I: pbuilder: network access will be disabled during build
I: Current time: Thu Jun 6 10:05:41 -12 2024
I: pbuilder-time-stamp: 1717711541
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-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 [hinge_0.5.0-7.dsc]
I: copying [./hinge_0.5.0.orig.tar.gz]
I: copying [./hinge_0.5.0-7.debian.tar.xz]
I: Extracting source
gpgv: Signature made Tue Dec 21 19:23:38 2021 -12
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 ./hinge_0.5.0-7.dsc: no acceptable signature found
dpkg-source: info: extracting hinge in hinge-0.5.0
dpkg-source: info: unpacking hinge_0.5.0.orig.tar.gz
dpkg-source: info: unpacking hinge_0.5.0-7.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying external-spdlog.patch
dpkg-source: info: applying libspdlog-14.0.patch
dpkg-source: info: applying libspdlog-1:1.3.0
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying spdlog-1.5.0.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/92327/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
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=16'
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='923b5733490a4d8bb716030c7732f3c7'
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='92327'
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.rmR9xBjv/pbuilderrc_PWAS --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rmR9xBjv/b1 --logfile b1/build.log hinge_0.5.0-7.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://85.184.249.68:3128'
I: uname -a
Linux ionos6-i386 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux
I: ls -l /bin
total 6036
-rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 42920 Sep 20 2022 cat
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chown
-rwxr-xr-x 1 root root 162024 Sep 20 2022 cp
-rwxr-xr-x 1 root root 136916 Jan 5 2023 dash
-rwxr-xr-x 1 root root 137160 Sep 20 2022 date
-rwxr-xr-x 1 root root 100364 Sep 20 2022 dd
-rwxr-xr-x 1 root root 108940 Sep 20 2022 df
-rwxr-xr-x 1 root root 162152 Sep 20 2022 dir
-rwxr-xr-x 1 root root 87760 Mar 22 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname
-rwxr-xr-x 1 root root 38760 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 2023 egrep
-rwxr-xr-x 1 root root 34664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep
-rwxr-xr-x 1 root root 84272 Mar 22 2023 findmnt
-rwsr-xr-x 1 root root 30240 Mar 22 2023 fusermount
-rwxr-xr-x 1 root root 218680 Jan 24 2023 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname
-rwxr-xr-x 1 root root 75756 Sep 20 2022 ln
-rwxr-xr-x 1 root root 55600 Mar 22 2023 login
-rwxr-xr-x 1 root root 162152 Sep 20 2022 ls
-rwxr-xr-x 1 root root 214568 Mar 22 2023 lsblk
-rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 63016 Mar 22 2023 more
-rwsr-xr-x 1 root root 58912 Mar 22 2023 mount
-rwxr-xr-x 1 root root 13856 Mar 22 2023 mountpoint
-rwxr-xr-x 1 root root 157932 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash
-rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 75720 Sep 20 2022 rm
-rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 133224 Jan 5 2023 sed
lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash
-rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 87976 Sep 20 2022 stty
-rwsr-xr-x 1 root root 83492 Mar 22 2023 su
-rwxr-xr-x 1 root root 38792 Sep 20 2022 sync
-rwxr-xr-x 1 root root 598456 Apr 6 2023 tar
-rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 120776 Sep 20 2022 touch
-rwxr-xr-x 1 root root 34664 Sep 20 2022 true
-rwxr-xr-x 1 root root 17892 Mar 22 2023 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Mar 22 2023 umount
-rwxr-xr-x 1 root root 38760 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 71216 Mar 22 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/92327/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), cmake, libspdlog-dev, libboost-dev, libboost-graph-dev, libhdf5-dev, zlib1g-dev, pandoc, python3, daligner, dazzdb, dascrubber, python3-numpy, python3-ujson, python3-colormap, python3-pbcore, python3-networkx, python3-matplotlib
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19604 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 cmake; however:
Package cmake is not installed.
pbuilder-satisfydepends-dummy depends on libspdlog-dev; however:
Package libspdlog-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-dev; however:
Package libboost-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-graph-dev; however:
Package libboost-graph-dev is not installed.
pbuilder-satisfydepends-dummy depends on libhdf5-dev; however:
Package libhdf5-dev is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on pandoc; however:
Package pandoc is not installed.
pbuilder-satisfydepends-dummy depends on python3; however:
Package python3 is not installed.
pbuilder-satisfydepends-dummy depends on daligner; however:
Package daligner is not installed.
pbuilder-satisfydepends-dummy depends on dazzdb; however:
Package dazzdb is not installed.
pbuilder-satisfydepends-dummy depends on dascrubber; however:
Package dascrubber is not installed.
pbuilder-satisfydepends-dummy depends on python3-numpy; however:
Package python3-numpy is not installed.
pbuilder-satisfydepends-dummy depends on python3-ujson; however:
Package python3-ujson is not installed.
pbuilder-satisfydepends-dummy depends on python3-colormap; however:
Package python3-colormap is not installed.
pbuilder-satisfydepends-dummy depends on python3-pbcore; however:
Package python3-pbcore is not installed.
pbuilder-satisfydepends-dummy depends on python3-networkx; however:
Package python3-networkx is not installed.
pbuilder-satisfydepends-dummy depends on python3-matplotlib; however:
Package python3-matplotlib is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} catch2{a} cmake{a} cmake-data{a} daligner{a} dascrubber{a} dazzdb{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lyx{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} hdf5-helpers{a} icu-devtools{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13{a} libblas3{a} libboost-dev{a} libboost-graph-dev{a} libboost-graph1.74-dev{a} libboost-graph1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-serialization1.74-dev{a} libboost-serialization1.74.0{a} libboost-test1.74-dev{a} libboost-test1.74.0{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-openssl-dev{a} libdebhelper-perl{a} libdeflate0{a} libdouble-conversion3{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfmt-dev{a} libfmt9{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libhts3{a} libhtscodecs2{a} libicu-dev{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp25{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblua5.3-0{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libopenjp2-7{a} libpipeline1{a} libpng16-16{a} libproc2-0{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libspdlog-dev{a} libspdlog1.10{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libsz2{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libuv1{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxsimd-dev{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} pandoc{a} pandoc-data{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-attr{a} python3-beniget{a} python3-biopython{a} python3-brotli{a} python3-colorama{a} python3-colorlog{a} python3-colormap{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-easydev{a} python3-fonttools{a} python3-fs{a} python3-gast{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-mpmath{a} python3-networkx{a} python3-numpy{a} python3-packaging{a} python3-pbcore{a} python3-pexpect{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-ply{a} python3-ptyprocess{a} python3-pyparsing{a} python3-pysam{a} python3-pythran{a} python3-renderpm{a} python3-reportlab{a} python3-reportlab-accel{a} python3-scipy{a} python3-six{a} python3-sympy{a} python3-tk{a} python3-tz{a} python3-ufolib2{a} python3-ujson{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tk8.6-blt2.5{a} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl isympy-common javascript-common libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-bs4 python3-gdal python3-h5py python3-html5lib python3-olefile python3-pydot python3-pygraphviz python3-yaml shared-mime-info wget xdg-user-dirs
0 packages upgraded, 219 newly installed, 0 to remove and 0 not upgraded.
Need to get 205 MB of archives. After unpacking 1074 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB]
Get: 2 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB]
Get: 3 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB]
Get: 4 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB]
Get: 5 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB]
Get: 6 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB]
Get: 8 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB]
Get: 9 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB]
Get: 10 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B]
Get: 11 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB]
Get: 12 http://deb.debian.org/debian bookworm/main i386 sgml-base all 1.31 [15.4 kB]
Get: 13 http://deb.debian.org/debian bookworm/main i386 libproc2-0 i386 2:4.0.2-3 [63.7 kB]
Get: 14 http://deb.debian.org/debian bookworm/main i386 procps i386 2:4.0.2-3 [706 kB]
Get: 15 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 16 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB]
Get: 17 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB]
Get: 18 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB]
Get: 19 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB]
Get: 20 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 21 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB]
Get: 22 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB]
Get: 23 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB]
Get: 24 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB]
Get: 25 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB]
Get: 26 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB]
Get: 27 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 28 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 29 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB]
Get: 30 http://deb.debian.org/debian bookworm/main i386 libtcl8.6 i386 8.6.13+dfsg-2 [1095 kB]
Get: 31 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB]
Get: 32 http://deb.debian.org/debian bookworm/main i386 libpng16-16 i386 1.6.39-2 [283 kB]
Get: 33 http://deb.debian.org/debian bookworm/main i386 libfreetype6 i386 2.12.1+dfsg-5 [410 kB]
Get: 34 http://deb.debian.org/debian bookworm/main i386 fonts-dejavu-core all 2.37-6 [1068 kB]
Get: 35 http://deb.debian.org/debian bookworm/main i386 libfontenc1 i386 1:1.1.4-1 [24.5 kB]
Get: 36 http://deb.debian.org/debian bookworm/main i386 x11-common all 1:7.7+23 [252 kB]
Get: 37 http://deb.debian.org/debian bookworm/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get: 38 http://deb.debian.org/debian bookworm/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB]
Get: 39 http://deb.debian.org/debian bookworm/main i386 fonts-urw-base35 all 20200910-7 [10.8 MB]
Get: 40 http://deb.debian.org/debian bookworm/main i386 fontconfig-config i386 2.14.1-4 [315 kB]
Get: 41 http://deb.debian.org/debian bookworm/main i386 libfontconfig1 i386 2.14.1-4 [398 kB]
Get: 42 http://deb.debian.org/debian bookworm/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB]
Get: 43 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB]
Get: 44 http://deb.debian.org/debian bookworm/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB]
Get: 45 http://deb.debian.org/debian bookworm/main i386 libxcb1 i386 1.15-1 [148 kB]
Get: 46 http://deb.debian.org/debian bookworm/main i386 libx11-data all 2:1.8.4-2 [292 kB]
Get: 47 http://deb.debian.org/debian bookworm/main i386 libx11-6 i386 2:1.8.4-2 [782 kB]
Get: 48 http://deb.debian.org/debian bookworm/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB]
Get: 49 http://deb.debian.org/debian bookworm/main i386 libxft2 i386 2.3.6-1 [62.8 kB]
Get: 50 http://deb.debian.org/debian bookworm/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB]
Get: 51 http://deb.debian.org/debian bookworm/main i386 libxss1 i386 1:1.2.3-1 [18.1 kB]
Get: 52 http://deb.debian.org/debian bookworm/main i386 libtk8.6 i386 8.6.13-2 [824 kB]
Get: 53 http://deb.debian.org/debian bookworm/main i386 tk8.6-blt2.5 i386 2.5.3+dfsg-4.1 [622 kB]
Get: 54 http://deb.debian.org/debian bookworm/main i386 blt i386 2.5.3+dfsg-4.1 [14.9 kB]
Get: 55 http://deb.debian.org/debian bookworm/main i386 catch2 i386 2.13.10-1 [483 kB]
Get: 56 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB]
Get: 57 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB]
Get: 58 http://deb.debian.org/debian bookworm/main i386 libarchive13 i386 3.6.2-1 [385 kB]
Get: 59 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB]
Get: 60 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB]
Get: 61 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB]
Get: 62 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1 [79.8 kB]
Get: 63 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB]
Get: 64 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB]
Get: 65 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB]
Get: 66 http://deb.debian.org/debian bookworm/main i386 libcurl4 i386 7.88.1-9 [420 kB]
Get: 67 http://deb.debian.org/debian bookworm/main i386 libjsoncpp25 i386 1.9.5-4 [86.2 kB]
Get: 68 http://deb.debian.org/debian bookworm/main i386 librhash0 i386 1.4.3-3 [149 kB]
Get: 69 http://deb.debian.org/debian bookworm/main i386 libuv1 i386 1.44.2-1 [147 kB]
Get: 70 http://deb.debian.org/debian bookworm/main i386 cmake-data all 3.25.1-1 [2026 kB]
Get: 71 http://deb.debian.org/debian bookworm/main i386 cmake i386 3.25.1-1 [9767 kB]
Get: 72 http://deb.debian.org/debian bookworm/main i386 daligner i386 1.0+git20221215.bd26967-1 [226 kB]
Get: 73 http://deb.debian.org/debian bookworm/main i386 dascrubber i386 1.1-4 [161 kB]
Get: 74 http://deb.debian.org/debian bookworm/main i386 dazzdb i386 1.0+git20221215.aad3a46-1 [217 kB]
Get: 75 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 76 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB]
Get: 77 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 78 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 79 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B]
Get: 80 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 81 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 82 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB]
Get: 83 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB]
Get: 84 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB]
Get: 85 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 86 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 87 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB]
Get: 88 http://deb.debian.org/debian bookworm/main i386 fonts-lyx all 2.3.7-1 [186 kB]
Get: 89 http://deb.debian.org/debian bookworm/main i386 hdf5-helpers i386 1.10.8+repack1-1 [27.9 kB]
Get: 90 http://deb.debian.org/debian bookworm/main i386 icu-devtools i386 72.1-3 [214 kB]
Get: 91 http://deb.debian.org/debian bookworm/main i386 libaec0 i386 1.0.6-1+b1 [22.4 kB]
Get: 92 http://deb.debian.org/debian bookworm/main i386 libsz2 i386 1.0.6-1+b1 [7884 B]
Get: 93 http://deb.debian.org/debian bookworm/main i386 libaec-dev i386 1.0.6-1+b1 [21.5 kB]
Get: 94 http://deb.debian.org/debian bookworm/main i386 libblas3 i386 3.11.0-2 [139 kB]
Get: 95 http://deb.debian.org/debian bookworm/main i386 libboost1.74-dev i386 1.74.0+ds1-20 [9510 kB]
Get: 96 http://deb.debian.org/debian bookworm/main i386 libboost-dev i386 1.74.0.3 [4548 B]
Get: 97 http://deb.debian.org/debian bookworm/main i386 libboost-regex1.74.0 i386 1.74.0+ds1-20 [509 kB]
Get: 98 http://deb.debian.org/debian bookworm/main i386 libboost-graph1.74.0 i386 1.74.0+ds1-20 [307 kB]
Get: 99 http://deb.debian.org/debian bookworm/main i386 libicu-dev i386 72.1-3 [10.6 MB]
Get: 100 http://deb.debian.org/debian bookworm/main i386 libboost-regex1.74-dev i386 1.74.0+ds1-20 [585 kB]
Get: 101 http://deb.debian.org/debian bookworm/main i386 libboost-serialization1.74.0 i386 1.74.0+ds1-20 [325 kB]
Get: 102 http://deb.debian.org/debian bookworm/main i386 libboost-serialization1.74-dev i386 1.74.0+ds1-20 [368 kB]
Get: 103 http://deb.debian.org/debian bookworm/main i386 libboost-test1.74.0 i386 1.74.0+ds1-20 [460 kB]
Get: 104 http://deb.debian.org/debian bookworm/main i386 libboost-test1.74-dev i386 1.74.0+ds1-20 [539 kB]
Get: 105 http://deb.debian.org/debian bookworm/main i386 libboost-graph1.74-dev i386 1.74.0+ds1-20 [329 kB]
Get: 106 http://deb.debian.org/debian bookworm/main i386 libboost-graph-dev i386 1.74.0.3 [4436 B]
Get: 107 http://deb.debian.org/debian bookworm/main i386 libcurl3-gnutls i386 7.88.1-9 [412 kB]
Get: 108 http://deb.debian.org/debian bookworm/main i386 libcurl4-openssl-dev i386 7.88.1-9 [534 kB]
Get: 109 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB]
Get: 110 http://deb.debian.org/debian bookworm/main i386 libdouble-conversion3 i386 3.2.1-1 [45.7 kB]
Get: 111 http://deb.debian.org/debian bookworm/main i386 libexpat1-dev i386 2.5.0-1 [158 kB]
Get: 112 http://deb.debian.org/debian bookworm/main i386 libfmt9 i386 9.1.0+ds1-2 [119 kB]
Get: 113 http://deb.debian.org/debian bookworm/main i386 libfmt-dev i386 9.1.0+ds1-2 [171 kB]
Get: 114 http://deb.debian.org/debian bookworm/main i386 libfribidi0 i386 1.0.8-2.1 [65.6 kB]
Get: 115 http://deb.debian.org/debian bookworm/main i386 libgfortran5 i386 12.2.0-14 [698 kB]
Get: 116 http://deb.debian.org/debian bookworm/main i386 libglib2.0-0 i386 2.74.6-2 [1467 kB]
Get: 117 http://deb.debian.org/debian bookworm/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB]
Get: 118 http://deb.debian.org/debian bookworm/main i386 libharfbuzz0b i386 6.0.0+dfsg-3 [1966 kB]
Get: 119 http://deb.debian.org/debian bookworm/main i386 libhdf5-103-1 i386 1.10.8+repack1-1 [1175 kB]
Get: 120 http://deb.debian.org/debian bookworm/main i386 libhdf5-cpp-103-1 i386 1.10.8+repack1-1 [136 kB]
Get: 121 http://deb.debian.org/debian bookworm/main i386 libhdf5-fortran-102 i386 1.10.8+repack1-1 [101 kB]
Get: 122 http://deb.debian.org/debian bookworm/main i386 libhdf5-hl-100 i386 1.10.8+repack1-1 [79.3 kB]
Get: 123 http://deb.debian.org/debian bookworm/main i386 libhdf5-hl-fortran-100 i386 1.10.8+repack1-1 [46.2 kB]
Get: 124 http://deb.debian.org/debian bookworm/main i386 libhdf5-hl-cpp-100 i386 1.10.8+repack1-1 [26.0 kB]
Get: 125 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB]
Get: 126 http://deb.debian.org/debian bookworm/main i386 libjpeg62-turbo i386 1:2.1.5-2 [169 kB]
Get: 127 http://deb.debian.org/debian bookworm/main i386 libjpeg62-turbo-dev i386 1:2.1.5-2 [304 kB]
Get: 128 http://deb.debian.org/debian bookworm/main i386 libjpeg-dev i386 1:2.1.5-2 [71.8 kB]
Get: 129 http://deb.debian.org/debian bookworm/main i386 libssl-dev i386 3.0.8-1 [2487 kB]
Get: 130 http://deb.debian.org/debian bookworm/main i386 libhdf5-dev i386 1.10.8+repack1-1 [2754 kB]
Get: 131 http://deb.debian.org/debian bookworm/main i386 libhtscodecs2 i386 1.3.0-4 [67.4 kB]
Get: 132 http://deb.debian.org/debian bookworm/main i386 libhts3 i386 1.16+ds-3 [469 kB]
Get: 133 http://deb.debian.org/debian bookworm/main i386 libimagequant0 i386 2.17.0-1 [32.9 kB]
Get: 134 http://deb.debian.org/debian bookworm/main i386 libjbig0 i386 2.1-6.1 [31.6 kB]
Get: 135 http://deb.debian.org/debian bookworm/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 136 http://deb.debian.org/debian bookworm/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 137 http://deb.debian.org/debian bookworm/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 138 http://deb.debian.org/debian bookworm/main i386 libjs-sphinxdoc all 5.3.0-4 [130 kB]
Get: 139 http://deb.debian.org/debian bookworm/main i386 libopenblas0-pthread i386 0.3.21+ds-4 [5148 kB]
Get: 140 http://deb.debian.org/debian bookworm/main i386 liblapack3 i386 3.11.0-2 [2092 kB]
Get: 141 http://deb.debian.org/debian bookworm/main i386 liblbfgsb0 i386 3.0+dfsg.4-1 [28.5 kB]
Get: 142 http://deb.debian.org/debian bookworm/main i386 liblcms2-2 i386 2.14-2 [165 kB]
Get: 143 http://deb.debian.org/debian bookworm/main i386 liblerc4 i386 4.0.0+ds-2 [181 kB]
Get: 144 http://deb.debian.org/debian bookworm/main i386 liblua5.3-0 i386 5.3.6-2 [144 kB]
Get: 145 http://deb.debian.org/debian bookworm/main i386 libopenblas0 i386 0.3.21+ds-4 [32.6 kB]
Get: 146 http://deb.debian.org/debian bookworm/main i386 libopenblas-pthread-dev i386 0.3.21+ds-4 [3447 kB]
Get: 147 http://deb.debian.org/debian bookworm/main i386 libopenblas-dev i386 0.3.21+ds-4 [44.9 kB]
Get: 148 http://deb.debian.org/debian bookworm/main i386 libopenjp2-7 i386 2.5.0-1+b1 [196 kB]
Get: 149 http://deb.debian.org/debian bookworm/main i386 libpython3.11 i386 3.11.2-6 [2013 kB]
Get: 150 http://deb.debian.org/debian bookworm/main i386 libpython3.11-dev i386 3.11.2-6 [4906 kB]
Get: 151 http://deb.debian.org/debian bookworm/main i386 libpython3-dev i386 3.11.2-1+b1 [9580 B]
Get: 152 http://deb.debian.org/debian bookworm/main i386 libpython3-all-dev i386 3.11.2-1+b1 [1068 B]
Get: 153 http://deb.debian.org/debian bookworm/main i386 libqhull-r8.0 i386 2020.2-5 [260 kB]
Get: 154 http://deb.debian.org/debian bookworm/main i386 libraqm0 i386 0.7.0-4.1 [11.1 kB]
Get: 155 http://deb.debian.org/debian bookworm/main i386 libspdlog1.10 i386 1:1.10.0+ds-0.4 [142 kB]
Get: 156 http://deb.debian.org/debian bookworm/main i386 libspdlog-dev i386 1:1.10.0+ds-0.4 [209 kB]
Get: 157 http://deb.debian.org/debian bookworm/main i386 libwebp7 i386 1.2.4-0.1 [293 kB]
Get: 158 http://deb.debian.org/debian bookworm/main i386 libtiff6 i386 4.5.0-5 [332 kB]
Get: 159 http://deb.debian.org/debian bookworm/main i386 libwebpdemux2 i386 1.2.4-0.1 [99.7 kB]
Get: 160 http://deb.debian.org/debian bookworm/main i386 libwebpmux3 i386 1.2.4-0.1 [111 kB]
Get: 161 http://deb.debian.org/debian bookworm/main i386 libxsimd-dev i386 8.1.0-7 [88.8 kB]
Get: 162 http://deb.debian.org/debian bookworm/main i386 libxslt1.1 i386 1.1.35-1 [253 kB]
Get: 163 http://deb.debian.org/debian bookworm/main i386 libyaml-0-2 i386 0.2.5-1 [55.9 kB]
Get: 164 http://deb.debian.org/debian bookworm/main i386 pandoc-data all 2.17.1.1-1.1 [417 kB]
Get: 165 http://deb.debian.org/debian bookworm/main i386 pandoc i386 2.17.1.1-1.1 [27.5 MB]
Get: 166 http://deb.debian.org/debian bookworm/main i386 python-matplotlib-data all 3.6.3-1 [2744 kB]
Get: 167 http://deb.debian.org/debian bookworm/main i386 python3-lib2to3 all 3.11.2-2 [76.2 kB]
Get: 168 http://deb.debian.org/debian bookworm/main i386 python3-distutils all 3.11.2-2 [131 kB]
Get: 169 http://deb.debian.org/debian bookworm/main i386 python3-all i386 3.11.2-1+b1 [1056 B]
Get: 170 http://deb.debian.org/debian bookworm/main i386 python3.11-dev i386 3.11.2-6 [615 kB]
Get: 171 http://deb.debian.org/debian bookworm/main i386 python3-dev i386 3.11.2-1+b1 [26.2 kB]
Get: 172 http://deb.debian.org/debian bookworm/main i386 python3-all-dev i386 3.11.2-1+b1 [1072 B]
Get: 173 http://deb.debian.org/debian bookworm/main i386 python3-appdirs all 1.4.4-3 [13.0 kB]
Get: 174 http://deb.debian.org/debian bookworm/main i386 python3-attr all 22.2.0-1 [65.4 kB]
Get: 175 http://deb.debian.org/debian bookworm/main i386 python3-gast all 0.5.2-2 [9364 B]
Get: 176 http://deb.debian.org/debian bookworm/main i386 python3-beniget all 0.4.1-3 [9920 B]
Get: 177 http://deb.debian.org/debian bookworm/main i386 python3-pkg-resources all 66.1.1-1 [296 kB]
Get: 178 http://deb.debian.org/debian bookworm/main i386 python3-numpy i386 1:1.24.2-1 [6115 kB]
Get: 179 http://deb.debian.org/debian bookworm/main i386 python3-renderpm i386 3.6.12-1+b1 [81.4 kB]
Get: 180 http://deb.debian.org/debian bookworm/main i386 python3-reportlab-accel i386 3.6.12-1+b1 [39.4 kB]
Get: 181 http://deb.debian.org/debian bookworm/main i386 python3-tk i386 3.11.2-2 [99.1 kB]
Get: 182 http://deb.debian.org/debian bookworm/main i386 python3-pil.imagetk i386 9.4.0-1.1+b1 [74.7 kB]
Get: 183 http://deb.debian.org/debian bookworm/main i386 python3-pil i386 9.4.0-1.1+b1 [473 kB]
Get: 184 http://deb.debian.org/debian bookworm/main i386 python3-reportlab all 3.6.12-1 [564 kB]
Get: 185 http://deb.debian.org/debian bookworm/main i386 xml-core all 0.18+nmu1 [23.8 kB]
Get: 186 http://deb.debian.org/debian bookworm/main i386 w3c-sgml-lib all 1.3-3 [273 kB]
Get: 187 http://deb.debian.org/debian bookworm/main i386 python3-biopython i386 1.80+dfsg-4+b1 [1589 kB]
Get: 188 http://deb.debian.org/debian bookworm/main i386 python3-brotli i386 1.0.9-2+b6 [295 kB]
Get: 189 http://deb.debian.org/debian bookworm/main i386 python3-colorama all 0.4.6-2 [36.8 kB]
Get: 190 http://deb.debian.org/debian bookworm/main i386 python3-colorlog all 6.7.0-1 [26.5 kB]
Get: 191 http://deb.debian.org/debian bookworm/main i386 python3-six all 1.16.0-4 [17.5 kB]
Get: 192 http://deb.debian.org/debian bookworm/main i386 python3-dateutil all 2.8.2-2 [78.3 kB]
Get: 193 http://deb.debian.org/debian bookworm/main i386 python3-pyparsing all 3.0.9-1 [138 kB]
Get: 194 http://deb.debian.org/debian bookworm/main i386 python3-contourpy i386 1.0.7-1+b1 [184 kB]
Get: 195 http://deb.debian.org/debian bookworm/main i386 python3-cycler all 0.11.0-1 [8020 B]
Get: 196 http://deb.debian.org/debian bookworm/main i386 python3-decorator all 5.1.1-3 [14.9 kB]
Get: 197 http://deb.debian.org/debian bookworm/main i386 python3-ply all 3.11-5 [65.8 kB]
Get: 198 http://deb.debian.org/debian bookworm/main i386 python3-pythran i386 0.11.0+ds-7 [427 kB]
Get: 199 http://deb.debian.org/debian bookworm/main i386 python3-scipy i386 1.10.1-2 [15.2 MB]
Get: 200 http://deb.debian.org/debian bookworm/main i386 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB]
Get: 201 http://deb.debian.org/debian bookworm/main i386 python3-mpmath all 1.2.1-2 [418 kB]
Get: 202 http://deb.debian.org/debian bookworm/main i386 python3-sympy all 1.11.1-1 [4358 kB]
Get: 203 http://deb.debian.org/debian bookworm/main i386 python3-tz all 2022.7.1-3 [30.1 kB]
Get: 204 http://deb.debian.org/debian bookworm/main i386 python3-fs all 2.4.16-2 [95.2 kB]
Get: 205 http://deb.debian.org/debian bookworm/main i386 python3-lxml i386 4.9.2-1+b1 [1182 kB]
Get: 206 http://deb.debian.org/debian bookworm/main i386 python3-lz4 i386 4.0.2+dfsg-1+b2 [25.1 kB]
Get: 207 http://deb.debian.org/debian bookworm/main i386 unicode-data all 15.0.0-1 [7984 kB]
Get: 208 http://deb.debian.org/debian bookworm/main i386 python3-fonttools i386 4.38.0-1+b1 [1010 kB]
Get: 209 http://deb.debian.org/debian bookworm/main i386 python3-kiwisolver i386 1.4.4-1+b1 [63.0 kB]
Get: 210 http://deb.debian.org/debian bookworm/main i386 python3-packaging all 23.0-1 [32.5 kB]
Get: 211 http://deb.debian.org/debian bookworm/main i386 python3-matplotlib i386 3.6.3-1+b1 [6891 kB]
Get: 212 http://deb.debian.org/debian bookworm/main i386 python3-ptyprocess all 0.7.0-5 [14.7 kB]
Get: 213 http://deb.debian.org/debian bookworm/main i386 python3-pexpect all 4.8.0-4 [52.9 kB]
Get: 214 http://deb.debian.org/debian bookworm/main i386 python3-easydev all 0.12.0+dfsg-4 [35.0 kB]
Get: 215 http://deb.debian.org/debian bookworm/main i386 python3-colormap all 1.0.4-3 [15.4 kB]
Get: 216 http://deb.debian.org/debian bookworm/main i386 python3-networkx all 2.8.8-1 [1425 kB]
Get: 217 http://deb.debian.org/debian bookworm/main i386 python3-pysam i386 0.20.0+ds-3+b1 [1708 kB]
Get: 218 http://deb.debian.org/debian bookworm/main i386 python3-pbcore all 2.1.2+dfsg-5 [2830 kB]
Get: 219 http://deb.debian.org/debian bookworm/main i386 python3-ujson i386 5.7.0-1 [26.1 kB]
Fetched 205 MB in 3s (67.5 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libpython3.11-minimal:i386 (3.11.2-6) ...
Setting up libexpat1:i386 (2.5.0-1) ...
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update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/i386-linux-gnu/libopenblas.so (libopenblas.so-i386-linux-gnu) in auto mode
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/hinge-0.5.0/ && 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 > ../hinge_0.5.0-7_source.changes
dpkg-buildpackage: info: source package hinge
dpkg-buildpackage: info: source version 0.5.0-7
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
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
cd obj-i686-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu ..
-- The C compiler identification is GNU 12.2.0
-- The CXX compiler identification is GNU 12.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found ZLIB: /usr/lib/i386-linux-gnu/libz.so (found version "1.2.13")
-- Found Boost: /usr/lib/i386-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: graph
-- Configuring done
CMake Warning (dev) at src/filter/CMakeLists.txt:4 (add_executable):
Policy CMP0115 is not set: Source file extensions must be explicit. Run
"cmake --help-policy CMP0115" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
File:
/build/hinge-0.5.0/src/filter/filter.cpp
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at src/maximal/CMakeLists.txt:4 (add_executable):
Policy CMP0115 is not set: Source file extensions must be explicit. Run
"cmake --help-policy CMP0115" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
File:
/build/hinge-0.5.0/src/maximal/maximal.cpp
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at src/consensus/CMakeLists.txt:4 (add_executable):
Policy CMP0115 is not set: Source file extensions must be explicit. Run
"cmake --help-policy CMP0115" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
File:
/build/hinge-0.5.0/src/consensus/draft.cpp
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at src/layout/CMakeLists.txt:9 (add_executable):
Policy CMP0115 is not set: Source file extensions must be explicit. Run
"cmake --help-policy CMP0115" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
File:
/build/hinge-0.5.0/src/layout/hinging.cpp
This warning is for project developers. Use -Wno-dev to suppress it.
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
CMAKE_INSTALL_LIBDIR
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
FETCHCONTENT_FULLY_DISCONNECTED
-- Build files have been written to: /build/hinge-0.5.0/obj-i686-linux-gnu
dh_auto_build
cd obj-i686-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
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make -f CMakeFiles/Makefile2 all
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make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/depend
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make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin /build/hinge-0.5.0/obj-i686-linux-gnu/bin/CMakeFiles/man.dir/DependInfo.cmake --color=
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cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake --color=
make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake --color=
make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/kmer_lookup.dir/DependInfo.cmake --color=
make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
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make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
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make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build
make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
[ 3%] Building C object bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o
[ 10%] Building C object bin/lib/CMakeFiles/DB.dir/QV.c.o
[ 10%] Building C object bin/lib/CMakeFiles/DB.dir/DB.c.o
[ 13%] Building C object bin/lib/CMakeFiles/ini.dir/ini.c.o
[ 20%] Generating hinge.1
[ 20%] Building C object bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -MF CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o.d -o CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -c /build/hinge-0.5.0/src/lib/kmer_lookup.c
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/QV.c.o -MF CMakeFiles/DB.dir/QV.c.o.d -o CMakeFiles/DB.dir/QV.c.o -c /build/hinge-0.5.0/src/lib/QV.c
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/ini.c.o -MF CMakeFiles/ini.dir/ini.c.o.d -o CMakeFiles/ini.dir/ini.c.o -c /build/hinge-0.5.0/src/lib/ini.c
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o -MF CMakeFiles/DW_banded.dir/DW_banded.c.o.d -o CMakeFiles/DW_banded.dir/DW_banded.c.o -c /build/hinge-0.5.0/src/lib/DW_banded.c
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/DB.c.o -MF CMakeFiles/DB.dir/DB.c.o.d -o CMakeFiles/DB.dir/DB.c.o -c /build/hinge-0.5.0/src/lib/DB.c
[ 24%] Building C object bin/lib/CMakeFiles/LA.dir/align.c.o
[ 27%] Building CXX object bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin && /usr/bin/pandoc --from markdown --to man -s /build/hinge-0.5.0/src/hinge.1.md -o hinge.1
[ 31%] Building C object bin/lib/CMakeFiles/PAF.dir/paf.c.o
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/c++ -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o -MF CMakeFiles/ini.dir/INIReader.cpp.o.d -o CMakeFiles/ini.dir/INIReader.cpp.o -c /build/hinge-0.5.0/src/lib/INIReader.cpp
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/LA.dir/align.c.o -MF CMakeFiles/LA.dir/align.c.o.d -o CMakeFiles/LA.dir/align.c.o -c /build/hinge-0.5.0/src/lib/align.c
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/PAF.dir/paf.c.o -MF CMakeFiles/PAF.dir/paf.c.o.d -o CMakeFiles/PAF.dir/paf.c.o -c /build/hinge-0.5.0/src/lib/paf.c
/build/hinge-0.5.0/src/lib/QV.c: In function 'Build_Table':
/build/hinge-0.5.0/src/lib/QV.c:164:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
164 | { uint64 symbol = (uint64) (node->lft);
| ^
/build/hinge-0.5.0/src/lib/QV.c: In function 'Huffman':
/build/hinge-0.5.0/src/lib/QV.c:211:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
211 | node[value].lft = (HTree *) (uint64) i;
| ^
/build/hinge-0.5.0/src/lib/DB.c: In function 'Load_QVs':
/build/hinge-0.5.0/src/lib/DB.c:916:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
916 | fscanf(istub,DB_NFILE,&nfiles);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/hinge-0.5.0/src/lib/DB.c:920:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
920 | { fscanf(istub,DB_FDATA,&last,fname,prolog);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/hinge-0.5.0/src/lib/DB.c:925:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
925 | { fscanf(istub,DB_FDATA,&last,fname,prolog);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 34%] Linking C static library libPAF.a
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/PAF.dir/cmake_clean_target.cmake
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/PAF.dir/link.txt --verbose=1
[ 37%] Linking C static library libDW_banded.a
/build/hinge-0.5.0/src/lib/kmer_lookup.c: In function 'find_best_aln_range':
/build/hinge-0.5.0/src/lib/kmer_lookup.c:347:14: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
347 | q_coor = calloc( km_ptr->count, sizeof(seq_coor_t) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/hinge-0.5.0/src/lib/kmer_lookup.c:56:
/usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here
556 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
/build/hinge-0.5.0/src/lib/kmer_lookup.c:348:14: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
348 | t_coor = calloc( km_ptr->count, sizeof(seq_coor_t) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here
556 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DW_banded.dir/cmake_clean_target.cmake
/usr/bin/ar qc libPAF.a CMakeFiles/PAF.dir/paf.c.o
/usr/bin/ranlib libPAF.a
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[ 37%] Built target PAF
/usr/bin/ar qc libDW_banded.a CMakeFiles/DW_banded.dir/DW_banded.c.o
/usr/bin/ranlib libDW_banded.a
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[ 37%] Built target man
[ 37%] Built target DW_banded
/build/hinge-0.5.0/src/lib/DB.c: In function 'Open_DB':
/build/hinge-0.5.0/src/lib/DB.c:533:11: warning: 'free' called on pointer 'p' with nonzero offset 32 [-Wfree-nonheap-object]
533 | free(reads);
| ^~~~~~~~~~~
In function 'Malloc',
inlined from 'Open_DB' at /build/hinge-0.5.0/src/lib/DB.c:525:29:
/build/hinge-0.5.0/src/lib/DB.c:84:12: note: returned from 'malloc'
84 | if ((p = malloc(size)) == NULL)
| ^~~~~~~~~~~~
[ 41%] Linking C static library libkmer_lookup.a
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/kmer_lookup.dir/cmake_clean_target.cmake
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kmer_lookup.dir/link.txt --verbose=1
/usr/bin/ar qc libkmer_lookup.a CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o
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make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/depend
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make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/build
make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
[ 44%] Building C object bin/lib/CMakeFiles/falcon.dir/falcon.c.o
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/falcon.dir/falcon.c.o -MF CMakeFiles/falcon.dir/falcon.c.o.d -o CMakeFiles/falcon.dir/falcon.c.o -c /build/hinge-0.5.0/src/lib/falcon.c
[ 48%] Linking C static library libfalcon.a
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/falcon.dir/cmake_clean_target.cmake
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/falcon.dir/link.txt --verbose=1
/usr/bin/ar qc libfalcon.a CMakeFiles/falcon.dir/falcon.c.o
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[ 48%] Built target falcon
/build/hinge-0.5.0/src/lib/DB.c: In function 'Read_All_Sequences':
/build/hinge-0.5.0/src/lib/DB.c:1587:15: warning: 'free' called on pointer 'p' with nonzero offset 1 [-Wfree-nonheap-object]
1587 | free(seq);
| ^~~~~~~~~
In function 'Malloc',
inlined from 'Read_All_Sequences' at /build/hinge-0.5.0/src/lib/DB.c:1564:18:
/build/hinge-0.5.0/src/lib/DB.c:84:12: note: returned from 'malloc'
84 | if ((p = malloc(size)) == NULL)
| ^~~~~~~~~~~~
[ 51%] Linking CXX static library libini.a
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cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/ini.dir/link.txt --verbose=1
/usr/bin/ar qc libini.a CMakeFiles/ini.dir/ini.c.o CMakeFiles/ini.dir/INIReader.cpp.o
[ 55%] Linking C static library libDB.a
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/usr/bin/ranlib libini.a
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[ 55%] Built target ini
/usr/bin/ar qc libDB.a CMakeFiles/DB.dir/DB.c.o CMakeFiles/DB.dir/QV.c.o
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[ 58%] Linking C static library libLA.a
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/usr/bin/ar qc libLA.a CMakeFiles/LA.dir/align.c.o
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make -f bin/lib/CMakeFiles/LAInterface.dir/build.make bin/lib/CMakeFiles/LAInterface.dir/depend
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[ 62%] Building CXX object bin/lib/CMakeFiles/LAInterface.dir/LAInterface.cpp.o
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/c++ -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/lib/CMakeFiles/LAInterface.dir/LAInterface.cpp.o -MF CMakeFiles/LAInterface.dir/LAInterface.cpp.o.d -o CMakeFiles/LAInterface.dir/LAInterface.cpp.o -c /build/hinge-0.5.0/src/lib/LAInterface.cpp
/build/hinge-0.5.0/src/lib/LAInterface.cpp: In member function 'void LAInterface::getOverlapw(std::vector<LOverlap*>&, int, int)':
/build/hinge-0.5.0/src/lib/LAInterface.cpp:1666:22: warning: format '%d' expects argument of type 'int', but argument 2 has type 'int64' {aka 'long long int'} [-Wformat=]
1666 | printf("%d percent finished\n", j/(novl/100));
| ~^ ~~~~~~~~~~~~
| | |
| int int64 {aka long long int}
| %lld
[ 65%] Linking CXX static library libLAInterface.a
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/LAInterface.dir/cmake_clean_target.cmake
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/usr/bin/ar qc libLAInterface.a CMakeFiles/LAInterface.dir/LAInterface.cpp.o
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make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/depend
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[ 68%] Building CXX object bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o
[ 72%] Building CXX object bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/filter && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o -MF CMakeFiles/Reads_filter.dir/filter.cpp.o.d -o CMakeFiles/Reads_filter.dir/filter.cpp.o -c /build/hinge-0.5.0/src/filter/filter.cpp
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/maximal && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -MF CMakeFiles/get_maximal_reads.dir/maximal.cpp.o.d -o CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -c /build/hinge-0.5.0/src/maximal/maximal.cpp
[ 75%] Building CXX object bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o
[ 79%] Building CXX object bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o -MF CMakeFiles/draft_assembly.dir/draft.cpp.o.d -o CMakeFiles/draft_assembly.dir/draft.cpp.o -c /build/hinge-0.5.0/src/consensus/draft.cpp
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o -MF CMakeFiles/consensus.dir/consensus.cpp.o.d -o CMakeFiles/consensus.dir/consensus.cpp.o -c /build/hinge-0.5.0/src/consensus/consensus.cpp
[ 82%] Building CXX object bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/layout && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o -MF CMakeFiles/hinging.dir/hinging.cpp.o.d -o CMakeFiles/hinging.dir/hinging.cpp.o -c /build/hinge-0.5.0/src/layout/hinging.cpp
/build/hinge-0.5.0/src/consensus/consensus.cpp: In function 'int main(int, char**)':
/build/hinge-0.5.0/src/consensus/consensus.cpp:126:15: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<LAlignment*>::size_type' {aka 'unsigned int'} [-Wformat=]
126 | printf("%lu\n", res.size());
| ~~^ ~~~~~~~~~~
| | |
| | std::vector<LAlignment*>::size_type {aka unsigned int}
| long unsigned int
| %u
/build/hinge-0.5.0/src/consensus/consensus.cpp:137:22: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<LAlignment*>::size_type' {aka 'unsigned int'} [-Wformat=]
137 | printf("%d %lu\n", i, idx[i].size());
| ~~^ ~~~~~~~~~~~~~
| | |
| long unsigned int std::vector<LAlignment*>::size_type {aka unsigned int}
| %u
[ 86%] Linking CXX executable consensus
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus && /usr/bin/cmake -E cmake_link_script CMakeFiles/consensus.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/consensus.dir/consensus.cpp.o -o consensus -lfmt ../lib/libLAInterface.a ../lib/libfalcon.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz ../lib/libkmer_lookup.a ../lib/libDW_banded.a
make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
[ 86%] Built target consensus
/build/hinge-0.5.0/src/consensus/draft.cpp: In function 'int draft_assembly_ctg(std::vector<std::tuple<Node, Node, int> >&, LAInterface&, std::vector<LAlignment*>&, std::unordered_map<int, std::vector<LOverlap*> >&, std::unordered_map<int, std::unordered_map<int, std::vector<LOverlap*> > >&, std::vector<Read*>&, int, int, int, int, int, bool, bool, std::string&)':
/build/hinge-0.5.0/src/consensus/draft.cpp:514:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<std::vector<std::pair<int, int> > >::size_type' {aka 'unsigned int'} [-Wformat=]
514 | printf("In total %lu lanes\n", lanes.size());
| ~~^ ~~~~~~~~~~~~
| | |
| long unsigned int std::vector<std::vector<std::pair<int, int> > >::size_type {aka unsigned int}
| %u
[ 89%] Linking CXX executable get_maximal_reads
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/maximal && /usr/bin/cmake -E cmake_link_script CMakeFiles/get_maximal_reads.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -o get_maximal_reads -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz
make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
[ 89%] Built target get_maximal_reads
[ 93%] Linking CXX executable draft_assembly
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus && /usr/bin/cmake -E cmake_link_script CMakeFiles/draft_assembly.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/draft_assembly.dir/draft.cpp.o -o draft_assembly -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libfalcon.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz ../lib/libkmer_lookup.a ../lib/libDW_banded.a
make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
[ 93%] Built target draft_assembly
[ 96%] Linking CXX executable Reads_filter
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/filter && /usr/bin/cmake -E cmake_link_script CMakeFiles/Reads_filter.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/Reads_filter.dir/filter.cpp.o -o Reads_filter -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz
make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
[ 96%] Built target Reads_filter
[100%] Linking CXX executable hinging
cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/layout && /usr/bin/cmake -E cmake_link_script CMakeFiles/hinging.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hinging.dir/hinging.cpp.o -o hinging -lfmt ../lib/libLAInterface.a ../lib/libini.a /usr/lib/i386-linux-gnu/libboost_graph.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz /usr/lib/i386-linux-gnu/libboost_regex.a
make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
[100%] Built target hinging
make[2]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
/usr/bin/cmake -E cmake_progress_start /build/hinge-0.5.0/obj-i686-linux-gnu/CMakeFiles 0
make[1]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
dh_auto_test
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/hinge/
cd obj-i686-linux-gnu && make -j16 install DESTDIR=/build/hinge-0.5.0/debian/hinge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
/usr/bin/cmake -S/build/hinge-0.5.0 -B/build/hinge-0.5.0/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region_find_bridges.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/random_condensation.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_single_strand.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_annotate_clip_ends.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/download_NCTC_pipeline.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_alignment.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/interface_utils.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth_json.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_consensus_gfa.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_bandage_file.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw.sh
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly_not_perfect.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/correct_head.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_region.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/unitig.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/merge_hinges.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/Visualise_graph.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping_nanopore.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pileup.ipynb
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/connected.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path_norevcomp.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_alignment.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_nctc.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_create_gfa_compute_n50.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/longest_path.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping3.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/fasta_to_fastq.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_read.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/compute_n50_from_draft.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_and_annotate.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/clip_ends.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_w_repeat.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph_nogt.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw_large.sh
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping2.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_with_gt.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/repeat_annotate_reads.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_annotation.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_qv.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/split_las.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus_norevcomp.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_read.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_NCTC_json.py
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/share/man/man1/hinge.1
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/bin/hinge
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/Reads_filter
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_maximal_reads
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/consensus
-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/hinging
make[1]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu'
dh_installdocs
dh_installchangelogs
debian/rules override_dh_installexamples
make[1]: Entering directory '/build/hinge-0.5.0'
dh_installexamples
# only install nominal.ini from the utils/ directory, but preserve
# the directory structure (since demo scripts expect it)
mkdir -p debian/hinge/usr/share/doc/hinge/examples/utils \
&& cp utils/nominal.ini debian/hinge/usr/share/doc/hinge/examples/utils
make[1]: Leaving directory '/build/hinge-0.5.0'
dh_installman
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
dh_md5sums
dh_builddeb
dpkg-deb: building package 'hinge-dbgsym' in '../hinge-dbgsym_0.5.0-7_i386.deb'.
dpkg-deb: building package 'hinge' in '../hinge_0.5.0-7_i386.deb'.
dpkg-genbuildinfo --build=binary -O../hinge_0.5.0-7_i386.buildinfo
dpkg-genchanges --build=binary -O../hinge_0.5.0-7_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/92327 and its subdirectories
I: Current time: Thu Jun 6 10:09:18 -12 2024
I: pbuilder-time-stamp: 1717711758