Wed Dec 25 12:31:03 UTC 2024  I: starting to build reapr/trixie/i386 on jenkins on '2024-12-25 12:30'
Wed Dec 25 12:31:03 UTC 2024  I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_9/38496/console.log
Wed Dec 25 12:31:03 UTC 2024  I: Downloading source for trixie/reapr=1.0.18+dfsg-7
--2024-12-25 12:31:04--  http://deb.debian.org/debian/pool/main/r/reapr/reapr_1.0.18%2bdfsg-7.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2160 (2.1K) [text/prs.lines.tag]
Saving to: ‘reapr_1.0.18+dfsg-7.dsc’

     0K ..                                                    100%  325M=0s

2024-12-25 12:31:04 (325 MB/s) - ‘reapr_1.0.18+dfsg-7.dsc’ saved [2160/2160]

Wed Dec 25 12:31:04 UTC 2024  I: reapr_1.0.18+dfsg-7.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 3.0 (quilt)
Source: reapr
Binary: reapr
Architecture: any
Version: 1.0.18+dfsg-7
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Sascha Steinbiss <satta@debian.org>
Homepage: https://www.sanger.ac.uk/science/tools/reapr
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/reapr
Vcs-Git: https://salsa.debian.org/med-team/reapr.git
Testsuite: autopkgtest
Testsuite-Triggers: samtools
Build-Depends: debhelper-compat (= 13), libbamtools-dev, libtabixpp-dev, libhts-dev, zlib1g-dev, asciidoctor, samtools, bamtools, smalt, r-base, snpomatic, tabix, libfile-copy-link-perl
Package-List:
 reapr deb science optional arch=any
Checksums-Sha1:
 3534f93653fc8eb621226e51ef212835b1281af9 74636 reapr_1.0.18+dfsg.orig.tar.gz
 93fe0a13504a5824646a65d5041835af2a729ea9 319912 reapr_1.0.18+dfsg-7.debian.tar.xz
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 58a388622ee433e4ca53a72d4feb6ea651498310b5c11ccfe3c857a0a5361103 319912 reapr_1.0.18+dfsg-7.debian.tar.xz
Files:
 061dfbfe97a0bdffe3a4b9e4be8142d3 74636 reapr_1.0.18+dfsg.orig.tar.gz
 9e4855aac3352f5b7fcbf6e8a6d4532d 319912 reapr_1.0.18+dfsg-7.debian.tar.xz

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Wed Dec 25 12:31:04 UTC 2024  I: Checking whether the package is not for us
Wed Dec 25 12:31:04 UTC 2024  I: Starting 1st build on remote node ionos2-i386.debian.net.
Wed Dec 25 12:31:04 UTC 2024  I: Preparing to do remote build '1' on ionos2-i386.debian.net.
Wed Dec 25 12:34:57 UTC 2024  I: Deleting $TMPDIR on ionos2-i386.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Wed Dec 25 00:31:06 -12 2024
I: pbuilder-time-stamp: 1735129866
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: using eatmydata during job
I: Copying source file
I: copying [reapr_1.0.18+dfsg-7.dsc]
I: copying [./reapr_1.0.18+dfsg.orig.tar.gz]
I: copying [./reapr_1.0.18+dfsg-7.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sat Dec 21 22:15:37 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-7.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-7.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/20103/tmp/hooks/D02_print_environment starting
I: set
  BUILDDIR='/build/reproducible-path'
  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
  BUILDUSERNAME='pbuilder1'
  BUILD_ARCH='i386'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 '
  DISTRIBUTION='trixie'
  HOME='/root'
  HOST_ARCH='i386'
  IFS=' 	
  '
  INVOCATION_ID='2f3e6e0f57d44f60a8967ef6b1f471f8'
  LANG='C'
  LANGUAGE='en_US:en'
  LC_ALL='C'
  LD_LIBRARY_PATH='/usr/lib/libeatmydata'
  LD_PRELOAD='libeatmydata.so'
  MAIL='/var/mail/root'
  OPTIND='1'
  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
  PBCURRENTCOMMANDLINEOPERATION='build'
  PBUILDER_OPERATION='build'
  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
  PBUILDER_SYSCONFDIR='/etc'
  PPID='20103'
  PS1='# '
  PS2='> '
  PS4='+ '
  PWD='/'
  SHELL='/bin/bash'
  SHLVL='2'
  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.W279HGSC/pbuilderrc_A3iL --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.W279HGSC/b1 --logfile b1/build.log reapr_1.0.18+dfsg-7.dsc'
  SUDO_GID='112'
  SUDO_UID='107'
  SUDO_USER='jenkins'
  TERM='unknown'
  TZ='/usr/share/zoneinfo/Etc/GMT+12'
  USER='root'
  _='/usr/bin/systemd-run'
  http_proxy='http://46.16.76.132:3128'
I: uname -a
  Linux ionos2-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/20103/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: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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 ... 19953 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} libproc2-0{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} procps{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 linux-sysctl-defaults lynx psmisc 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, 196 newly installed, 0 to remove and 0 not upgraded.
Need to get 116 MB of archives. After unpacking 300 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 tzdata all 2024b-4 [256 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB]
Get: 3 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-6 [876 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-6 [69.4 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 openssl i386 3.3.2-2 [1387 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20240203 [158 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-3 [201 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-6 [1198 kB]
Get: 14 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-12 [95.9 kB]
Get: 15 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 ucf all 3.0045 [45.2 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 rubygems-integration all 1.18 [6704 B]
Get: 19 http://deb.debian.org/debian trixie/main i386 rake all 13.2.1-1 [65.2 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 ruby-net-telnet all 0.2.0-1 [13.1 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 ruby-webrick all 1.8.1-1 [51.4 kB]
Get: 22 http://deb.debian.org/debian trixie/main i386 ruby-xmlrpc all 0.3.3-2 [24.4 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 libruby i386 1:3.1+nmu1 [4664 B]
Get: 24 http://deb.debian.org/debian trixie/main i386 ruby-sdbm i386 1.0.0-5+b5 [16.8 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 libedit2 i386 3.1-20240808-1 [98.0 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 libncurses6 i386 6.5-2+b1 [112 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 libyaml-0-2 i386 0.2.5-2 [55.8 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 libruby3.1t64 i386 3.1.2-8.4 [5470 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 ruby3.1 i386 3.1.2-8.4 [664 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 ruby-rubygems all 3.4.20-1 [309 kB]
Get: 31 http://deb.debian.org/debian trixie/main i386 ruby i386 1:3.1+nmu1 [5584 B]
Get: 32 http://deb.debian.org/debian trixie/main i386 ruby-asciidoctor all 2.0.23-1 [214 kB]
Get: 33 http://deb.debian.org/debian trixie/main i386 asciidoctor all 2.0.23-1 [88.7 kB]
Get: 34 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB]
Get: 35 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 36 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 37 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 38 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-3 [723 kB]
Get: 39 http://deb.debian.org/debian trixie/main i386 libbamtools2.5.2 i386 2.5.2+dfsg-6+b1 [178 kB]
Get: 40 http://deb.debian.org/debian trixie/main i386 libjsoncpp26 i386 1.9.6-3 [90.0 kB]
Get: 41 http://deb.debian.org/debian trixie/main i386 bamtools i386 2.5.2+dfsg-6+b1 [219 kB]
Get: 42 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.2~rc1-2 [24.0 kB]
Get: 43 http://deb.debian.org/debian trixie/main i386 comerr-dev i386 2.1-1.47.2~rc1-2 [55.9 kB]
Get: 44 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB]
Get: 45 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB]
Get: 46 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 47 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 48 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 49 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 50 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 51 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 52 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB]
Get: 53 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 54 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-3 [1631 kB]
Get: 55 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 56 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 57 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB]
Get: 58 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 59 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB]
Get: 60 http://deb.debian.org/debian trixie/main i386 libpng16-16t64 i386 1.6.44-3 [288 kB]
Get: 61 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB]
Get: 62 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 63 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 64 http://deb.debian.org/debian trixie/main i386 fontconfig-config i386 2.15.0-1.1+b1 [318 kB]
Get: 65 http://deb.debian.org/debian trixie/main i386 libfontconfig1 i386 2.15.0-1.1+b1 [402 kB]
Get: 66 http://deb.debian.org/debian trixie/main i386 fontconfig i386 2.15.0-1.1+b1 [463 kB]
Get: 67 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB]
Get: 68 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB]
Get: 69 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B]
Get: 70 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-3 [350 kB]
Get: 71 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB]
Get: 72 http://deb.debian.org/debian trixie/main i386 libgssrpc4t64 i386 1.21.3-3 [63.1 kB]
Get: 73 http://deb.debian.org/debian trixie/main i386 libkadm5clnt-mit12 i386 1.21.3-3 [43.2 kB]
Get: 74 http://deb.debian.org/debian trixie/main i386 libkdb5-10t64 i386 1.21.3-3 [45.1 kB]
Get: 75 http://deb.debian.org/debian trixie/main i386 libkadm5srv-mit12 i386 1.21.3-3 [57.0 kB]
Get: 76 http://deb.debian.org/debian trixie/main i386 krb5-multidev i386 1.21.3-3 [126 kB]
Get: 77 http://deb.debian.org/debian trixie/main i386 libbambamc0 i386 0.0.50-6+b2 [43.7 kB]
Get: 78 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Get: 79 http://deb.debian.org/debian trixie/main i386 libbamtools-dev i386 2.5.2+dfsg-6+b1 [242 kB]
Get: 80 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-4 [143 kB]
Get: 81 http://deb.debian.org/debian trixie/main i386 libbrotli-dev i386 1.1.0-2+b6 [313 kB]
Get: 82 http://deb.debian.org/debian trixie/main i386 libbz2-dev i386 1.0.8-6 [32.1 kB]
Get: 83 http://deb.debian.org/debian trixie/main i386 libpixman-1-0 i386 0.44.0-3 [246 kB]
Get: 84 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.11-1 [20.7 kB]
Get: 85 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.5-1 [28.2 kB]
Get: 86 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.17.0-2+b1 [148 kB]
Get: 87 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.10-2 [337 kB]
Get: 88 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.10-2 [834 kB]
Get: 89 http://deb.debian.org/debian trixie/main i386 libxcb-render0 i386 1.17.0-2+b1 [116 kB]
Get: 90 http://deb.debian.org/debian trixie/main i386 libxcb-shm0 i386 1.17.0-2+b1 [105 kB]
Get: 91 http://deb.debian.org/debian trixie/main i386 libxext6 i386 2:1.3.4-1+b2 [52.6 kB]
Get: 92 http://deb.debian.org/debian trixie/main i386 libxrender1 i386 1:0.9.10-1.1+b3 [28.8 kB]
Get: 93 http://deb.debian.org/debian trixie/main i386 libcairo2 i386 1.18.2-2 [591 kB]
Get: 94 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB]
Get: 95 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB]
Get: 96 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3+b1 [200 kB]
Get: 97 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB]
Get: 98 http://deb.debian.org/debian trixie/main i386 libnghttp3-9 i386 1.6.0-2 [75.9 kB]
Get: 99 http://deb.debian.org/debian trixie/main i386 libngtcp2-16 i386 1.9.1-1 [151 kB]
Get: 100 http://deb.debian.org/debian trixie/main i386 libngtcp2-crypto-gnutls8 i386 1.9.1-1 [19.1 kB]
Get: 101 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB]
Get: 102 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB]
Get: 103 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB]
Get: 104 http://deb.debian.org/debian trixie/main i386 libcurl3t64-gnutls i386 8.11.1-1 [404 kB]
Get: 105 http://deb.debian.org/debian trixie/main i386 libevent-2.1-7t64 i386 2.1.12-stable-10+b1 [195 kB]
Get: 106 http://deb.debian.org/debian trixie/main i386 libunbound8 i386 1.22.0-1 [632 kB]
Get: 107 http://deb.debian.org/debian trixie/main i386 libgnutls-dane0t64 i386 3.8.8-2 [447 kB]
Get: 108 http://deb.debian.org/debian trixie/main i386 libgnutls-openssl27t64 i386 3.8.8-2 [447 kB]
Get: 109 http://deb.debian.org/debian trixie/main i386 libidn2-dev i386 2.3.7-2+b1 [126 kB]
Get: 110 http://deb.debian.org/debian trixie/main i386 libp11-kit-dev i386 0.25.5-2+b1 [208 kB]
Get: 111 http://deb.debian.org/debian trixie/main i386 libtasn1-6-dev i386 4.19.0-3+b3 [102 kB]
Get: 112 http://deb.debian.org/debian trixie/main i386 libgmpxx4ldbl i386 2:6.3.0+dfsg-3 [329 kB]
Get: 113 http://deb.debian.org/debian trixie/main i386 libgmp-dev i386 2:6.3.0+dfsg-3 [661 kB]
Get: 114 http://deb.debian.org/debian trixie/main i386 nettle-dev i386 3.10-1+b1 [1334 kB]
Get: 115 http://deb.debian.org/debian trixie/main i386 libgnutls28-dev i386 3.8.8-2 [1453 kB]
Get: 116 http://deb.debian.org/debian trixie/main i386 libkrb5-dev i386 1.21.3-3 [15.7 kB]
Get: 117 http://deb.debian.org/debian trixie/main i386 libldap-dev i386 2.5.18+dfsg-3+b1 [324 kB]
Get: 118 http://deb.debian.org/debian trixie/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB]
Get: 119 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB]
Get: 120 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-4 [26.2 kB]
Get: 121 http://deb.debian.org/debian trixie/main i386 libnghttp2-dev i386 1.64.0-1 [123 kB]
Get: 122 http://deb.debian.org/debian trixie/main i386 libnghttp3-dev i386 1.6.0-2 [101 kB]
Get: 123 http://deb.debian.org/debian trixie/main i386 libngtcp2-crypto-gnutls-dev i386 1.9.1-1 [24.0 kB]
Get: 124 http://deb.debian.org/debian trixie/main i386 libngtcp2-dev i386 1.9.1-1 [202 kB]
Get: 125 http://deb.debian.org/debian trixie/main i386 libpsl-dev i386 0.21.2-1.1+b1 [78.4 kB]
Get: 126 http://deb.debian.org/debian trixie/main i386 librtmp-dev i386 2.4+20151223.gitfa8646d.1-2+b5 [72.3 kB]
Get: 127 http://deb.debian.org/debian trixie/main i386 libssl-dev i386 3.3.2-2 [2790 kB]
Get: 128 http://deb.debian.org/debian trixie/main i386 libssh2-1-dev i386 1.11.1-1 [407 kB]
Get: 129 http://deb.debian.org/debian trixie/main i386 libzstd-dev i386 1.5.6+dfsg-1+b1 [355 kB]
Get: 130 http://deb.debian.org/debian trixie/main i386 libcurl4-gnutls-dev i386 8.11.1-1 [535 kB]
Get: 131 http://deb.debian.org/debian trixie/main i386 libcurl4t64 i386 8.11.1-1 [393 kB]
Get: 132 http://deb.debian.org/debian trixie/main i386 libdatrie1 i386 0.2.13-3+b1 [39.9 kB]
Get: 133 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.22-1 [48.1 kB]
Get: 134 http://deb.debian.org/debian trixie/main i386 libdeflate-dev i386 1.22-1 [57.2 kB]
Get: 135 http://deb.debian.org/debian trixie/main i386 libfile-copy-link-perl all 0.140-5 [13.2 kB]
Get: 136 http://deb.debian.org/debian trixie/main i386 libfribidi0 i386 1.0.16-1 [27.0 kB]
Get: 137 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14.2.0-8 [735 kB]
Get: 138 http://deb.debian.org/debian trixie/main i386 libglib2.0-0t64 i386 2.82.4-1 [1572 kB]
Get: 139 http://deb.debian.org/debian trixie/main i386 libgraphite2-3 i386 1.3.14-2+b1 [77.8 kB]
Get: 140 http://deb.debian.org/debian trixie/main i386 libharfbuzz0b i386 10.1.0-1 [503 kB]
Get: 141 http://deb.debian.org/debian trixie/main i386 libhtscodecs2 i386 1.6.1-1 [70.8 kB]
Get: 142 http://deb.debian.org/debian trixie/main i386 libhts3t64 i386 1.20+ds-2 [500 kB]
Get: 143 http://deb.debian.org/debian trixie/main i386 liblzma-dev i386 5.6.3-1+b1 [328 kB]
Get: 144 http://deb.debian.org/debian trixie/main i386 libhts-dev i386 1.20+ds-2 [1693 kB]
Get: 145 http://deb.debian.org/debian trixie/main i386 x11-common all 1:7.7+23.1 [216 kB]
Get: 146 http://deb.debian.org/debian trixie/main i386 libice6 i386 2:1.1.1-1 [67.8 kB]
Get: 147 http://deb.debian.org/debian trixie/main i386 libjbig0 i386 2.1-6.1+b2 [32.2 kB]
Get: 148 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-3+b1 [171 kB]
Get: 149 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-4 [2194 kB]
Get: 150 http://deb.debian.org/debian trixie/main i386 liblerc4 i386 4.0.0+ds-5 [191 kB]
Get: 151 http://deb.debian.org/debian trixie/main i386 libthai-data all 0.1.29-2 [168 kB]
Get: 152 http://deb.debian.org/debian trixie/main i386 libthai0 i386 0.1.29-2+b1 [50.3 kB]
Get: 153 http://deb.debian.org/debian trixie/main i386 libpango-1.0-0 i386 1.55.0+ds-3 [233 kB]
Get: 154 http://deb.debian.org/debian trixie/main i386 libpangoft2-1.0-0 i386 1.55.0+ds-3 [58.2 kB]
Get: 155 http://deb.debian.org/debian trixie/main i386 libpangocairo-1.0-0 i386 1.55.0+ds-3 [36.2 kB]
Get: 156 http://deb.debian.org/debian trixie/main i386 libpaper1 i386 1.1.29+b2 [13.0 kB]
Get: 157 http://deb.debian.org/debian trixie/main i386 libpaper-utils i386 1.1.29+b2 [9304 B]
Get: 158 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-6 [173 kB]
Get: 159 http://deb.debian.org/debian trixie/main i386 libsharpyuv0 i386 1.4.0-0.1+b1 [113 kB]
Get: 160 http://deb.debian.org/debian trixie/main i386 libsm6 i386 2:1.2.4-1 [35.9 kB]
Get: 161 http://deb.debian.org/debian trixie/main i386 libtabixpp0t64 i386 1.1.2-2.1+b1 [10.6 kB]
Get: 162 http://deb.debian.org/debian trixie/main i386 libtabixpp-dev i386 1.1.2-2.1+b1 [10.1 kB]
Get: 163 http://deb.debian.org/debian trixie/main i386 libtcl8.6 i386 8.6.15+dfsg-2 [1103 kB]
Get: 164 http://deb.debian.org/debian trixie/main i386 libwebp7 i386 1.4.0-0.1+b1 [322 kB]
Get: 165 http://deb.debian.org/debian trixie/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB]
Get: 166 http://deb.debian.org/debian trixie/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 167 http://deb.debian.org/debian trixie/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB]
Get: 168 http://deb.debian.org/debian trixie/main i386 libxft2 i386 2.3.6-1+b3 [55.3 kB]
Get: 169 http://deb.debian.org/debian trixie/main i386 libxss1 i386 1:1.2.3-1+b2 [17.3 kB]
Get: 170 http://deb.debian.org/debian trixie/main i386 libtk8.6 i386 8.6.15-1 [833 kB]
Get: 171 http://deb.debian.org/debian trixie/main i386 libxt6t64 i386 1:1.2.1-1.2+b1 [193 kB]
Get: 172 http://deb.debian.org/debian trixie/main i386 zip i386 3.0-14 [239 kB]
Get: 173 http://deb.debian.org/debian trixie/main i386 unzip i386 6.0-28 [166 kB]
Get: 174 http://deb.debian.org/debian trixie/main i386 xdg-utils all 1.2.1-2 [75.8 kB]
Get: 175 http://deb.debian.org/debian trixie/main i386 r-base-core i386 4.4.2-1 [28.3 MB]
Get: 176 http://deb.debian.org/debian trixie/main i386 r-cran-boot all 1.3-31-1 [639 kB]
Get: 177 http://deb.debian.org/debian trixie/main i386 r-cran-cluster i386 2.1.8-1 [583 kB]
Get: 178 http://deb.debian.org/debian trixie/main i386 r-cran-foreign i386 0.8.87-1 [256 kB]
Get: 179 http://deb.debian.org/debian trixie/main i386 r-cran-mass i386 7.3-61-1 [1113 kB]
Get: 180 http://deb.debian.org/debian trixie/main i386 r-cran-kernsmooth i386 2.23-24-1 [92.0 kB]
Get: 181 http://deb.debian.org/debian trixie/main i386 r-cran-lattice i386 0.22-6-1 [1393 kB]
Get: 182 http://deb.debian.org/debian trixie/main i386 r-cran-nlme i386 3.1.166-1 [2329 kB]
Get: 183 http://deb.debian.org/debian trixie/main i386 r-cran-matrix i386 1.7-1-1 [4156 kB]
Get: 184 http://deb.debian.org/debian trixie/main i386 r-cran-mgcv i386 1.9-1-1 [3256 kB]
Get: 185 http://deb.debian.org/debian trixie/main i386 r-cran-survival i386 3.7-0-1 [6316 kB]
Get: 186 http://deb.debian.org/debian trixie/main i386 r-cran-rpart i386 4.1.23-1 [689 kB]
Get: 187 http://deb.debian.org/debian trixie/main i386 r-cran-class i386 7.3-22-2 [87.7 kB]
Get: 188 http://deb.debian.org/debian trixie/main i386 r-cran-nnet i386 7.3-19-2 [113 kB]
Get: 189 http://deb.debian.org/debian trixie/main i386 r-cran-spatial i386 7.3-17-1 [129 kB]
Get: 190 http://deb.debian.org/debian trixie/main i386 r-cran-codetools all 0.2-20-1 [91.1 kB]
Get: 191 http://deb.debian.org/debian trixie/main i386 r-recommended all 4.4.2-1 [2572 B]
Get: 192 http://deb.debian.org/debian trixie/main i386 r-base all 4.4.2-1 [14.7 kB]
Get: 193 http://deb.debian.org/debian trixie/main i386 samtools i386 1.20-3 [688 kB]
Get: 194 http://deb.debian.org/debian trixie/main i386 smalt i386 0.7.6-13 [127 kB]
Get: 195 http://deb.debian.org/debian trixie/main i386 snpomatic i386 1.0-7 [87.9 kB]
Get: 196 http://deb.debian.org/debian trixie/main i386 tabix i386 1.20+ds-2 [536 kB]
Fetched 116 MB in 3s (41.1 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package tzdata.
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(Reading database ... 19953 files and directories currently installed.)
Preparing to unpack .../000-tzdata_2024b-4_all.deb ...
Unpacking tzdata (2024b-4) ...
Selecting previously unselected package libproc2-0:i386.
Preparing to unpack .../001-libproc2-0_2%3a4.0.4-6_i386.deb ...
Unpacking libproc2-0:i386 (2:4.0.4-6) ...
Selecting previously unselected package procps.
Preparing to unpack .../002-procps_2%3a4.0.4-6_i386.deb ...
Unpacking procps (2:4.0.4-6) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../003-readline-common_8.2-6_all.deb ...
Unpacking readline-common (8.2-6) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package openssl.
Preparing to unpack .../005-openssl_3.3.2-2_i386.deb ...
Unpacking openssl (3.3.2-2) ...
Selecting previously unselected package ca-certificates.
Preparing to unpack .../006-ca-certificates_20240203_all.deb ...
Unpacking ca-certificates (20240203) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../007-libmagic-mgc_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:i386.
Preparing to unpack .../008-libmagic1t64_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic1t64:i386 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../009-file_1%3a5.45-3+b1_i386.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../010-gettext-base_0.22.5-3_i386.deb ...
Unpacking gettext-base (0.22.5-3) ...
Selecting previously unselected package libuchardet0:i386.
Preparing to unpack .../011-libuchardet0_0.0.8-1+b2_i386.deb ...
Unpacking libuchardet0:i386 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../012-groff-base_1.23.0-6_i386.deb ...
Unpacking groff-base (1.23.0-6) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../013-bsdextrautils_2.40.2-12_i386.deb ...
Unpacking bsdextrautils (2.40.2-12) ...
Selecting previously unselected package libpipeline1:i386.
Preparing to unpack .../014-libpipeline1_1.5.8-1_i386.deb ...
Unpacking libpipeline1:i386 (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../015-man-db_2.13.0-1_i386.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package ucf.
Preparing to unpack .../016-ucf_3.0045_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0045) ...
Selecting previously unselected package rubygems-integration.
Preparing to unpack .../017-rubygems-integration_1.18_all.deb ...
Unpacking rubygems-integration (1.18) ...
Selecting previously unselected package rake.
Preparing to unpack .../018-rake_13.2.1-1_all.deb ...
Unpacking rake (13.2.1-1) ...
Selecting previously unselected package ruby-net-telnet.
Preparing to unpack .../019-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 .../020-ruby-webrick_1.8.1-1_all.deb ...
Unpacking ruby-webrick (1.8.1-1) ...
Selecting previously unselected package ruby-xmlrpc.
Preparing to unpack .../021-ruby-xmlrpc_0.3.3-2_all.deb ...
Unpacking ruby-xmlrpc (0.3.3-2) ...
Selecting previously unselected package libruby:i386.
Preparing to unpack .../022-libruby_1%3a3.1+nmu1_i386.deb ...
Unpacking libruby:i386 (1:3.1+nmu1) ...
Selecting previously unselected package ruby-sdbm:i386.
Preparing to unpack .../023-ruby-sdbm_1.0.0-5+b5_i386.deb ...
Unpacking ruby-sdbm:i386 (1.0.0-5+b5) ...
Selecting previously unselected package libedit2:i386.
Preparing to unpack .../024-libedit2_3.1-20240808-1_i386.deb ...
Unpacking libedit2:i386 (3.1-20240808-1) ...
Selecting previously unselected package libncurses6:i386.
Preparing to unpack .../025-libncurses6_6.5-2+b1_i386.deb ...
Unpacking libncurses6:i386 (6.5-2+b1) ...
Selecting previously unselected package libyaml-0-2:i386.
Preparing to unpack .../026-libyaml-0-2_0.2.5-2_i386.deb ...
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Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
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Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
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Setting up libpixman-1-0:i386 (0.44.0-3) ...
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Setting up libxdmcp6:i386 (1:1.1.5-1) ...
Setting up libkeyutils1:i386 (1.6.3-4) ...
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Setting up libfile-copy-link-perl (0.140-5) ...
Setting up libicu72:i386 (72.1-5+b1) ...
Setting up libzstd-dev:i386 (1.5.6+dfsg-1+b1) ...
Setting up liblerc4:i386 (4.0.0+ds-5) ...
Setting up bsdextrautils (2.40.2-12) ...
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Setting up unzip (6.0-28) ...
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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:i386 (0.21.2-1.1+b1) ...
Setting up libnghttp2-14:i386 (1.64.0-1) ...
Setting up libdeflate0:i386 (1.22-1) ...
Setting up gettext-base (0.22.5-3) ...
Setting up m4 (1.4.19-4) ...
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Setting up libxcb-shm0:i386 (1.17.0-2+b1) ...
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Setting up tzdata (2024b-4) ...

Current default time zone: 'Etc/UTC'
Local time is now:      Wed Dec 25 12:31:45 UTC 2024.
Universal Time is now:  Wed Dec 25 12:31:45 UTC 2024.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

Setting up zip (3.0-14) ...
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No schema files found: doing nothing.
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update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode
Setting up libunbound8:i386 (1.22.0-1) ...
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Setting up libidn2-dev:i386 (2.3.7-2+b1) ...
Setting up libsasl2-2:i386 (2.1.28+dfsg1-8) ...
Setting up libgfortran5:i386 (14.2.0-8) ...
Setting up autoconf (2.72-3) ...
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Setting up libwebp7:i386 (1.4.0-0.1+b1) ...
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Setting up ruby-webrick (1.8.1-1) ...
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update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
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Setting up libp11-kit-dev:i386 (0.25.5-2+b1) ...
Setting up libbz2-dev:i386 (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:i386 (2:1.1.1-1) ...
Setting up liblapack3:i386 (3.12.0-4) ...
update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode
Setting up gettext (0.22.5-3) ...
Setting up libgmp-dev:i386 (2:6.3.0+dfsg-3) ...
Setting up nettle-dev:i386 (3.10-1+b1) ...
Setting up libxrender1:i386 (1:0.9.10-1.1+b3) ...
Setting up libtool (2.4.7-8) ...
Setting up fontconfig-config (2.15.0-1.1+b1) ...
Setting up libxext6:i386 (2:1.3.4-1+b2) ...
Setting up libngtcp2-crypto-gnutls-dev:i386 (1.9.1-1) ...
Setting up libngtcp2-dev:i386 (1.9.1-1) ...
Setting up libldap-2.5-0:i386 (2.5.18+dfsg-3+b1) ...
Setting up pkgconf:i386 (1.8.1-4) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
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Setting up ca-certificates (20240203) ...
Updating certificates in /etc/ssl/certs...
146 added, 0 removed; done.
Setting up libfreetype6:i386 (2.13.3+dfsg-1) ...
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Setting up ucf (3.0045) ...
Setting up libssh2-1-dev:i386 (1.11.1-1) ...
Setting up libreadline8t64:i386 (8.2-6) ...
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up groff-base (1.23.0-6) ...
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Setting up libxss1:i386 (1:1.2.3-1+b2) ...
Setting up libfontconfig1:i386 (2.15.0-1.1+b1) ...
Setting up libsm6:i386 (2:1.2.4-1) ...
Setting up libgnutls28-dev:i386 (3.8.8-2) ...
Setting up libpaper1:i386 (1.1.29+b2) ...
Creating config file /etc/papersize with new version
Setting up libnghttp2-dev:i386 (1.64.0-1) ...
Setting up fontconfig (2.15.0-1.1+b1) ...
Regenerating fonts cache... done.
Setting up libxft2:i386 (2.3.6-1+b3) ...
Setting up libcurl4t64:i386 (8.11.1-1) ...
Setting up libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libtk8.6:i386 (8.6.15-1) ...
Setting up libpango-1.0-0:i386 (1.55.0+ds-3) ...
Setting up libcurl3t64-gnutls:i386 (8.11.1-1) ...
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:i386 (1.18.2-2) ...
Setting up libgssrpc4t64:i386 (1.21.3-3) ...
Setting up libxt6t64:i386 (1:1.2.1-1.2+b1) ...
Setting up librtmp-dev:i386 (2.4+20151223.gitfa8646d.1-2+b5) ...
Setting up libhts3t64:i386 (1.20+ds-2) ...
Setting up libpangoft2-1.0-0:i386 (1.55.0+ds-3) ...
Setting up libpangocairo-1.0-0:i386 (1.55.0+ds-3) ...
Setting up libkadm5clnt-mit12:i386 (1.21.3-3) ...
Setting up libkdb5-10t64:i386 (1.21.3-3) ...
Setting up debhelper (13.20) ...
Setting up samtools (1.20-3) ...
Setting up r-base-core (4.4.2-1) ...
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 (2.1.8-1) ...
Setting up libkadm5srv-mit12:i386 (1.21.3-3) ...
Setting up libtabixpp0t64:i386 (1.1.2-2.1+b1) ...
Setting up r-cran-nnet (7.3-19-2) ...
Setting up krb5-multidev:i386 (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:i386 (1.21.3-3) ...
Setting up r-cran-matrix (1.7-1-1) ...
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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:i386 (8.11.1-1) ...
Setting up r-cran-rpart (4.1.23-1) ...
Setting up libhts-dev:i386 (1.20+ds-2) ...
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Setting up ruby-rubygems (3.4.20-1) ...
Processing triggers for libc-bin (2.40-4) ...
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...
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Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/reapr-1.0.18+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../reapr_1.0.18+dfsg-7_source.changes
dpkg-buildpackage: info: source package reapr
dpkg-buildpackage: info: source version 1.0.18+dfsg-7
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
 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 -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++ -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 -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++ -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 -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++ -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 -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<string, list<pair<unsigned long, unsigned long> > >::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 -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++ -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 -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++
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 -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++ -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 -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++ -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 -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++ -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 -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++ -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 -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++ -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 -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++ -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 -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++ -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 -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++ -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 -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++ -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 -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++ -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 -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<Histogram>&, 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 -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++ -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 -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++ -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 -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++ -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 -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++ -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 -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++ -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 -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++ -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 -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++ -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 -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++ -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 -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++ -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 -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++ -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 -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++ -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 -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++ -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 -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++ -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 -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++
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 -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++ -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 -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<long unsigned int, BamTools::BamAlignment>&, 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 -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:/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	-
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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.34069.smaltmap.smalt_index foo1.fasta
# Command line:  smalt index -k 13 -s 2 out.bam.tmp.34069.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: 1 seconds
[REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.34069.smaltmap.smalt_sample out.bam.tmp.34069.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq
# Command line:  smalt sample -u 1000 -o out.bam.tmp.34069.smaltmap.smalt_sample out.bam.tmp.34069.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:2 seconds
# smalt: Total elapsed wall clock time: 2 seconds
[REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5   -g out.bam.tmp.34069.smaltmap.smalt_sample -f samsoft out.bam.tmp.34069.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/'   | samtools view -S -T foo1.fasta -b - > out.bam.tmp.34069.smaltmap.raw.bam
# Command line:  smalt map -r 0 -x -y 0.5 -g out.bam.tmp.34069.smaltmap.smalt_sample -f samsoft out.bam.tmp.34069.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:23 seconds
# smalt: Total elapsed wall clock time: 23 seconds
[REAPR smaltmap] Running: samtools sort out.bam.tmp.34069.smaltmap.raw.bam -O bam -o out.bam.tmp.34069.smaltmap.raw.bam.sort.bam
[REAPR smaltmap] Running: samtools rmdup out.bam.tmp.34069.smaltmap.raw.bam.sort.bam out.bam.tmp.34069.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.34069.smaltmap.header
[REAPR smaltmap] Running: samtools view -H out.bam.tmp.34069.smaltmap.rmdup.bam >> out.bam.tmp.34069.smaltmap.header
[REAPR smaltmap] Running: samtools reheader out.bam.tmp.34069.smaltmap.header out.bam.tmp.34069.smaltmap.rmdup.bam > out.bam
[REAPR smaltmap] Running: samtools index out.bam
[REAPR smaltmap] Running: rm out.bam.tmp.34069.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-dbgsym' in '../reapr-dbgsym_1.0.18+dfsg-7_i386.deb'.
dpkg-deb: building package 'reapr' in '../reapr_1.0.18+dfsg-7_i386.deb'.
 dpkg-genbuildinfo --build=binary -O../reapr_1.0.18+dfsg-7_i386.buildinfo
 dpkg-genchanges --build=binary -O../reapr_1.0.18+dfsg-7_i386.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: 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/20103 and its subdirectories
I: Current time: Wed Dec 25 00:34:56 -12 2024
I: pbuilder-time-stamp: 1735130096
Wed Dec 25 12:34:57 UTC 2024  I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net.
Wed Dec 25 12:34:57 UTC 2024  I: Preparing to do remote build '2' on ionos6-i386.debian.net.
Wed Dec 25 13:02:19 UTC 2024  I: Deleting $TMPDIR on ionos6-i386.debian.net.
Wed Dec 25 13:02:41 UTC 2024  I: reapr_1.0.18+dfsg-7_i386.changes:
Format: 1.8
Date: Sat, 21 Dec 2024 22:47:35 +0100
Source: reapr
Binary: reapr reapr-dbgsym
Architecture: i386
Version: 1.0.18+dfsg-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 reapr      - universal tool for genome assembly evaluation
Closes: 1045461
Changes:
 reapr (1.0.18+dfsg-7) unstable; urgency=medium
 .
   [ Michael R. Crusoe ]
   * Team upload.
   * d/watch: https is now an option for the Sanger FTP site.
 .
   [ Andreas Tille ]
   * Fix clean target
     Closes: #1045461
   * Standards-Version: 4.7.0 (routine-update)
Checksums-Sha1:
 81d3825f1fc361f30f78f837092b5d0854858a79 3693460 reapr-dbgsym_1.0.18+dfsg-7_i386.deb
 5f70f707f9cfb199b506a312ea2fa43f4e6bb32b 10133 reapr_1.0.18+dfsg-7_i386.buildinfo
 4bf410bc4fb1e9bbbc6832467abce84e992d2697 217912 reapr_1.0.18+dfsg-7_i386.deb
Checksums-Sha256:
 4d7d2a2fd5eaa05dadd6d5ee65b7490e6df0dcac9db6727d25cb1f56ea260079 3693460 reapr-dbgsym_1.0.18+dfsg-7_i386.deb
 6697fd5b734cee53e009826079572a60f346a7fd989c7bf15023263d2f2adcd5 10133 reapr_1.0.18+dfsg-7_i386.buildinfo
 be4d62bd92882f718828b265d92ded23edd35cbd8b68ba47d6dc5039d4d7d753 217912 reapr_1.0.18+dfsg-7_i386.deb
Files:
 212b8f23801e7a17408a65d4f06d3454 3693460 debug optional reapr-dbgsym_1.0.18+dfsg-7_i386.deb
 980c22754acc64be38d2e8f62bb6726b 10133 science optional reapr_1.0.18+dfsg-7_i386.buildinfo
 481cf2bb221a6caa8c4d49e6f368df43 217912 science optional reapr_1.0.18+dfsg-7_i386.deb
Wed Dec 25 13:02:42 UTC 2024  I: diffoscope 284 will be used to compare the two builds:
Running as unit: rb-diffoscope-i386_9-38496.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.W279HGSC/reapr_1.0.18+dfsg-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.W279HGSC/reapr_1.0.18+dfsg-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.W279HGSC/reapr_1.0.18+dfsg-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.W279HGSC/b1/reapr_1.0.18+dfsg-7_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.W279HGSC/b2/reapr_1.0.18+dfsg-7_i386.changes

## command (total time: 0.000s)
       0.000s      1 call     cmp (internal)

## has_same_content_as (total time: 0.000s)
       0.000s      1 call     abc.DotChangesFile

## main (total time: 0.368s)
       0.368s      2 calls    outputs
       0.000s      1 call     cleanup

## recognizes (total time: 0.049s)
       0.049s     12 calls    diffoscope.comparators.binary.FilesystemFile

## specialize (total time: 0.000s)
       0.000s      1 call     specialize
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 683ms
CPU time consumed: 683ms
Wed Dec 25 13:02:43 UTC 2024  I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists.
Wed Dec 25 13:02:43 UTC 2024  I: reapr from trixie built successfully and reproducibly on i386.
Wed Dec 25 13:02:45 UTC 2024  I: Submitting .buildinfo files to external archives:
Wed Dec 25 13:02:45 UTC 2024  I: Submitting 12K	b1/reapr_1.0.18+dfsg-7_i386.buildinfo.asc
Wed Dec 25 13:02:45 UTC 2024  I: Submitting 12K	b2/reapr_1.0.18+dfsg-7_i386.buildinfo.asc
Wed Dec 25 13:02:46 UTC 2024  I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Wed Dec 25 13:02:46 UTC 2024  I: Done submitting .buildinfo files.
Wed Dec 25 13:02:46 UTC 2024  I: Removing signed reapr_1.0.18+dfsg-7_i386.buildinfo.asc files:
removed './b1/reapr_1.0.18+dfsg-7_i386.buildinfo.asc'
removed './b2/reapr_1.0.18+dfsg-7_i386.buildinfo.asc'