I: pbuilder: network access will be disabled during build I: Current time: Wed Nov 13 08:35:36 +14 2024 I: pbuilder-time-stamp: 1731436536 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/615444/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Nov 12 18:35 /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/615444/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/615444/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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=0f5c46b5d0e34070858bd293dda340fd LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=615444 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.jCWNMOcd/pbuilderrc_xZVp --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jCWNMOcd/b2 --logfile b2/build.log reapr_1.0.18+dfsg-6.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/615444/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-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 ... 19970 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} comerr-dev{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} krb5-multidev{a} libarchive-zip-perl{a} libbambamc0{a} libbamtools-dev{a} libbamtools2.5.2{a} libblas3{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{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} libevent-2.1-7t64{a} libexpat1{a} libfile-copy-link-perl{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libharfbuzz0b{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libice6{a} libicu72{a} libidn2-dev{a} libjbig0{a} libjpeg62-turbo{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} libldap-dev{a} liblerc4{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{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} libpkgconf3{a} libpng16-16t64{a} libpsl-dev{a} libpsl5t64{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libruby{a} libruby3.1t64{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtabixpp-dev{a} libtabixpp0t64{a} libtasn1-6-dev{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libunbound8{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} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} openssl{a} pkgconf{a} pkgconf-bin{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: bzip2-doc curl fonts-lato krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libjs-jquery libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libtasn1-doc 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, 194 newly installed, 0 to remove and 0 not upgraded. Need to get 114 MB of archives. After unpacking 301 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-3 [255 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-9 [97.2 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 rubygems-integration all 1.18 [6704 B] Get: 17 http://deb.debian.org/debian trixie/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 ruby-sdbm amd64 1.0.0-5+b5 [15.6 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libruby3.1t64 amd64 3.1.2-8.4 [5411 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 ruby3.1 amd64 3.1.2-8.4 [664 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get: 30 http://deb.debian.org/debian trixie/main amd64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6+b1 [161 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-2 [81.6 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 bamtools amd64 2.5.2+dfsg-6+b1 [207 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 comerr-dev amd64 2.1-1.47.1-1+b1 [54.8 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 48 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.3-2 [105 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b5 [307 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 68 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libgssrpc4t64 amd64 1.21.3-3 [59.5 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libkadm5clnt-mit12 amd64 1.21.3-3 [41.7 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libkdb5-10t64 amd64 1.21.3-3 [42.0 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libkadm5srv-mit12 amd64 1.21.3-3 [53.5 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 krb5-multidev amd64 1.21.3-3 [126 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libbambamc0 amd64 0.0.50-6+b2 [38.2 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libbamtools-dev amd64 2.5.2+dfsg-6+b1 [222 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3+b1 [152 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libbrotli-dev amd64 1.1.0-2+b5 [316 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b2 [24.4 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.4.0-1+b1 [63.6 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.11.0-1 [359 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libunbound8 amd64 1.22.0-1 [598 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libgnutls-dane0t64 amd64 3.8.6-2+b1 [439 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libgnutls-openssl27t64 amd64 3.8.6-2+b1 [439 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libp11-kit-dev amd64 0.25.5-2+b1 [208 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b2 [329 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b2 [642 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libgnutls28-dev amd64 3.8.6-2+b1 [1385 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libkrb5-dev amd64 1.21.3-3 [15.7 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libldap-dev amd64 2.5.18+dfsg-3+b1 [303 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libnghttp3-dev amd64 1.4.0-1+b1 [87.2 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.6.0-1 [23.8 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libngtcp2-dev amd64 1.6.0-1 [170 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.3.2-2 [2742 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.6+dfsg-1+b1 [365 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libcurl4-gnutls-dev amd64 8.11.0-1 [472 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.22-1 [55.8 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libfile-copy-link-perl all 0.140-5 [13.2 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libhts-dev amd64 1.20+ds-2 [1701 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3+b1 [2450 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get: 156 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libtabixpp0t64 amd64 1.1.2-2.1+b1 [10.3 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libtabixpp-dev amd64 1.1.2-2.1+b1 [9528 B] Get: 161 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.1-3 [28.3 MB] Get: 174 http://deb.debian.org/debian trixie/main amd64 r-cran-boot all 1.3-31-1 [639 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 r-cran-cluster amd64 2.1.6-1 [568 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 r-cran-foreign amd64 0.8.87-1 [253 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 r-cran-mass amd64 7.3-61-1 [1112 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 r-cran-kernsmooth amd64 2.23-24-1 [92.7 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 r-cran-nlme amd64 3.1.166-1 [2330 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 r-cran-matrix amd64 1.7-1-1 [4138 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 r-cran-survival amd64 3.7-0-1 [6305 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 r-cran-rpart amd64 4.1.23-1 [685 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 r-cran-class amd64 7.3-22-2 [87.3 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 r-cran-nnet amd64 7.3-19-2 [111 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 r-cran-spatial amd64 7.3-17-1 [128 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 r-recommended all 4.4.1-3 [2580 B] Get: 190 http://deb.debian.org/debian trixie/main amd64 r-base all 4.4.1-3 [14.6 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.20-3 [653 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 smalt amd64 0.7.6-13 [115 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 snpomatic amd64 1.0-7 [85.6 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 tabix amd64 1.20+ds-2 [486 kB] Fetched 114 MB in 7s (16.4 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 ... 19970 files and directories currently installed.) Preparing to unpack .../000-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package readline-common. Preparing to unpack .../001-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.3.2-2_amd64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../009-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.40.2-9_amd64.deb ... Unpacking bsdextrautils (2.40.2-9) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../012-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package ucf. Preparing to unpack .../014-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../015-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package rake. Preparing to unpack .../016-rake_13.2.1-1_all.deb ... Unpacking rake (13.2.1-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../017-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../018-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../019-ruby-xmlrpc_0.3.3-2_all.deb ... Unpacking ruby-xmlrpc (0.3.3-2) ... Selecting previously unselected package libruby:amd64. Preparing to unpack .../020-libruby_1%3a3.1+nmu1_amd64.deb ... Unpacking libruby:amd64 (1:3.1+nmu1) ... Selecting previously unselected package ruby-sdbm:amd64. Preparing to unpack .../021-ruby-sdbm_1.0.0-5+b5_amd64.deb ... Unpacking ruby-sdbm:amd64 (1.0.0-5+b5) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../022-libedit2_3.1-20240808-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20240808-1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../023-libncurses6_6.5-2+b1_amd64.deb ... Unpacking libncurses6:amd64 (6.5-2+b1) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../024-libyaml-0-2_0.2.5-1+b2_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1+b2) ... Selecting previously unselected package libruby3.1t64:amd64. Preparing to unpack .../025-libruby3.1t64_3.1.2-8.4_amd64.deb ... Unpacking libruby3.1t64:amd64 (3.1.2-8.4) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../026-ruby3.1_3.1.2-8.4_amd64.deb ... Unpacking ruby3.1 (3.1.2-8.4) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../027-ruby-rubygems_3.4.20-1_all.deb ... Unpacking ruby-rubygems (3.4.20-1) ... Selecting previously unselected package ruby. Preparing to unpack .../028-ruby_1%3a3.1+nmu1_amd64.deb ... Unpacking ruby (1:3.1+nmu1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../029-ruby-asciidoctor_2.0.23-1_all.deb ... Unpacking ruby-asciidoctor (2.0.23-1) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../030-asciidoctor_2.0.23-1_all.deb ... Unpacking asciidoctor (2.0.23-1) ... Selecting previously unselected package m4. Preparing to unpack .../031-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../032-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../033-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... 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Unpacking libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Selecting previously unselected package libpaper1:amd64. Preparing to unpack .../153-libpaper1_1.1.29+b2_amd64.deb ... Unpacking libpaper1:amd64 (1.1.29+b2) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../154-libpaper-utils_1.1.29+b2_amd64.deb ... Unpacking libpaper-utils (1.1.29+b2) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../155-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../156-libsharpyuv0_1.4.0-0.1+b1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../157-libsm6_2%3a1.2.4-1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.4-1) ... Selecting previously unselected package libtabixpp0t64:amd64. 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Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../164-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../165-libxft2_2.3.6-1+b2_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b2) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../166-libxss1_1%3a1.2.3-1+b2_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b2) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../167-libtk8.6_8.6.15-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.15-1) ... Selecting previously unselected package libxt6t64:amd64. 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Setting up libexpat1:amd64 (2.6.3-2) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libgraphite2-3:amd64 (1.3.14-2+b1) ... Setting up libgnutls-openssl27t64:amd64 (3.8.6-2+b1) ... Setting up libpixman-1-0:amd64 (0.42.2-1+b1) ... Setting up libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b2) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up libfile-copy-link-perl (0.140-5) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up libzstd-dev:amd64 (1.5.6+dfsg-1+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up bsdextrautils (2.40.2-9) ... Setting up libdatrie1:amd64 (0.2.13-3+b1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1+b2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b5) ... Setting up libedit2:amd64 (3.1-20240808-1) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libcom-err2:amd64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Nov 12 18:36:49 UTC 2024. Universal Time is now: Tue Nov 12 18:36:49 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-14) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.82.2-2) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libunbound8:amd64 (1.22.0-1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b2) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.6-2+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libjsoncpp26:amd64 (1.9.6-2) ... Setting up libncurses6:amd64 (6.5-2+b1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libfribidi0:amd64 (1.0.15-1) ... Setting up comerr-dev:amd64 (2.1-1.47.1-1+b1) ... Setting up libbambamc0:amd64 (0.0.50-6+b2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libssl-dev:amd64 (3.3.2-2) ... Setting up libpng16-16t64:amd64 (1.6.44-2) ... Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... Setting up autopoint (0.22.5-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libbamtools2.5.2:amd64 (2.5.2+dfsg-6+b1) ... Setting up libidn2-dev:amd64 (2.3.7-2+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.4.0-1+b1) ... Setting up libwebp7:amd64 (1.4.0-0.1+b1) ... Setting up libnghttp3-dev:amd64 (1.4.0-1+b1) ... Setting up ruby-webrick (1.8.1-1) ... Setting up liblzma-dev:amd64 (5.6.3-1+b1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up bamtools (2.5.2+dfsg-6+b1) ... Setting up snpomatic (1.0-7) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libtasn1-6-dev:amd64 (4.19.0-3+b3) ... Setting up openssl (3.3.2-2) ... Setting up libdeflate-dev:amd64 (1.22-1) ... Setting up tabix (1.20+ds-2) ... Setting up readline-common (8.2-5) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... 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 libbrotli-dev:amd64 (1.1.0-2+b5) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-2+b1) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... 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 (1.14.0-1) ... Setting up smalt (0.7.6-13) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up liblapack3:amd64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2+b2) ... Setting up nettle-dev:amd64 (3.10-1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.6.0-1) ... Setting up libngtcp2-dev:amd64 (1.6.0-1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libldap-dev:amd64 (2.5.18+dfsg-3+b1) ... Setting up libbamtools-dev:amd64 (2.5.2+dfsg-6+b1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up ucf (3.0043+nmu1) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up libgnutls28-dev:amd64 (3.8.6-2+b1) ... Setting up libpaper1:amd64 (1.1.29+b2) ... Creating config file /etc/papersize with new version Setting up libnghttp2-dev:amd64 (1.64.0-1) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b2) ... Setting up libcurl4t64:amd64 (8.11.0-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libcurl3t64-gnutls:amd64 (8.11.0-1) ... Setting up rubygems-integration (1.18) ... Setting up libpaper-utils (1.1.29+b2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libgssrpc4t64:amd64 (1.21.3-3) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-3) ... Setting up libkdb5-10t64:amd64 (1.21.3-3) ... Setting up debhelper (13.20) ... Setting up samtools (1.20-3) ... Setting up r-base-core (4.4.1-3) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-lattice (0.22-6-1) ... Setting up r-cran-nlme (3.1.166-1) ... Setting up r-cran-cluster (2.1.6-1) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-3) ... Setting up libtabixpp0t64:amd64 (1.1.2-2.1+b1) ... Setting up r-cran-nnet (7.3-19-2) ... Setting up krb5-multidev:amd64 (1.21.3-3) ... Setting up r-cran-codetools (0.2-20-1) ... Setting up r-cran-boot (1.3-31-1) ... Setting up r-cran-spatial (7.3-17-1) ... Setting up r-cran-mass (7.3-61-1) ... Setting up r-cran-foreign (0.8.87-1) ... Setting up libkrb5-dev:amd64 (1.21.3-3) ... Setting up r-cran-matrix (1.7-1-1) ... Setting up r-cran-kernsmooth (2.23-24-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up r-cran-class (7.3-22-2) ... Setting up r-cran-survival (3.7-0-1) ... Setting up libcurl4-gnutls-dev:amd64 (8.11.0-1) ... Setting up r-cran-rpart (4.1.23-1) ... Setting up libhts-dev:amd64 (1.20+ds-2) ... Setting up libtabixpp-dev:amd64 (1.1.2-2.1+b1) ... Setting up r-recommended (4.4.1-3) ... Setting up r-base (4.4.1-3) ... Setting up libruby:amd64 (1:3.1+nmu1) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b5) ... Setting up libruby3.1t64:amd64 (3.1.2-8.4) ... Setting up ruby3.1 (3.1.2-8.4) ... Setting up ruby (1:3.1+nmu1) ... Setting up ruby-asciidoctor (2.0.23-1) ... Setting up rake (13.2.1-1) ... Setting up asciidoctor (2.0.23-1) ... Setting up ruby-rubygems (3.4.20-1) ... Processing triggers for libc-bin (2.40-3) ... 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/615444/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/615444/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 amd64 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++ -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 -fcf-protection -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++ -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 -fcf-protection -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++ -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 -fcf-protection -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++ -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 -fcf-protection -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); | ^ g++ -o task_score -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 -fcf-protection -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++ -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 -fcf-protection -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++ g++ -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 -fcf-protection -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++ -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 -fcf-protection -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++ -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 -fcf-protection -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++ -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 -fcf-protection -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++ -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 -fcf-protection -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++ -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 -fcf-protection -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++ -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 -fcf-protection -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++ -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 -fcf-protection -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++ -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 -fcf-protection -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++ -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 -fcf-protection -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++ -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 -fcf-protection -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++) | ~~^~~~~~~~~~~~~~~~ g++ -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 -fcf-protection -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++ -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 -fcf-protection -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++ -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 -fcf-protection -Wall -O3 -I /usr/include/bamtools -I /usr/include make_plots.o -o make_plots -Wl,-z,relro -Wl,-z,now g++ -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 -fcf-protection -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++ -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 -fcf-protection -Wall -O3 -I /usr/include/bamtools -I /usr/include fa2gaps.o fasta.o -o fa2gaps -Wl,-z,relro -Wl,-z,now g++ -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 -fcf-protection -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++ -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 -fcf-protection -Wall -O3 -I /usr/include/bamtools -I /usr/include fa2gc.o fasta.o -o fa2gc -Wl,-z,relro -Wl,-z,now g++ -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 -fcf-protection -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++ -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 -fcf-protection -Wall -O3 -I /usr/include/bamtools -I /usr/include scaff2contig.o fasta.o -o scaff2contig -Wl,-z,relro -Wl,-z,now g++ -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 -fcf-protection -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++ -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 -fcf-protection -Wall -O3 -I /usr/include/bamtools -I /usr/include n50.o fasta.o -o n50 -Wl,-z,relro -Wl,-z,now g++ -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 -fcf-protection -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++ task_gapresize.cpp: In function 'int main(int, char**)': task_gapresize.cpp:129:127: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int64_t' {aka 'long int'} [-Wsign-compare] 129 | if (!bamAlign.IsReverseStrand() && pairOrientation == INNIE && bamAlign.InsertSize > 0 && gapIter->second < fragEnd && fragEnd <= gapIter->second + options.maxFragLength) | ~~~~~~~~~~~~~~~~^~~~~~~~~ task_gapresize.cpp:129:148: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'long unsigned int' [-Wsign-compare] 129 | if (!bamAlign.IsReverseStrand() && pairOrientation == INNIE && bamAlign.InsertSize > 0 && gapIter->second < fragEnd && fragEnd <= gapIter->second + options.maxFragLength) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -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 -fcf-protection -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++ -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 -fcf-protection -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++ g++ -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 -fcf-protection -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++ -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 -fcf-protection -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++ -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 -fcf-protection -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.675219.smaltmap.smalt_index foo1.fasta # Command line: smalt index -k 13 -s 2 out.bam.tmp.675219.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: 0 seconds [REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.675219.smaltmap.smalt_sample out.bam.tmp.675219.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Command line: smalt sample -u 1000 -o out.bam.tmp.675219.smaltmap.smalt_sample out.bam.tmp.675219.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:3 seconds # smalt: Total elapsed wall clock time: 3 seconds [REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.675219.smaltmap.smalt_sample -f samsoft out.bam.tmp.675219.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.675219.smaltmap.raw.bam # Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.675219.smaltmap.smalt_sample -f samsoft out.bam.tmp.675219.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:17 seconds # smalt: Total elapsed wall clock time: 17 seconds [REAPR smaltmap] Running: samtools sort out.bam.tmp.675219.smaltmap.raw.bam -O bam -o out.bam.tmp.675219.smaltmap.raw.bam.sort.bam [REAPR smaltmap] Running: samtools rmdup out.bam.tmp.675219.smaltmap.raw.bam.sort.bam out.bam.tmp.675219.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.675219.smaltmap.header [REAPR smaltmap] Running: samtools view -H out.bam.tmp.675219.smaltmap.rmdup.bam >> out.bam.tmp.675219.smaltmap.header [REAPR smaltmap] Running: samtools reheader out.bam.tmp.675219.smaltmap.header out.bam.tmp.675219.smaltmap.rmdup.bam > out.bam [REAPR smaltmap] Running: samtools index out.bam [REAPR smaltmap] Running: rm out.bam.tmp.675219.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 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' in '../reapr_1.0.18+dfsg-6_amd64.deb'. dpkg-deb: building package 'reapr-dbgsym' in '../reapr-dbgsym_1.0.18+dfsg-6_amd64.deb'. dpkg-genbuildinfo --build=binary -O../reapr_1.0.18+dfsg-6_amd64.buildinfo dpkg-genchanges --build=binary -O../reapr_1.0.18+dfsg-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/615444/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/615444/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/615444 and its subdirectories I: Current time: Wed Nov 13 08:39:48 +14 2024 I: pbuilder-time-stamp: 1731436788