools_2.5.2+dfsg-5_armhf.deb ... Unpacking bamtools (2.5.2+dfsg-5) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../040-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../041-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../042-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../043-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../044-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../045-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../046-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../047-libelf1t64_0.191-1_armhf.deb ... Unpacking libelf1t64:armhf (0.191-1) ... Selecting previously unselected package dwz. Preparing to unpack .../048-dwz_0.15-1+b1_armhf.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../049-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../050-libxml2_2.9.14+dfsg-1.3+b2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../051-gettext_0.21-14+b1_armhf.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../052-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../053-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../054-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../055-libexpat1_2.6.2-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.2-1) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../056-libbrotli1_1.1.0-2+b3_armhf.deb ... Unpacking libbrotli1:armhf (1.1.0-2+b3) ... Selecting previously unselected package libpng16-16t64:armhf. Preparing to unpack .../057-libpng16-16t64_1.6.43-5_armhf.deb ... Unpacking libpng16-16t64:armhf (1.6.43-5) ... Selecting previously unselected package libfreetype6:armhf. Preparing to unpack .../058-libfreetype6_2.13.2+dfsg-1+b2_armhf.deb ... Unpacking libfreetype6:armhf (2.13.2+dfsg-1+b2) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../059-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../060-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../061-fontconfig-config_2.15.0-1.1_armhf.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package libfontconfig1:armhf. Preparing to unpack .../062-libfontconfig1_2.15.0-1.1_armhf.deb ... Unpacking libfontconfig1:armhf (2.15.0-1.1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../063-fontconfig_2.15.0-1.1_armhf.deb ... Unpacking fontconfig (2.15.0-1.1) ... Selecting previously unselected package libbambamc0:armhf. Preparing to unpack .../064-libbambamc0_0.0.50-6+b1_armhf.deb ... Unpacking libbambamc0:armhf (0.0.50-6+b1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../065-zlib1g-dev_1%3a1.3.dfsg-3.1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.3.dfsg-3.1) ... Selecting previously unselected package libbamtools-dev:armhf. Preparing to unpack .../066-libbamtools-dev_2.5.2+dfsg-5_armhf.deb ... Unpacking libbamtools-dev:armhf (2.5.2+dfsg-5) ... Selecting previously unselected package libblas3:armhf. Preparing to unpack .../067-libblas3_3.12.0-3_armhf.deb ... Unpacking libblas3:armhf (3.12.0-3) ... Selecting previously unselected package libpixman-1-0:armhf. Preparing to unpack .../068-libpixman-1-0_0.42.2-1+b1_armhf.deb ... Unpacking libpixman-1-0:armhf (0.42.2-1+b1) ... Selecting previously unselected package libxau6:armhf. Preparing to unpack .../069-libxau6_1%3a1.0.9-1_armhf.deb ... Unpacking libxau6:armhf (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:armhf. Preparing to unpack .../070-libxdmcp6_1%3a1.1.2-3_armhf.deb ... Unpacking libxdmcp6:armhf (1:1.1.2-3) ... Selecting previously unselected package libxcb1:armhf. Preparing to unpack .../071-libxcb1_1.15-1_armhf.deb ... Unpacking libxcb1:armhf (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../072-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:armhf. Preparing to unpack .../073-libx11-6_2%3a1.8.7-1_armhf.deb ... Unpacking libx11-6:armhf (2:1.8.7-1) ... Selecting previously unselected package libxcb-render0:armhf. Preparing to unpack .../074-libxcb-render0_1.15-1_armhf.deb ... Unpacking libxcb-render0:armhf (1.15-1) ... Selecting previously unselected package libxcb-shm0:armhf. Preparing to unpack .../075-libxcb-shm0_1.15-1_armhf.deb ... Unpacking libxcb-shm0:armhf (1.15-1) ... Selecting previously unselected package libxext6:armhf. Preparing to unpack .../076-libxext6_2%3a1.3.4-1+b1_armhf.deb ... Unpacking libxext6:armhf (2:1.3.4-1+b1) ... Selecting previously unselected package libxrender1:armhf. Preparing to unpack .../077-libxrender1_1%3a0.9.10-1.1_armhf.deb ... Unpacking libxrender1:armhf (1:0.9.10-1.1) ... Selecting previously unselected package libcairo2:armhf. Preparing to unpack .../078-libcairo2_1.18.0-3_armhf.deb ... Unpacking libcairo2:armhf (1.18.0-3) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../079-libcom-err2_1.47.0-2.4_armhf.deb ... Unpacking libcom-err2:armhf (1.47.0-2.4) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../080-libkrb5support0_1.20.1-6+b1_armhf.deb ... Unpacking libkrb5support0:armhf (1.20.1-6+b1) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../081-libk5crypto3_1.20.1-6+b1_armhf.deb ... Unpacking libk5crypto3:armhf (1.20.1-6+b1) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../082-libkeyutils1_1.6.3-3_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-3) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../083-libkrb5-3_1.20.1-6+b1_armhf.deb ... Unpacking libkrb5-3:armhf (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../084-libgssapi-krb5-2_1.20.1-6+b1_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.20.1-6+b1) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../085-libnghttp2-14_1.61.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.61.0-1) ... Selecting previously unselected package libpsl5t64:armhf. 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Unpacking libcurl4t64:armhf (8.7.1-2) ... Selecting previously unselected package libdatrie1:armhf. Preparing to unpack .../092-libdatrie1_0.2.13-3_armhf.deb ... Unpacking libdatrie1:armhf (0.2.13-3) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../093-libdeflate0_1.20-1_armhf.deb ... Unpacking libdeflate0:armhf (1.20-1) ... Selecting previously unselected package libdeflate-dev:armhf. Preparing to unpack .../094-libdeflate-dev_1.20-1_armhf.deb ... Unpacking libdeflate-dev:armhf (1.20-1) ... Selecting previously unselected package libfile-copy-link-perl. Preparing to unpack .../095-libfile-copy-link-perl_0.140-5_all.deb ... Unpacking libfile-copy-link-perl (0.140-5) ... Selecting previously unselected package libfribidi0:armhf. Preparing to unpack .../096-libfribidi0_1.0.13-3+b1_armhf.deb ... Unpacking libfribidi0:armhf (1.0.13-3+b1) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../097-libgfortran5_14-20240330-1_armhf.deb ... Unpacking libgfortran5:armhf (14-20240330-1) ... Selecting previously unselected package libglib2.0-0t64:armhf. Preparing to unpack .../098-libglib2.0-0t64_2.78.4-6_armhf.deb ... Unpacking libglib2.0-0t64:armhf (2.78.4-6) ... Selecting previously unselected package libgraphite2-3:armhf. Preparing to unpack .../099-libgraphite2-3_1.3.14-2_armhf.deb ... Unpacking libgraphite2-3:armhf (1.3.14-2) ... Selecting previously unselected package libharfbuzz0b:armhf. Preparing to unpack .../100-libharfbuzz0b_8.3.0-2+b1_armhf.deb ... Unpacking libharfbuzz0b:armhf (8.3.0-2+b1) ... Selecting previously unselected package libhtscodecs2:armhf. Preparing to unpack .../101-libhtscodecs2_1.6.0-1+b1_armhf.deb ... Unpacking libhtscodecs2:armhf (1.6.0-1+b1) ... Selecting previously unselected package libhts3t64:armhf. Preparing to unpack .../102-libhts3t64_1.19+ds-1.1+b1_armhf.deb ... Unpacking libhts3t64:armhf (1.19+ds-1.1+b1) ... Selecting previously unselected package liblzma-dev:armhf. Preparing to unpack .../103-liblzma-dev_5.6.1+really5.4.5-1_armhf.deb ... Unpacking liblzma-dev:armhf (5.6.1+really5.4.5-1) ... Selecting previously unselected package libhts-dev:armhf. Preparing to unpack .../104-libhts-dev_1.19+ds-1.1+b1_armhf.deb ... Unpacking libhts-dev:armhf (1.19+ds-1.1+b1) ... Selecting previously unselected package x11-common. Preparing to unpack .../105-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package libice6:armhf. Preparing to unpack .../106-libice6_2%3a1.0.10-1_armhf.deb ... Unpacking libice6:armhf (2:1.0.10-1) ... Selecting previously unselected package libjbig0:armhf. Preparing to unpack .../107-libjbig0_2.1-6.1+b1_armhf.deb ... Unpacking libjbig0:armhf (2.1-6.1+b1) ... Selecting previously unselected package libjpeg62-turbo:armhf. Preparing to unpack .../108-libjpeg62-turbo_1%3a2.1.5-2+b2_armhf.deb ... Unpacking libjpeg62-turbo:armhf (1:2.1.5-2+b2) ... Selecting previously unselected package liblapack3:armhf. Preparing to unpack .../109-liblapack3_3.12.0-3_armhf.deb ... Unpacking liblapack3:armhf (3.12.0-3) ... Selecting previously unselected package liblerc4:armhf. Preparing to unpack .../110-liblerc4_4.0.0+ds-4+b1_armhf.deb ... Unpacking liblerc4:armhf (4.0.0+ds-4+b1) ... Selecting previously unselected package libthai-data. Preparing to unpack .../111-libthai-data_0.1.29-2_all.deb ... Unpacking libthai-data (0.1.29-2) ... Selecting previously unselected package libthai0:armhf. Preparing to unpack .../112-libthai0_0.1.29-2_armhf.deb ... Unpacking libthai0:armhf (0.1.29-2) ... Selecting previously unselected package libpango-1.0-0:armhf. Preparing to unpack .../113-libpango-1.0-0_1.52.1+ds-1_armhf.deb ... Unpacking libpango-1.0-0:armhf (1.52.1+ds-1) ... Selecting previously unselected package libpangoft2-1.0-0:armhf. Preparing to unpack .../114-libpangoft2-1.0-0_1.52.1+ds-1_armhf.deb ... Unpacking libpangoft2-1.0-0:armhf (1.52.1+ds-1) ... Selecting previously unselected package libpangocairo-1.0-0:armhf. Preparing to unpack .../115-libpangocairo-1.0-0_1.52.1+ds-1_armhf.deb ... Unpacking libpangocairo-1.0-0:armhf (1.52.1+ds-1) ... Selecting previously unselected package libpaper1:armhf. Preparing to unpack .../116-libpaper1_1.1.29_armhf.deb ... Unpacking libpaper1:armhf (1.1.29) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../117-libpaper-utils_1.1.29_armhf.deb ... Unpacking libpaper-utils (1.1.29) ... Selecting previously unselected package libreadline8t64:armhf. Preparing to unpack .../118-libreadline8t64_8.2-4_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-4) ... Selecting previously unselected package libsharpyuv0:armhf. Preparing to unpack .../119-libsharpyuv0_1.3.2-0.4+b1_armhf.deb ... Unpacking libsharpyuv0:armhf (1.3.2-0.4+b1) ... Selecting previously unselected package libsm6:armhf. Preparing to unpack .../120-libsm6_2%3a1.2.3-1_armhf.deb ... Unpacking libsm6:armhf (2:1.2.3-1) ... Selecting previously unselected package libtabixpp0t64:armhf. Preparing to unpack .../121-libtabixpp0t64_1.1.2-2.1_armhf.deb ... Unpacking libtabixpp0t64:armhf (1.1.2-2.1) ... Selecting previously unselected package libtabixpp-dev:armhf. Preparing to unpack .../122-libtabixpp-dev_1.1.2-2.1_armhf.deb ... Unpacking libtabixpp-dev:armhf (1.1.2-2.1) ... Selecting previously unselected package libtcl8.6:armhf. Preparing to unpack .../123-libtcl8.6_8.6.14+dfsg-1_armhf.deb ... Unpacking libtcl8.6:armhf (8.6.14+dfsg-1) ... Selecting previously unselected package libwebp7:armhf. Preparing to unpack .../124-libwebp7_1.3.2-0.4+b1_armhf.deb ... Unpacking libwebp7:armhf (1.3.2-0.4+b1) ... Selecting previously unselected package libtiff6:armhf. Preparing to unpack .../125-libtiff6_4.5.1+git230720-4_armhf.deb ... Unpacking libtiff6:armhf (4.5.1+git230720-4) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../126-libtirpc-common_1.3.4+ds-1.2_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.2) ... Selecting previously unselected package libtirpc3t64:armhf. Preparing to unpack .../127-libtirpc3t64_1.3.4+ds-1.2_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:armhf (1.3.4+ds-1.2) ... Selecting previously unselected package libxft2:armhf. Preparing to unpack .../128-libxft2_2.3.6-1+b1_armhf.deb ... Unpacking libxft2:armhf (2.3.6-1+b1) ... Selecting previously unselected package libxss1:armhf. Preparing to unpack .../129-libxss1_1%3a1.2.3-1_armhf.deb ... Unpacking libxss1:armhf (1:1.2.3-1) ... Selecting previously unselected package libtk8.6:armhf. Preparing to unpack .../130-libtk8.6_8.6.14-1_armhf.deb ... Unpacking libtk8.6:armhf (8.6.14-1) ... Selecting previously unselected package libxt6t64:armhf. Preparing to unpack .../131-libxt6t64_1%3a1.2.1-1.2_armhf.deb ... Unpacking libxt6t64:armhf (1:1.2.1-1.2) ... Selecting previously unselected package zip. Preparing to unpack .../132-zip_3.0-13_armhf.deb ... Unpacking zip (3.0-13) ... Selecting previously unselected package unzip. Preparing to unpack .../133-unzip_6.0-28_armhf.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../134-xdg-utils_1.1.3-4.1_all.deb ... Unpacking xdg-utils (1.1.3-4.1) ... Selecting previously unselected package r-base-core. Preparing to unpack .../135-r-base-core_4.3.3-3_armhf.deb ... Unpacking r-base-core (4.3.3-3) ... Selecting previously unselected package r-cran-boot. Preparing to unpack .../136-r-cran-boot_1.3-30-1_all.deb ... Unpacking r-cran-boot (1.3-30-1) ... Selecting previously unselected package r-cran-cluster. Preparing to unpack .../137-r-cran-cluster_2.1.6-1_armhf.deb ... Unpacking r-cran-cluster (2.1.6-1) ... Selecting previously unselected package r-cran-foreign. Preparing to unpack .../138-r-cran-foreign_0.8.86-1_armhf.deb ... Unpacking r-cran-foreign (0.8.86-1) ... Selecting previously unselected package r-cran-mass. Preparing to unpack .../139-r-cran-mass_7.3-60.0.1-1_armhf.deb ... Unpacking r-cran-mass (7.3-60.0.1-1) ... Selecting previously unselected package r-cran-kernsmooth. Preparing to unpack .../140-r-cran-kernsmooth_2.23-22-1_armhf.deb ... Unpacking r-cran-kernsmooth (2.23-22-1) ... Selecting previously unselected package r-cran-lattice. Preparing to unpack .../141-r-cran-lattice_0.22-6-1_armhf.deb ... Unpacking r-cran-lattice (0.22-6-1) ... Selecting previously unselected package r-cran-nlme. Preparing to unpack .../142-r-cran-nlme_3.1.164-1_armhf.deb ... Unpacking r-cran-nlme (3.1.164-1) ... Selecting previously unselected package r-cran-matrix. Preparing to unpack .../143-r-cran-matrix_1.6-5-1_armhf.deb ... Unpacking r-cran-matrix (1.6-5-1) ... Selecting previously unselected package r-cran-mgcv. Preparing to unpack .../144-r-cran-mgcv_1.9-1-1_armhf.deb ... Unpacking r-cran-mgcv (1.9-1-1) ... Selecting previously unselected package r-cran-survival. Preparing to unpack .../145-r-cran-survival_3.5-8-1_armhf.deb ... Unpacking r-cran-survival (3.5-8-1) ... Selecting previously unselected package r-cran-rpart. Preparing to unpack .../146-r-cran-rpart_4.1.23-1_armhf.deb ... Unpacking r-cran-rpart (4.1.23-1) ... Selecting previously unselected package r-cran-class. Preparing to unpack .../147-r-cran-class_7.3-22-2_armhf.deb ... Unpacking r-cran-class (7.3-22-2) ... Selecting previously unselected package r-cran-nnet. Preparing to unpack .../148-r-cran-nnet_7.3-19-2_armhf.deb ... Unpacking r-cran-nnet (7.3-19-2) ... Selecting previously unselected package r-cran-spatial. Preparing to unpack .../149-r-cran-spatial_7.3-17-1_armhf.deb ... Unpacking r-cran-spatial (7.3-17-1) ... Selecting previously unselected package r-cran-codetools. Preparing to unpack .../150-r-cran-codetools_0.2-20-1_all.deb ... Unpacking r-cran-codetools (0.2-20-1) ... Selecting previously unselected package r-recommended. Preparing to unpack .../151-r-recommended_4.3.3-3_all.deb ... Unpacking r-recommended (4.3.3-3) ... Selecting previously unselected package r-base. Preparing to unpack .../152-r-base_4.3.3-3_all.deb ... Unpacking r-base (4.3.3-3) ... Selecting previously unselected package samtools. Preparing to unpack .../153-samtools_1.19.2-1+b1_armhf.deb ... Unpacking samtools (1.19.2-1+b1) ... Selecting previously unselected package smalt. Preparing to unpack .../154-smalt_0.7.6-13_armhf.deb ... Unpacking smalt (0.7.6-13) ... Selecting previously unselected package snpomatic. Preparing to unpack .../155-snpomatic_1.0-7_armhf.deb ... Unpacking snpomatic (1.0-7) ... Selecting previously unselected package tabix. Preparing to unpack .../156-tabix_1.19+ds-1.1+b1_armhf.deb ... Unpacking tabix (1.19+ds-1.1+b1) ... Setting up libhtscodecs2:armhf (1.6.0-1+b1) ... Setting up libexpat1:armhf (2.6.2-1) ... Setting up libpipeline1:armhf (1.5.7-2) ... Setting up libgraphite2-3:armhf (1.3.14-2) ... Setting up libpixman-1-0:armhf (0.42.2-1+b1) ... Setting up libsharpyuv0:armhf (1.3.2-0.4+b1) ... Setting up libxau6:armhf (1:1.0.9-1) ... Setting up libkeyutils1:armhf (1.6.3-3) ... Setting up libfile-copy-link-perl (0.140-5) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up liblerc4:armhf (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.39.3-11) ... Setting up libdatrie1:armhf (0.2.13-3) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:armhf (0.2.5-1) ... Setting up libtirpc-common (1.3.4+ds-1.2) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:armhf (1.1.0-2+b3) ... Setting up libmagic1t64:armhf (1:5.45-3) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libpsl5t64:armhf (0.21.2-1.1) ... Setting up libnghttp2-14:armhf (1.61.0-1) ... Setting up libdeflate0:armhf (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:armhf (1.47.0-2.4) ... Setting up file (1:5.45-3) ... Setting up libjbig0:armhf (2.1-6.1+b1) ... Setting up libelf1t64:armhf (0.191-1) ... Setting up libkrb5support0:armhf (1.20.1-6+b1) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Apr 5 12:48:32 UTC 2024. Universal Time is now: Fri Apr 5 12:48:32 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-13) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:armhf (2.78.4-6) ... No schema files found: doing nothing. Setting up libblas3:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libjpeg62-turbo:armhf (1:2.1.5-2+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b3) ... Setting up libncurses6:armhf (6.4+20240113-1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libfribidi0:armhf (1.0.13-3+b1) ... Setting up libbambamc0:armhf (0.0.50-6+b1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:armhf (1.6.43-5) ... Setting up libtcl8.6:armhf (8.6.14+dfsg-1) ... Setting up autopoint (0.21-14) ... Setting up libjsoncpp25:armhf (1.9.5-6+b2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:armhf (1.20.1-6+b1) ... Setting up libbamtools2.5.2:armhf (2.5.2+dfsg-5) ... Setting up libgfortran5:armhf (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:armhf (1.3.2-0.4+b1) ... Setting up ruby-webrick (1.8.1-1) ... Setting up liblzma-dev:armhf (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libtiff6:armhf (4.5.1+git230720-4) ... Setting up bamtools (2.5.2+dfsg-5) ... Setting up snpomatic (1.0-7) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libthai-data (0.1.29-2) ... Setting up libkrb5-3:armhf (1.20.1-6+b1) ... Setting up libssh2-1t64:armhf (1.11.0-4.1+b1) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:armhf (0.12.2-1) ... Setting up libdeflate-dev:armhf (1.20-1) ... Setting up tabix (1.19+ds-1.1+b1) ... Setting up readline-common (8.2-4) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up smalt (0.7.6-13) ... Setting up libice6:armhf (2:1.0.10-1) ... Setting up libxdmcp6:armhf (1:1.1.2-3) ... Setting up liblapack3:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libxcb1:armhf (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:armhf (1.15-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libedit2:armhf (3.1-20230828-1) ... Setting up libxcb-shm0:armhf (1.15-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:armhf (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libfreetype6:armhf (2.13.2+dfsg-1+b2) ... Setting up libbamtools-dev:armhf (2.5.2+dfsg-5) ... Setting up libgssapi-krb5-2:armhf (1.20.1-6+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up libreadline8t64:armhf (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up libx11-6:armhf (2:1.8.7-1) ... Setting up libharfbuzz0b:armhf (8.3.0-2+b1) ... Setting up libfontconfig1:armhf (2.15.0-1.1) ... Setting up libsm6:armhf (2:1.2.3-1) ... Setting up libpaper1:armhf (1.1.29) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libxrender1:armhf (1:0.9.10-1.1) ... Setting up libcurl4t64:armhf (8.7.1-2) ... Setting up libtirpc3t64:armhf (1.3.4+ds-1.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:armhf (1.52.1+ds-1) ... Setting up libcurl3t64-gnutls:armhf (8.7.1-2) ... Setting up libxext6:armhf (2:1.3.4-1+b1) ... Setting up rubygems-integration (1.18) ... Setting up libpaper-utils (1.1.29) ... Setting up libcurl4-gnutls-dev:armhf (8.7.1-2) ... Setting up man-db (2.12.0-4) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:armhf (1.18.0-3) ... Setting up libxt6t64:armhf (1:1.2.1-1.2) ... Setting up libhts3t64:armhf (1.19+ds-1.1+b1) ... Setting up libxss1:armhf (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:armhf (1.52.1+ds-1) ... Setting up libpangocairo-1.0-0:armhf (1.52.1+ds-1) ... Setting up libxft2:armhf (2.3.6-1+b1) ... Setting up libtk8.6:armhf (8.6.14-1) ... Setting up libhts-dev:armhf (1.19+ds-1.1+b1) ... Setting up debhelper (13.15.3) ... Setting up samtools (1.19.2-1+b1) ... Setting up r-base-core (4.3.3-3) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-lattice (0.22-6-1) ... Setting up r-cran-nlme (3.1.164-1) ... Setting up r-cran-cluster (2.1.6-1) ... Setting up libtabixpp0t64:armhf (1.1.2-2.1) ... Setting up r-cran-nnet (7.3-19-2) ... Setting up r-cran-codetools (0.2-20-1) ... Setting up r-cran-boot (1.3-30-1) ... Setting up r-cran-spatial (7.3-17-1) ... Setting up r-cran-mass (7.3-60.0.1-1) ... Setting up r-cran-foreign (0.8.86-1) ... Setting up r-cran-matrix (1.6-5-1) ... Setting up r-cran-kernsmooth (2.23-22-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up libtabixpp-dev:armhf (1.1.2-2.1) ... Setting up r-cran-class (7.3-22-2) ... Setting up r-cran-survival (3.5-8-1) ... Setting up r-cran-rpart (4.1.23-1) ... Setting up r-recommended (4.3.3-3) ... Setting up r-base (4.3.3-3) ... Setting up rake (13.2.0-1) ... Setting up ruby-sdbm:armhf (1.0.0-5+b3) ... Setting up libruby3.1t64:armhf (3.1.2-8.3) ... Setting up ruby3.1 (3.1.2-8.3) ... Setting up libruby:armhf (1:3.1+nmu1) ... Setting up ruby (1:3.1+nmu1) ... Setting up ruby-asciidoctor (2.0.20-1) ... Setting up asciidoctor (2.0.20-1) ... Setting up ruby-rubygems (3.4.20-1) ... Processing triggers for libc-bin (2.37-15.1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/8061/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/8061/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/reapr-1.0.18+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../reapr_1.0.18+dfsg-6_source.changes dpkg-buildpackage: info: source package reapr dpkg-buildpackage: info: source version 1.0.18+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/reapr-1.0.18+dfsg' rm -rf /build/reproducible-path/reapr-1.0.18+dfsg/debian/man_src/*.html /build/reproducible-path/reapr-1.0.18+dfsg/debian/man_src/*.? rm -rf /build/reproducible-path/reapr-1.0.18+dfsg/debian/man rm -rf /build/reproducible-path/reapr-1.0.18+dfsg/debian/test dh_auto_clean -- make[1]: Leaving directory '/build/reproducible-path/reapr-1.0.18+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/reapr-1.0.18+dfsg' cd src && /usr/bin/make make[2]: Entering directory '/build/reproducible-path/reapr-1.0.18+dfsg/src' g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c errorWindow.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c utils.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c histogram.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_score.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ task_score.cpp: In function 'int main(int, char**)': task_score.cpp:235:79: warning: variable 'p' set but not used [-Wunused-but-set-variable] 235 | map > >::iterator p = globalGaps.find(currentRefID); | ^ In file included from /usr/include/c++/13/map:62, from task_score.cpp:10: /usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, Histogram>; _KeyOfValue = std::_Select1st, Histogram> >; _Compare = std::less >; _Alloc = std::allocator, Histogram> >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, Histogram>, std::_Select1st, Histogram> >, std::less >, std::allocator, Histogram> > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:63: /usr/include/c++/13/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = Histogram; _Compare = std::less >; _Alloc = std::allocator, Histogram> >]': /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, Histogram>, std::_Select1st, Histogram> >, std::less >, std::allocator, Histogram> > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = Histogram; _Compare = std::less >; _Alloc = std::allocator, Histogram> >]', inlined from 'void bam2possibleLink(CmdLineOptions&, std::string&, long unsigned int, long unsigned int, std::string&, long unsigned int&, long unsigned int&, BAMdata&)' at task_score.cpp:1032:28: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, Histogram>, std::_Select1st, Histogram> >, std::less >, std::allocator, Histogram> > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = Histogram; _Compare = std::less >; _Alloc = std::allocator, Histogram> >]', inlined from 'void bam2possibleLink(CmdLineOptions&, std::string&, long unsigned int, long unsigned int, std::string&, long unsigned int&, long unsigned int&, BAMdata&)' at task_score.cpp:1060:37: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, Histogram>, std::_Select1st, Histogram> >, std::less >, std::allocator, Histogram> > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = Histogram; _Compare = std::less >; _Alloc = std::allocator, Histogram> >]', inlined from 'void bam2possibleLink(CmdLineOptions&, std::string&, long unsigned int, long unsigned int, std::string&, long unsigned int&, long unsigned int&, BAMdata&)' at task_score.cpp:1061:37: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, Histogram>, std::_Select1st, Histogram> >, std::less >, std::allocator, Histogram> > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -o task_score -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_score.o errorWindow.o utils.o histogram.o -lbamtools -ltabixpp -lhts -lz -Wl,-z,relro -Wl,-z,now g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c trianglePlot.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/include/c++/13/vector:72, from trianglePlot.h:11, from trianglePlot.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void TrianglePlot::getHeights(long unsigned int, std::vector&, std::vector&)' at trianglePlot.cpp:144:30: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void TrianglePlot::getHeights(long unsigned int, std::vector&, std::vector&)' at trianglePlot.cpp:149:31: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c coveragePlot.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fasta.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_stats.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ task_stats.cpp: In function 'int main(int, char**)': task_stats.cpp:262:34: warning: 'ti_perfect' may be used uninitialized [-Wmaybe-uninitialized] 262 | getPerfectMapping(ti_perfect, currentRefIDstring, stats.perfectCov, references[currentRefID].RefLength); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ task_stats.cpp:150:12: note: 'ti_perfect' was declared here 150 | Tabix* ti_perfect; | ^~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_stats.o trianglePlot.o coveragePlot.o fasta.o histogram.o utils.o -lbamtools -ltabixpp -lhts -lz -o task_stats -Wl,-z,relro -Wl,-z,now g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_break.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_break.o -lbamtools fasta.o utils.o -lbamtools -ltabixpp -lhts -lz -o task_break -Wl,-z,relro -Wl,-z,now g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2fragCov.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2fragCov.o -lbamtools coveragePlot.o utils.o -lbamtools -ltabixpp -lhts -lz -o bam2fragCov -Wl,-z,relro -Wl,-z,now g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2insert.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2insert.o -lbamtools histogram.o utils.o -lbamtools -ltabixpp -lhts -lz -o bam2insert -Wl,-z,relro -Wl,-z,now g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2fcdEstimate.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ bam2fcdEstimate.cpp: In function 'int main(int, char**)': bam2fcdEstimate.cpp:84:34: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'long unsigned int' [-Wsign-compare] 84 | while (bamAlign.Position > triplot.centreCoord()) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ bam2fcdEstimate.cpp: In function 'void initialiseFCDHists(std::vector&, CmdLineOptions&)': bam2fcdEstimate.cpp:210:33: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'long int' [-Wsign-compare] 210 | for (unsigned long i = 0; i <= ops.maxInsert; i++) | ~~^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from bam2fcdEstimate.cpp:5: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Histogram}; _Tp = Histogram; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Histogram}; _Tp = Histogram; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Histogram; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void initialiseFCDHists(std::vector&, CmdLineOptions&)' at bam2fcdEstimate.cpp:212:20: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2fcdEstimate.o -lbamtools histogram.o utils.o trianglePlot.o -ltabixpp -lhts -lz -o bam2fcdEstimate -Wl,-z,relro -Wl,-z,now g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c make_plots.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include make_plots.o -o make_plots -Wl,-z,relro -Wl,-z,now g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fa2gaps.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include fa2gaps.o fasta.o -o fa2gaps -Wl,-z,relro -Wl,-z,now g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fa2gc.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include fa2gc.o fasta.o -o fa2gc -Wl,-z,relro -Wl,-z,now g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c scaff2contig.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include scaff2contig.o fasta.o -o scaff2contig -Wl,-z,relro -Wl,-z,now g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c n50.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include n50.o fasta.o -o n50 -Wl,-z,relro -Wl,-z,now g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_gapresize.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_gapresize.o -lbamtools utils.o trianglePlot.o fasta.o -ltabixpp -lhts -lz -o task_gapresize -Wl,-z,relro -Wl,-z,now g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_fcdrate.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from task_fcdrate.cpp:8: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from task_fcdrate.cpp:6: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void getGradient(std::vector&, std::vector&, std::vector&, std::vector&)' at task_fcdrate.cpp:304:22: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void getGradient(std::vector&, std::vector&, std::vector&, std::vector&)' at task_fcdrate.cpp:305:22: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'int main(int, char**)' at task_fcdrate.cpp:107:25: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'int main(int, char**)' at task_fcdrate.cpp:107:25: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'int main(int, char**)' at task_fcdrate.cpp:126:45: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'int main(int, char**)' at task_fcdrate.cpp:127:45: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_fcdrate.o -ltabixpp -lhts -lz histogram.o utils.o -lbamtools -o task_fcdrate -Wl,-z,relro -Wl,-z,now g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2perfect.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ bam2perfect.cpp: In function 'void writeAlignments(std::multimap&, BamTools::BamWriter&, long unsigned int)': bam2perfect.cpp:213:32: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'long unsigned int' [-Wsign-compare] 213 | if (p->second.Position >= endPos) break; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/reapr-1.0.18+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2perfect.o -lbamtools utils.o -lbamtools -ltabixpp -lhts -lz -o bam2perfect -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/reapr-1.0.18+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/reapr-1.0.18+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/reapr-1.0.18+dfsg' mkdir /build/reproducible-path/reapr-1.0.18+dfsg/debian/test ln -s /build/reproducible-path/reapr-1.0.18+dfsg/src/reapr.pl /build/reproducible-path/reapr-1.0.18+dfsg/debian/test/reapr PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path:/build/reproducible-path/reapr-1.0.18+dfsg/src:/build/reproducible-path/reapr-1.0.18+dfsg/debian/test /build/reproducible-path/reapr-1.0.18+dfsg/debian/tests/test-example [wgsim] seed = 42 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 1 sequences, total length: 1000111 foo 1384 T K + foo 4961 T W + foo 5885 - T - foo 9598 A C - foo 10177 G R + foo 11305 G K + foo 11592 G R + foo 13931 T - - foo 15907 C A - foo 17264 G K + foo 17780 A - - foo 18711 A W + foo 19249 T W + foo 19522 C S + foo 23053 T K + foo 23681 A R + foo 23730 C S + foo 24075 G S + foo 24555 G C - foo 26775 G K + foo 26896 C M + foo 27253 G K + foo 28210 T Y + foo 28224 A W + foo 28377 - G + foo 29035 G K + foo 29898 C M + foo 30274 A R + foo 30542 G K + foo 31566 A C - foo 32252 - A - foo 33303 T K + foo 33390 - G + foo 34073 A R + foo 34171 G R + foo 34718 T Y + foo 34801 - C + foo 35204 T W + foo 35342 G S + foo 35489 G T - foo 36153 A M + foo 36273 C S + foo 37356 G T - foo 37596 C S + foo 39308 T - - foo 40333 C G - foo 42295 T K + foo 42372 T Y + foo 44433 C G - foo 44630 - AG + foo 44902 T C - foo 47156 C A - foo 48210 C M + foo 48390 A R + foo 49652 C M + foo 52739 T Y + foo 52858 A M + foo 54737 A G - foo 55306 C T - foo 55434 C T - foo 59204 A W + foo 59300 G C - foo 59335 T Y + foo 59444 T - - foo 59531 C S + foo 59766 C Y + foo 61950 C S + foo 62887 G S + foo 63390 A G - foo 64365 G K + foo 64703 C S + foo 64932 C Y + foo 68383 - CG + foo 68464 A W + foo 68727 A W + foo 69080 A M + foo 72071 T C - foo 72720 - G - foo 73354 C T - foo 73637 G T - foo 74741 A M + foo 75101 C T - foo 75207 T K + foo 76400 T Y + foo 76780 A C - foo 77172 A W + foo 78385 C Y + foo 80705 C M + foo 82440 A R + foo 83021 G K + foo 83116 A - - foo 83846 T K + foo 84633 G S + foo 85891 G S + foo 87759 A C - foo 87778 T W + foo 88581 T K + foo 88606 T Y + foo 88880 A G - foo 89945 G C - foo 90728 T K + foo 91798 G R + foo 95957 G C - foo 96173 T W + foo 96665 A M + foo 98019 - G + foo 98131 A M + foo 98669 A R + foo 98719 G T - foo 99062 A W + foo 99590 A T - foo 100532 - TC + foo 103015 A W + foo 103172 G S + foo 103609 G R + foo 106549 T Y + foo 108808 C Y + foo 109191 G C - foo 111686 C G - foo 113436 C A - foo 113763 A W + foo 115671 C T - foo 117460 - A - foo 118193 G - - foo 118585 T K + foo 121219 A M + foo 121876 T K + foo 122071 T A - foo 124918 C G - foo 125300 G S + foo 125967 C S + foo 127443 G S + foo 127565 C Y + foo 128700 C A - foo 129912 G A - foo 130847 T W + foo 131677 G S + foo 132189 T C - foo 135878 CGGC - - foo 136825 T K + foo 138881 TGT - - foo 139288 A W + foo 141054 A W + foo 141055 - T + foo 141101 C S + foo 141404 A R + foo 142698 T C - foo 143990 C A - foo 144167 T Y + foo 144814 C Y + foo 146381 T Y + foo 146393 C A - foo 146510 A C - foo 147182 A W + foo 148783 T C - foo 149068 G S + foo 150208 T K + foo 151554 T W + foo 151709 C G - foo 153072 G R + foo 153307 T Y + foo 154050 G S + foo 154415 C S + foo 154594 G R + foo 155839 G T - foo 156106 G A - foo 159356 T W + foo 159926 A W + foo 160303 T K + foo 161323 C Y + foo 161904 G S + foo 162533 - ACC - foo 164738 C G - foo 165413 A R + foo 166944 C M + foo 167464 T Y + foo 168420 T C - foo 168579 A M + foo 168787 T W + foo 168959 A T - foo 169884 G S + foo 170032 G T - foo 172058 G K + foo 174942 A R + foo 175014 G K + foo 178406 G A - foo 179028 - A + foo 182394 C M + foo 182735 T Y + foo 183384 T K + foo 183893 - AT - foo 185360 G A - foo 185538 - G - foo 187948 G S + foo 188120 T G - foo 188179 T W + foo 188316 T Y + foo 189963 - G + foo 190093 C Y + foo 192220 C M + foo 192368 A W + foo 192782 T K + foo 193307 A R + foo 193501 G K + foo 194276 G S + foo 194930 C S + foo 196728 A W + foo 197559 G C - foo 198467 T W + foo 199042 C Y + foo 199259 AA - - foo 199687 TT - - foo 200287 C A - foo 200678 A R + foo 201208 C T - foo 201882 A - - foo 204456 T K + foo 206327 G R + foo 207311 G T - foo 209184 G A - foo 209279 C Y + foo 211459 C Y + foo 213807 T Y + foo 213846 T Y + foo 214635 A G - foo 214884 C A - foo 216244 A M + foo 216652 A M + foo 216745 T - - foo 216909 A T - foo 217579 A G - foo 217895 C Y + foo 218870 G K + foo 223098 T A - foo 223283 - C + foo 223666 C A - foo 224011 - C + foo 225681 C S + foo 227345 T C - foo 228778 T G - foo 229926 C - - foo 230778 T K + foo 230939 CG - - foo 231988 CT - - foo 234593 T W + foo 235496 C S + foo 235705 G K + foo 235758 A G - foo 236852 T C - foo 238790 A M + foo 238865 T K + foo 239329 A M + foo 239576 - C + foo 243058 G S + foo 244147 T - - foo 244462 C G - foo 245443 - A + foo 246544 C Y + foo 246744 T W + foo 247473 C M + foo 248129 C T - foo 249060 A C - foo 249515 G T - foo 250138 G S + foo 250567 C A - foo 254381 G R + foo 257864 C M + foo 257879 C Y + foo 259859 A M + foo 260643 C S + foo 261681 C G - foo 262645 T Y + foo 263279 A R + foo 263575 A - - foo 264587 - TA + foo 264689 T K + foo 265758 G K + foo 266272 A M + foo 268550 C M + foo 269986 G S + foo 270321 AC - - foo 273346 C S + foo 275367 C A - foo 277334 C G - foo 277629 G T - foo 278431 C Y + foo 281456 T Y + foo 281556 T G - foo 281737 G K + foo 282290 AC - - foo 282851 - C - foo 284405 A C - foo 288751 A C - foo 290501 TAAA - - foo 291315 A W + foo 291368 C - - foo 292154 A C - foo 292385 C M + foo 292555 G K + foo 297709 G C - foo 298183 A W + foo 298228 T W + foo 299902 T G - foo 302575 A T - foo 304823 G R + foo 305308 T Y + foo 305487 G S + foo 305697 G T - foo 306098 C G - foo 306882 T Y + foo 308201 A M + foo 308833 A T - foo 312033 A - - foo 312895 C G - foo 313889 C - - foo 315109 A R + foo 316083 C - - foo 316466 A R + foo 318040 G C - foo 319446 T C - foo 320236 C S + foo 320652 A - - foo 320716 T K + foo 323644 A - - foo 325359 G T - foo 329476 - CA + foo 329706 T G - foo 330181 T Y + foo 330703 C Y + foo 331315 G S + foo 332351 C A - foo 333408 A R + foo 333468 C S + foo 336247 A G - foo 336586 A M + foo 337364 G K + foo 337686 A T - foo 338043 A - - foo 338292 C G - foo 338962 A C - foo 339353 G K + foo 340647 - A + foo 341705 G R + foo 344283 C M + foo 345898 - AG - foo 347959 T - - foo 349162 C M + foo 352072 T Y + foo 354614 C Y + foo 359304 T - - foo 359312 - G + foo 360972 C S + foo 363857 C Y + foo 366226 A C - foo 367259 C M + foo 372502 T Y + foo 372747 A M + foo 375140 C S + foo 376298 T W + foo 376313 C - - foo 376760 T W + foo 378494 A W + foo 381137 T G - foo 381186 A R + foo 381701 A G - foo 382614 A W + foo 382761 C T - foo 382854 T C - foo 383201 C T - foo 385104 G S + foo 385233 - A + foo 386138 C T - foo 386316 A W + foo 387072 A R + foo 387642 - A + foo 388232 T C - foo 388890 GGG - - foo 390508 C S + foo 390625 C M + foo 391921 C G - foo 395256 G T - foo 395542 G S + foo 397015 A - - foo 397516 C Y + foo 397528 GC - - foo 398152 C T - foo 399802 A W + foo 400972 T K + foo 401419 - T + foo 401477 T W + foo 402437 A M + foo 402722 G R + foo 403452 C M + foo 404234 - A + foo 405344 A W + foo 407040 G S + foo 408483 G R + foo 408586 A C - foo 408721 A R + foo 409494 A M + foo 410078 A G - foo 411170 C A - foo 415342 T Y + foo 416265 C G - foo 417740 C A - foo 418622 C S + foo 420232 A W + foo 420288 T Y + foo 420908 A W + foo 421109 T A - foo 421357 A R + foo 422799 G A - foo 424383 C S + foo 424871 - GCA + foo 427273 T A - foo 429822 C M + foo 429846 T W + foo 432015 A G - foo 432414 G K + foo 433606 C Y + foo 433831 T Y + foo 437721 - A - foo 438402 G - - foo 438799 A T - foo 439422 C M + foo 440734 C A - foo 441840 T G - foo 442021 - C + foo 445021 T A - foo 445591 G A - foo 446138 T W + foo 447757 A W + foo 449156 T - - foo 449161 G K + foo 450114 A W + foo 450688 A W + foo 454421 C G - foo 454718 T Y + foo 455675 TC - - foo 461721 G R + foo 462526 G S + foo 467296 G A - foo 467510 G K + foo 468267 T K + foo 469118 G R + foo 469830 C Y + foo 471073 G T - foo 472056 G A - foo 472773 - A + foo 473046 G R + foo 473188 G A - foo 473742 C - - foo 474789 T A - foo 477763 G R + foo 478246 T W + foo 478975 T G - foo 479038 A R + foo 480275 T Y + foo 480317 G A - foo 481512 T K + foo 482069 G S + foo 482534 A R + foo 483760 C Y + foo 485281 T W + foo 486255 T C - foo 487038 T K + foo 487225 T A - foo 488012 C Y + foo 488795 T C - foo 490241 A R + foo 492595 - CGG + foo 493224 C A - foo 494284 A T - foo 495990 - T - foo 497306 A R + foo 497403 T Y + foo 499569 C Y + foo 499651 T K + foo 503139 T C - foo 504660 A R + foo 508679 C - - foo 513643 G K + foo 515668 CC - - foo 515836 G R + foo 516488 C S + foo 517602 G R + foo 517962 G K + foo 517975 T K + foo 519144 A T - foo 520068 T K + foo 520926 A W + foo 521562 C S + foo 522076 CG - - foo 522838 T Y + foo 523513 - C + foo 523907 - TA + foo 526271 T A - foo 526533 AC - - foo 526767 C Y + foo 528217 C Y + foo 531924 G S + foo 532333 - TT + foo 533132 C M + foo 534689 A T - foo 534779 A W + foo 535594 C A - foo 535795 G R + foo 538368 A R + foo 540879 G K + foo 542530 A - - foo 543620 G R + foo 544733 - C - foo 546300 - TT + foo 548196 A T - foo 548878 C M + foo 548885 G R + foo 549459 T K + foo 550908 A G - foo 551170 A - - foo 553130 T Y + foo 555293 T G - foo 556198 G R + foo 556355 A T - foo 557688 G K + foo 558415 G C - foo 558461 - G + foo 559287 T Y + foo 559465 C M + foo 560184 T W + foo 560252 T W + foo 562579 A M + foo 562961 G A - foo 566986 C A - foo 568134 C A - foo 569698 T C - foo 570180 T K + foo 570451 TG - - foo 570832 - A - foo 571589 A W + foo 572208 C M + foo 572871 C S + foo 574334 G - - foo 575673 T Y + foo 576797 G S + foo 578486 - C - foo 578494 C S + foo 579257 G A - foo 580103 G T - foo 580872 A W + foo 580925 G S + foo 580950 G C - foo 581637 T Y + foo 581654 A G - foo 582538 A T - foo 582691 C M + foo 582938 A W + foo 583104 T K + foo 584763 T W + foo 585723 T W + foo 588253 T Y + foo 588972 T C - foo 589438 - C - foo 591131 C Y + foo 591950 G R + foo 592194 T G - foo 592310 G S + foo 593892 G A - foo 598556 A - - foo 601660 G S + foo 602112 G T - foo 602412 T Y + foo 607282 - C + foo 607394 A M + foo 608438 A T - foo 609255 A W + foo 609365 - T + foo 611161 G K + foo 612224 C G - foo 614493 G R + foo 614601 G A - foo 614607 C Y + foo 619507 C M + foo 619798 T C - foo 621872 C T - foo 622375 C Y + foo 623208 - G - foo 624366 C A - foo 625320 - ACA - foo 626664 - G + foo 627140 T C - foo 627353 G T - foo 628714 T Y + foo 628744 A - - foo 629152 A G - foo 630110 T G - foo 631744 G K + foo 632763 C S + foo 634419 G - - foo 634459 A G - foo 634571 G A - foo 635366 - A + foo 635604 G T - foo 637057 T C - foo 637525 A T - foo 638412 A R + foo 640547 A W + foo 641514 T K + foo 642219 A R + foo 642427 A G - foo 642612 A R + foo 643553 T W + foo 647316 - T + foo 647598 C - - foo 651093 G A - foo 651718 G R + foo 652235 A G - foo 652579 A C - foo 653355 A W + foo 655174 C M + foo 655487 A M + foo 656849 G S + foo 661081 T K + foo 661134 G C - foo 661935 A W + foo 662010 A M + foo 662040 G R + foo 663030 A W + foo 663268 - C + foo 664991 T - - foo 665489 T K + foo 665555 C M + foo 665965 C Y + foo 668725 A C - foo 668834 - G - foo 668873 C S + foo 669654 T W + foo 671041 G S + foo 671485 T W + foo 671690 C M + foo 673022 G R + foo 674137 - T + foo 674782 A C - foo 676373 G T - foo 676793 T C - foo 677409 G S + foo 677536 - AA - foo 677620 G K + foo 677686 C Y + foo 678327 G S + foo 678704 G S + foo 678771 A C - foo 678866 C T - foo 679960 A W + foo 680447 - C + foo 682102 C T - foo 685497 T A - foo 686884 G S + foo 687324 ACA - - foo 687684 - AC + foo 687823 T C - foo 688590 G K + foo 690802 C M + foo 691388 T C - foo 691403 T G - foo 691790 G A - foo 692973 C A - foo 694058 G S + foo 694550 G R + foo 694968 T W + foo 695898 A T - foo 696721 C S + foo 696787 C S + foo 696935 A M + foo 698024 - C + foo 699813 A - - foo 700179 G R + foo 701421 A M + foo 701989 T A - foo 702862 C A - foo 707020 G A - foo 708420 A - - foo 708669 C G - foo 710521 T W + foo 711801 G C - foo 711913 T G - foo 715830 C M + foo 717664 TC - - foo 718845 A W + foo 719069 T Y + foo 719565 A W + foo 721136 T K + foo 726116 T K + foo 727809 T K + foo 728864 G K + foo 728918 G A - foo 730296 - T + foo 731988 C Y + foo 734658 A M + foo 734715 A W + foo 736618 C G - foo 737257 T Y + foo 740864 C A - foo 741640 G - - foo 741859 - TA - foo 742011 T K + foo 742237 A R + foo 742960 G K + foo 743731 G R + foo 743971 A W + foo 744635 T K + foo 746430 C G - foo 746489 - GC - foo 746881 C M + foo 756997 TC - - foo 757776 A M + foo 759870 A T - foo 760224 G K + foo 760799 G C - foo 761692 T C - foo 762569 G S + foo 763140 A G - foo 763842 - T - foo 764192 A M + foo 764334 G A - foo 764889 - AAT + foo 766464 G S + foo 768226 G A - foo 770272 T G - foo 771145 C Y + foo 772209 T A - foo 773672 T K + foo 773932 G C - foo 774658 C S + foo 775969 A M + foo 776816 T G - foo 777591 C Y + foo 777891 A M + foo 778164 C M + foo 778219 T W + foo 779260 G T - foo 779465 A W + foo 779779 G S + foo 780033 G K + foo 783243 C M + foo 783860 A R + foo 788345 A M + foo 789554 G - - foo 790025 G K + foo 791454 T K + foo 792009 C A - foo 792872 C G - foo 794616 T W + foo 795031 G R + foo 796919 C M + foo 797020 G S + foo 797042 G C - foo 797149 G A - foo 797177 A C - foo 799076 G C - foo 799580 G S + foo 800356 A R + foo 802297 G T - foo 802309 T Y + foo 802343 - C + foo 802769 A W + foo 803104 C G - foo 805819 C Y + foo 805972 T Y + foo 807503 T K + foo 807950 C M + foo 807994 - A - foo 809167 A G - foo 809658 A W + foo 810152 A M + foo 811506 G R + foo 813494 A M + foo 814035 G T - foo 814476 A W + foo 819399 T K + foo 820171 T W + foo 820445 G C - foo 822178 C G - foo 822504 C T - foo 823378 C M + foo 823591 CG - - foo 824229 C M + foo 824579 C T - foo 824858 C M + foo 826101 T K + foo 827593 C G - foo 827794 T Y + foo 828228 A M + foo 828367 T K + foo 828788 C M + foo 829002 C Y + foo 830345 C M + foo 831018 C A - foo 831459 T K + foo 832413 A T - foo 832782 T Y + foo 832908 T Y + foo 833130 T - - foo 833142 G S + foo 833241 G A - foo 836727 A T - foo 836829 G S + foo 838452 T G - foo 838543 A T - foo 838605 C M + foo 838954 G C - foo 841829 G K + foo 842324 - TC + foo 842996 - C + foo 844390 C A - foo 844793 A C - foo 844925 C A - foo 845082 G C - foo 846202 G R + foo 846707 A G - foo 848713 G A - foo 849372 C S + foo 849742 G A - foo 850499 C - - foo 850927 GT - - foo 851084 - G + foo 852247 A R + foo 852972 C A - foo 854808 T W + foo 855956 G K + foo 856225 G A - foo 856582 T K + foo 857351 C M + foo 857504 AC - - foo 858324 A T - foo 858858 T C - foo 859488 T Y + foo 862441 T Y + foo 863827 C Y + foo 864165 C A - foo 865997 C M + foo 866370 G S + foo 867653 G S + foo 867722 C Y + foo 868696 C M + foo 869005 T W + foo 869791 T Y + foo 875339 C Y + foo 875347 C M + foo 875584 T G - foo 876780 C T - foo 878368 A C - foo 878916 - CAG + foo 879005 A R + foo 880112 G T - foo 881021 - T - foo 881175 T W + foo 882168 - GGG + foo 882223 - G - foo 883033 TG - - foo 883381 C G - foo 884378 C - - foo 885075 A M + foo 885190 A W + foo 885568 A W + foo 885827 T Y + foo 887610 TG - - foo 889139 G R + foo 890978 T - - foo 891500 C Y + foo 892257 G C - foo 892642 G R + foo 892644 T W + foo 892757 C A - foo 893222 T - - foo 893348 T W + foo 894161 - C - foo 894447 A G - foo 894614 A W + foo 897817 T W + foo 899408 C S + foo 902450 A T - foo 902970 AT - - foo 905836 G K + foo 906524 GA - - foo 907484 A W + foo 907537 C M + foo 908515 G R + foo 908642 C T - foo 911145 T C - foo 912220 T Y + foo 912682 C Y + foo 914260 C S + foo 914757 T Y + foo 916413 G C - foo 916783 T G - foo 917033 G C - foo 917218 A - - foo 918225 G - - foo 918459 A - - foo 918732 A M + foo 919640 TC - - foo 920824 T W + foo 920836 G C - foo 924560 G R + foo 924659 GA - - foo 925868 T A - foo 928254 T G - foo 928369 - A - foo 928641 - AG + foo 929857 C M + foo 930211 T W + foo 930935 C T - foo 931986 A M + foo 932852 G T - foo 933965 T A - foo 935564 A W + foo 936034 T Y + foo 936221 AC - - foo 936670 C S + foo 936704 T A - foo 936786 T W + foo 939218 C S + foo 939312 A W + foo 939467 A W + foo 939934 C S + foo 941603 C Y + foo 942910 A W + foo 944654 T Y + foo 945301 A C - foo 945770 C T - foo 946078 G S + foo 948833 G K + foo 948999 A W + foo 949193 A R + foo 950276 C M + foo 950414 A W + foo 951285 G C - foo 953158 G R + foo 953287 A W + foo 954150 C G - foo 954258 G - - foo 955396 CC - - foo 956490 - AC + foo 958129 A R + foo 959027 T A - foo 959964 A W + foo 962042 A G - foo 962742 C G - foo 963306 T W + foo 963422 G K + foo 964082 G S + foo 965561 C S + foo 966531 T K + foo 967324 T W + foo 968419 - C - foo 969054 G - - foo 969158 G S + foo 972658 C M + foo 974266 T W + foo 974629 G K + foo 975034 A R + foo 975636 T W + foo 977078 - A - foo 978321 G T - foo 978595 C G - foo 979090 C M + foo 983855 TA - - foo 985725 T A - foo 988497 C Y + foo 990171 C M + foo 990804 - CA - foo 990941 T W + foo 991797 A W + foo 992469 A M + foo 994610 C Y + foo 998107 - T + foo 999725 G R + [REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.15610.smaltmap.smalt_index foo1.fasta # Command line: smalt index -k 13 -s 2 out.bam.tmp.15610.smaltmap.smalt_index foo1.fasta # Reading sequences ... # Writing sequence set ... # Setting up hash index with collisions ... # word length = 13 bases, skip step = 2 bases ... # number of bits for key = 18 with 0 perfect bits # Counting keys ... # Counting k-tuples ... # Allocating k-tuple arrays ... # Counting k-tuple occurrences ... # Setting the k-tuple positions in index ... # Hash table is set up. # =-=-=-=-= Hash Index Stats =-=-=-=-= # Hash index with collisions. # Word length: 13 bases # Skip step: 2 bases # Number of hash keys: 262144 # Number of word positions: 499970 # Number of different words: 498076 # Maximum number of words per key: 11 # Number of keys without words: 39377 # =-=-= End of Hash Index Stats =-=-= # Writing table to file ... # smalt: Total elapsed wall clock time: 2 seconds [REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.15610.smaltmap.smalt_sample out.bam.tmp.15610.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Command line: smalt sample -u 1000 -o out.bam.tmp.15610.smaltmap.smalt_sample out.bam.tmp.15610.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Opening read files ... # Reading reference sequences ... # Reading hash table ... # =-=-=-=-= Hash Index Stats =-=-=-=-= # Hash index with collisions. # Word length: 13 bases # Skip step: 2 bases # Number of hash keys: 262144 # Number of word positions: 499970 # Number of different words: 498076 # Maximum number of words per key: 11 # Number of keys without words: 39377 # =-=-= End of Hash Index Stats =-=-= # Check of read pairs ok ... # Mate names match ... # Sampling insert size distribution ... # Processed 9999 read pairs. # smalt: Time spent setting up hash index:0 seconds # smalt: Time spent mapping reads:14 seconds # smalt: Total elapsed wall clock time: 14 seconds [REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.15610.smaltmap.smalt_sample -f samsoft out.bam.tmp.15610.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.15610.smaltmap.raw.bam # Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.15610.smaltmap.smalt_sample -f samsoft out.bam.tmp.15610.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Reading distribution of insert sizes from file ... # Sampled histogram # Smoothed histogram # Opening read files ... # Reading reference sequences ... # Reading hash table ... # =-=-=-=-= Hash Index Stats =-=-=-=-= # Hash index with collisions. # Word length: 13 bases # Skip step: 2 bases # Number of hash keys: 262144 # Number of word positions: 499970 # Number of different words: 498076 # Maximum number of words per key: 11 # Number of keys without words: 39377 # =-=-= End of Hash Index Stats =-=-= # Processing query reads ... # Processed 10000 read pairs. # smalt: Time spent setting up hash index:0 seconds # smalt: Time spent mapping reads:1 minutes and 7 seconds # smalt: Total elapsed wall clock time: 1 minutes and 7 seconds [REAPR smaltmap] Running: samtools sort out.bam.tmp.15610.smaltmap.raw.bam -O bam -o out.bam.tmp.15610.smaltmap.raw.bam.sort.bam [REAPR smaltmap] Running: samtools rmdup out.bam.tmp.15610.smaltmap.raw.bam.sort.bam out.bam.tmp.15610.smaltmap.rmdup.bam [bam_rmdup_core] processing reference foo... [bam_rmdup_core] 1 / 10000 = 0.0001 in library ' ' [REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.15610.smaltmap.header [REAPR smaltmap] Running: samtools view -H out.bam.tmp.15610.smaltmap.rmdup.bam >> out.bam.tmp.15610.smaltmap.header [REAPR smaltmap] Running: samtools reheader out.bam.tmp.15610.smaltmap.header out.bam.tmp.15610.smaltmap.rmdup.bam > out.bam [REAPR smaltmap] Running: samtools index out.bam [REAPR smaltmap] Running: rm out.bam.tmp.15610.smaltmap.* Running reapr version 1.0.18 pipeline: reapr foo1.fasta out.bam result [REAPR pipeline] Running facheck [REAPR pipeline] Running preprocess [REAPR preprocess] sampling region foo:1169-3476. Already sampled 0 bases [REAPR preprocess] sampling region foo:3492-5726. Already sampled 2308 bases [REAPR preprocess] sampling region foo:5756-12551. Already sampled 4543 bases [REAPR preprocess] sampling region foo:12591-998105. Already sampled 11339 bases [REAPR preprocess] Sampled 996854 bases for GC/coverage estimation [REAPR pipeline] Running stats [REAPR pipeline] Running fcdrate [REAPR pipeline] Running score [REAPR pipeline] Running break [REAPR pipeline] Running summary rm -rf /build/reproducible-path/reapr-1.0.18+dfsg/debian/test make[1]: Leaving directory '/build/reproducible-path/reapr-1.0.18+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/reapr-1.0.18+dfsg' mkdir -p debian/reapr/usr/lib/reapr install src/reapr.pl debian/reapr/usr/lib/reapr/reapr.pl chmod -x src/*.cpp find src -executable -exec install {} debian/reapr/usr/lib/reapr \; install: omitting directory 'src' dh_auto_install -- make[1]: Leaving directory '/build/reproducible-path/reapr-1.0.18+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/reapr-1.0.18+dfsg' for pl in `grep -Rl '#!/usr/bin/env' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/reproducible-path/reapr-1.0.18+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/reapr-1.0.18+dfsg' mkdir -p /build/reproducible-path/reapr-1.0.18+dfsg/debian/man asciidoctor -a docdate='' -b manpage /build/reproducible-path/reapr-1.0.18+dfsg/debian/man_src/*.adoc cp /build/reproducible-path/reapr-1.0.18+dfsg/debian/man_src/*.? /build/reproducible-path/reapr-1.0.18+dfsg/debian/man dh_installman -- make[1]: Leaving directory '/build/reproducible-path/reapr-1.0.18+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_score contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_break contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_fcdrate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_gapresize contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_stats contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/bam2fcdEstimate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package reapr: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package reapr: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'reapr-dbgsym' in '../reapr-dbgsym_1.0.18+dfsg-6_armhf.deb'. dpkg-deb: building package 'reapr' in '../reapr_1.0.18+dfsg-6_armhf.deb'. dpkg-genbuildinfo --build=binary -O../reapr_1.0.18+dfsg-6_armhf.buildinfo dpkg-genchanges --build=binary -O../reapr_1.0.18+dfsg-6_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/8061/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/8061/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/8061 and its subdirectories I: Current time: Sat Apr 6 02:56:26 +14 2024 I: pbuilder-time-stamp: 1712321786