[Debian-med-packaging] Bug#949195: libsbml: FTBFS: dh: unable to load addon python3

Sat Jan 18 00:19:40 GMT 2020

Source: libsbml
Version: 5.17.2+dfsg-3
Severity: serious
Tags: ftbfs

Dear maintainer,

your package failed to rebuild in a standard sid/amd64 chroot.
Attached is the full build log, hopefully relevant excerpt follows:

dpkg-buildpackage: info: source package libsbml
dpkg-buildpackage: info: source version 5.17.2+dfsg-3
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
dpkg-source: info: using options from libsbml-5.17.2+dfsg/debian/source/options: --extend-diff-ignore=(^|/)(src/sbml/validator/constraints/.*|src/bindings/csharp/csharp-files.*|src/sbml/extension/SBMLExtensionRegistry.*|src/sbml/packages/comp/validator/constraints/CompIdBase.cpp|src/bindings/java/java-files/org/sbml/libsbml/SBMLExtensionRegistry.java|src/sbml/xml/XMLErrorLog.cpp|docs/src/doxygen-config-common.txt)$
 fakeroot debian/rules clean
dh  clean --with python3,cli
dh: unable to load addon python3: Can't locate Debian/Debhelper/Sequence/python3.pm in @INC (you may need to install the Debian::Debhelper::Sequence::python3 module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at (eval 12) line 1.
BEGIN failed--compilation aborted at (eval 12) line 1.

make: *** [debian/rules:33: clean] Error 255
dpkg-buildpackage: error: fakeroot debian/rules clean subprocess returned exit status 2

-- 
regards,
                        Mattia Rizzolo

GPG Key: 66AE 2B4A FCCF 3F52 DA18  4D18 4B04 3FCD B944 4540      .''`.
More about me:  https://mapreri.org                             : :'  :
Launchpad user: https://launchpad.net/~mapreri                  `. `'`
Debian QA page: https://qa.debian.org/developer.php?login=mattia  `-
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[0mI: Using pkgname logfile[0m
[0mI: Current time: Fri Jan 17 21:48:27 UTC 2020[0m
[0mI: pbuilder-time-stamp: 1579297707[0m
[0mI: Obtaining the cached apt archive contents[0m
[0mI: Copying source file[0m
[0mI: copying [pkgs/libsbml_5.17.2+dfsg-3.dsc][0m
[0mI: copying [pkgs/libsbml_5.17.2+dfsg.orig.tar.xz][0m
[0mI: copying [pkgs/libsbml_5.17.2+dfsg-3.debian.tar.xz][0m
[0mI: Extracting source[0m
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/home/mattia/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Jan 30 19:17:29 2019 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille at debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./libsbml_5.17.2+dfsg-3.dsc
dpkg-source: info: extracting libsbml in libsbml-5.17.2+dfsg
dpkg-source: info: unpacking libsbml_5.17.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking libsbml_5.17.2+dfsg-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying perl-installdirs.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying doxygen.patch
dpkg-source: info: applying swig-3.x.patch
dpkg-source: info: applying mips-compile-with-O1.patch
dpkg-source: info: applying javadoc_java9.patch
dpkg-source: info: applying javadoc.patch
dpkg-source: info: applying remove_SBMLDoclet.patch
dpkg-source: info: applying fix_cmake_configuration.patch
dpkg-source: info: applying fix_build_issue.patch
[0mI: using fakeroot in build.[0m
[0mI: Installing the build-deps[0m
[0mI: -> Attempting to satisfy build-dependencies[0m
Note, using file '/build/libsbml_5.17.2+dfsg-3.dsc' to get the build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
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update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
Setting up libuv1:amd64 (1.33.1-2) ...
Setting up liblog-log4perl-perl (1.49-1) ...
Setting up libexpat1-dev:amd64 (2.2.9-1) ...
Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+b1) ...
Setting up swig3.0 (3.0.12-2.2) ...
Setting up libx11-data (2:1.6.8-1) ...
Setting up libjpeg62-turbo-dev:amd64 (1:1.5.2-2+b1) ...
Setting up libnspr4:amd64 (2:4.24-1) ...
Setting up libfile-find-rule-perl (0.34-1) ...
Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b1) ...
Setting up libio-tiecombine-perl (1.005-1) ...
Setting up libmonoboehm-2.0-1 (5.18.0.240+dfsg-5) ...
Setting up cli-common (0.10) ...
Setting up libteckit0:amd64 (2.5.8+ds2-5) ...
Setting up libpathplan4:amd64 (2.42.2-3) ...
Setting up aglfn (1.7+git20191031.4036a9c-2) ...
Setting up libavahi-common-data:amd64 (0.7-5) ...
Setting up libann0 (1.1.2+doc-7) ...
Setting up libncurses6:amd64 (6.1+20191019-1) ...
Setting up libdbus-1-3:amd64 (1.12.16-2) ...
Setting up libsigsegv2:amd64 (2.12-2) ...
Setting up libfftw3-quad3:amd64 (3.3.8-2) ...
Setting up libfribidi0:amd64 (1.0.8-2) ...
Setting up libopus0:amd64 (1.3-1+b1) ...
Setting up t1utils (1.41-3) ...
Setting up libnewlib-dev (3.1.0.20181231-1) ...
Setting up libexif12:amd64 (0.6.21-5.1) ...
Setting up libpng16-16:amd64 (1.6.37-1) ...
Setting up libpcre32-3:amd64 (2:8.39-12+b1) ...
Setting up libvorbis0a:amd64 (1.3.6-2) ...
Setting up openjdk-11-doc (11.0.6+10-1) ...
Setting up libio-html-perl (1.001-1) ...
Setting up libtcl8.6:amd64 (8.6.10+dfsg-1) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libwebp6:amd64 (0.6.1-2+b1) ...
Setting up libb-hooks-op-check-perl (0.22-1+b2) ...
Setting up icu-devtools (63.2-2) ...
Setting up pkg-config (0.29-6) ...
Setting up fonts-dejavu-core (2.37-1) ...
Setting up libpcsclite1:amd64 (1.8.26-2) ...
Setting up libpcre2-posix2:amd64 (10.34-7) ...
Setting up libsensors5:amd64 (1:3.6.0-2) ...
Setting up libk5crypto3:amd64 (1.17-6) ...
Setting up libqt5core5a:amd64 (5.12.5+dfsg-5) ...
Setting up libltdl7:amd64 (2.4.6-11) ...
Setting up libfftw3-double3:amd64 (3.3.8-2) ...
Setting up libglapi-mesa:amd64 (19.3.2-1) ...
Setting up libparams-util-perl (1.07-3+b5) ...
Setting up libkpathsea6:amd64 (2019.20190605.51237-3) ...
Setting up libsasl2-2:amd64 (2.1.27+dfsg-2) ...
Setting up libgfortran5:amd64 (9.2.1-23) ...
Setting up libmtdev1:amd64 (1.1.5-1.1) ...
Setting up libcapture-tiny-perl (0.48-1) ...
Setting up libtimedate-perl (2.3100-1) ...
Setting up libexporter-lite-perl (0.08-1) ...
Setting up liblzma-dev:amd64 (5.2.4-1+b1) ...
Setting up libgif7:amd64 (5.1.9-1) ...
Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1+b1) ...
Setting up libparse-recdescent-perl (1.967015+dfsg-2) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libxshmfence1:amd64 (1.3-1) ...
Setting up libqt5dbus5:amd64 (5.12.5+dfsg-5) ...
Setting up librhash0:amd64 (1.3.9-1) ...
Setting up libpath-tiny-perl (0.108-1) ...
Setting up libuchardet0:amd64 (0.0.6-3) ...
Setting up liblua5.3-0:amd64 (5.3.3-1.1+b1) ...
Setting up procps (2:3.3.15-2+b1) ...
update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode
Setting up libjson-perl (4.02000-1) ...
Setting up libasound2:amd64 (1.1.9-1) ...
Setting up libmousex-strictconstructor-perl (0.02-2) ...
Setting up fonts-lmodern (2.004.5-6) ...
Setting up libsub-uplevel-perl (0.2800-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libthai-data (0.1.28-3) ...
Setting up libssh2-1:amd64 (1.8.0-2.1) ...
Setting up xorg-sgml-doctools (1:1.11-1) ...
Setting up netbase (6.0) ...
Setting up libcxsparse3:amd64 (1:5.6.0+dfsg-2) ...
Setting up cmake-data (3.15.4-1) ...
Setting up libcdt5:amd64 (2.42.2-3) ...
Setting up libkrb5-3:amd64 (1.17-6) ...
Setting up libcgraph6:amd64 (2.42.2-3) ...
Setting up libtiff5:amd64 (4.1.0+git191117-2) ...
Setting up libmpdec2:amd64 (2.4.2-2) ...
Setting up libexporter-tiny-perl (1.002001-1) ...
Setting up libtext-unidecode-perl (1.30-1) ...
Setting up libfile-homedir-perl (1.004-1) ...
Setting up libsamplerate0:amd64 (0.1.9-2) ...
Setting up openssl (1.1.1d-2) ...
Setting up libwebpmux3:amd64 (0.6.1-2+b1) ...
Setting up libbsd0:amd64 (0.10.0-1) ...
Setting up libdrm-common (2.4.100-4) ...
Setting up libelf1:amd64 (0.176-1.1) ...
Setting up libevdev2:amd64 (1.8.0+dfsg-2) ...
Setting up readline-common (8.0-3) ...
Setting up libicu-dev:amd64 (63.2-2) ...
Setting up libxml2:amd64 (2.9.4+dfsg1-8) ...
Setting up xdg-utils (1.1.3-1) ...
Setting up libsuitesparseconfig5:amd64 (1:5.6.0+dfsg-2) ...
Setting up liburi-perl (1.76-1) ...
Setting up libcarp-assert-perl (0.21-1) ...
Setting up libgudev-1.0-0:amd64 (233-1) ...
Setting up libblas-dev:amd64 (3.9.0-1) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode
Setting up libsz2:amd64 (1.0.4-1) ...
Setting up libvorbisenc2:amd64 (1.3.6-2) ...
Setting up libjsoncpp1:amd64 (1.7.4-3+b1) ...
Setting up libsynctex2:amd64 (2019.20190605.51237-3) ...
Setting up libwacom-common (1.1-2) ...
Setting up libmousex-nativetraits-perl (1.09-2) ...
Setting up libbz2-dev:amd64 (1.0.8-2) ...
Setting up libxkbcommon0:amd64 (0.9.1-1) ...
Setting up libwayland-client0:amd64 (1.17.0-1) ...
Setting up libnet-ssleay-perl (1.88-2) ...
Setting up x11proto-dev (2018.4-4) ...
Setting up libfile-stripnondeterminism-perl (1.6.3-1) ...
Setting up gnuplot-data (5.2.8+dfsg1-1) ...
Setting up libamd2:amd64 (1:5.6.0+dfsg-2) ...
Setting up libice6:amd64 (2:1.0.9-2) ...
Setting up libhttp-date-perl (6.05-1) ...
Setting up libxdmcp6:amd64 (1:1.1.2-3) ...
Setting up liblapack3:amd64 (3.9.0-1) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
Setting up libncurses-dev:amd64 (6.1+20191019-1) ...
Setting up libxcb1:amd64 (1.13.1-3) ...
Setting up swig (3.0.12-2.2) ...
Setting up libxcb-xfixes0:amd64 (1.13.1-3) ...
Setting up libfile-listing-perl (6.04-1) ...
Setting up libxau-dev:amd64 (1:1.0.8-1+b2) ...
Setting up libcolamd2:amd64 (1:5.6.0+dfsg-2) ...
Setting up libpcre2-dev:amd64 (10.34-7) ...
Setting up libmonosgen-2.0-dev (5.18.0.240+dfsg-5) ...
Setting up libxcb-xinput0:amd64 (1.13.1-3) ...
Setting up libtool (2.4.6-11) ...
Setting up libarchive13:amd64 (3.4.0-1+b1) ...
Setting up libxcb-render0:amd64 (1.13.1-3) ...
Setting up libfftw3-bin (3.3.8-2) ...
Setting up libpcre3-dev:amd64 (2:8.39-12+b1) ...
Setting up liblist-moreutils-perl (0.416-1+b5) ...
Setting up libxcb-glx0:amd64 (1.13.1-3) ...
Setting up libedit2:amd64 (3.1-20191231-1) ...
Setting up libreadline8:amd64 (8.0-3) ...
Setting up libpng-dev:amd64 (1.6.37-1) ...
Setting up libhash-merge-perl (0.300-1) ...
Setting up libsubunit-dev:amd64 (1.3.0-6) ...
Setting up libxcb-keysyms1:amd64 (0.4.0-1+b2) ...
Setting up libaec-dev:amd64 (1.0.4-1) ...
Setting up libarpack2:amd64 (3.7.0-3) ...
Setting up libxcb-shape0:amd64 (1.13.1-3) ...
Setting up libavahi-common3:amd64 (0.7-5) ...
Setting up libjpeg-dev (1:1.5.2-2) ...
Setting up libgfortran-9-dev:amd64 (9.2.1-23) ...
Setting up libldap-2.4-2:amd64 (2.4.48+dfsg-1+b2) ...
Setting up libnet-http-perl (6.19-1) ...
Setting up m4 (1.4.18-4) ...
Setting up libxcb-render-util0:amd64 (0.3.9-1+b1) ...
Setting up libnss3:amd64 (2:3.49-1) ...
Setting up libxcb-shm0:amd64 (1.13.1-3) ...
Setting up libxcb-icccm4:amd64 (0.4.1-1.1) ...
Setting up libxcb-util0:amd64 (0.3.8-3+b2) ...
Setting up libreadline-dev:amd64 (8.0-3) ...
Setting up default-jdk-doc (2:1.11-72) ...
Setting up libqrupdate1:amd64 (1.1.2-3) ...
Setting up libdevel-callchecker-perl (0.008-1+b1) ...
Setting up libqt5network5:amd64 (5.12.5+dfsg-5) ...
Setting up libxcb-xkb1:amd64 (1.13.1-3) ...
Setting up libxcb-image0:amd64 (0.4.0-1+b2) ...
Setting up libxcb-present0:amd64 (1.13.1-3) ...
Setting up libqt5sql5:amd64 (5.12.5+dfsg-5) ...
Setting up libthai0:amd64 (0.1.28-3) ...
Setting up ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
128 added, 0 removed; done.
Setting up libcamd2:amd64 (1:5.6.0+dfsg-2) ...
Setting up libxdmcp-dev:amd64 (1:1.1.2-3) ...
Setting up libqt5xml5:amd64 (5.12.5+dfsg-5) ...
Setting up libxml2-dev:amd64 (2.9.4+dfsg1-8) ...
Setting up libxcb-xinerama0:amd64 (1.13.1-3) ...
Setting up libptexenc1:amd64 (2019.20190605.51237-3) ...
Setting up libtest-exception-perl (0.43-1) ...
Setting up libfreetype6:amd64 (2.10.1-2) ...
Setting up libglpk40:amd64 (4.65-2) ...
Setting up libxcb-sync1:amd64 (1.13.1-3) ...
Setting up x11proto-core-dev (2018.4-4) ...
Setting up libhdf5-103:amd64 (1.10.4+repack-10) ...
Setting up bsdmainutils (11.1.2+b1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libxkbcommon-x11-0:amd64 (0.9.1-1) ...
Setting up liblapack-dev:amd64 (3.9.0-1) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode
Setting up check:amd64 (0.12.0-0.1) ...
Setting up libgssapi-krb5-2:amd64 (1.17-6) ...
Setting up libdata-optlist-perl (0.110-1) ...
Setting up libcroco3:amd64 (0.6.13-1) ...
Setting up ucf (3.0038+nmu1) ...
Setting up autoconf (2.69-11) ...
Setting up libxcb-dri2-0:amd64 (1.13.1-3) ...
Setting up dh-strip-nondeterminism (1.6.3-1) ...
Setting up libwww-robotrules-perl (6.02-1) ...
Setting up libjack-jackd2-0:amd64 (1.9.12~dfsg-2+b1) ...
Setting up libgvpr2:amd64 (2.42.2-3) ...
Setting up libdrm2:amd64 (2.4.100-4) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-4) ...
Setting up libccolamd2:amd64 (1:5.6.0+dfsg-2) ...
Setting up libxcb-randr0:amd64 (1.13.1-3) ...
Setting up libhtml-parser-perl (3.72-3+b4) ...
Setting up libcurl4:amd64 (7.67.0-2) ...
Setting up libx11-6:amd64 (2:1.6.8-1) ...
Setting up libharfbuzz0b:amd64 (2.6.4-1) ...
Setting up libsndfile1:amd64 (1.0.28-6) ...
Setting up libwacom2:amd64 (1.1-2) ...
Setting up libsm6:amd64 (2:1.2.3-1) ...
Setting up libfftw3-dev:amd64 (3.3.8-2) ...
Setting up libavahi-client3:amd64 (0.7-5) ...
Setting up libcholmod3:amd64 (1:5.6.0+dfsg-2) ...
Setting up libmono-2.0-dev (5.18.0.240+dfsg-5) ...
Setting up libllvm9:amd64 (1:9.0.1-6) ...
Setting up libxmuu1:amd64 (2:1.1.2-2+b3) ...
Setting up libio-socket-ssl-perl (2.066-1) ...
Setting up libsub-exporter-perl (0.987-1) ...
Setting up libhttp-message-perl (6.18-1) ...
Setting up libdrm-amdgpu1:amd64 (2.4.100-4) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libxcb-dri3-0:amd64 (1.13.1-3) ...
Setting up libpaper1:amd64 (1.1.28+b1) ...

Creating config file /etc/papersize with new version
Setting up libportaudio2:amd64 (19.6.0-1) ...
Setting up libhttp-negotiate-perl (6.01-1) ...
Setting up libcarp-assert-more-perl (1.20-1) ...
Setting up libpython3.7-stdlib:amd64 (3.7.6-1) ...
Setting up libdrm-nouveau2:amd64 (2.4.100-4) ...
Setting up gettext (0.19.8.1-10) ...
Setting up libharfbuzz-icu0:amd64 (2.6.4-1) ...
Setting up libxcb1-dev:amd64 (1.13.1-3) ...
Setting up libxpm4:amd64 (1:3.5.12-1) ...
Setting up libxrender1:amd64 (1:0.9.10-1) ...
Setting up gfortran-9 (9.2.1-23) ...
Setting up libpython3.7:amd64 (3.7.6-1) ...
Setting up libgbm1:amd64 (19.3.2-1) ...
Setting up libhttp-cookies-perl (6.08-1) ...
Setting up libwmf0.2-7:amd64 (0.2.8.4-17) ...
Setting up libdrm-radeon1:amd64 (2.4.100-4) ...
Setting up libclang1-9 (1:9.0.1-6) ...
Setting up fontconfig-config (2.13.1-2) ...
Setting up libpython3.7-dev:amd64 (3.7.6-1) ...
Setting up libhtml-tree-perl (5.07-2) ...
Setting up libparams-classify-perl (0.015-1+b2) ...
Setting up libdrm-intel1:amd64 (2.4.100-4) ...
Setting up libgl1-mesa-dri:amd64 (19.3.2-1) ...
Setting up libhdf5-cpp-103:amd64 (1.10.4+repack-10) ...
Setting up libx11-dev:amd64 (2:1.6.8-1) ...
Setting up libxext6:amd64 (2:1.3.3-1+b2) ...
Setting up libcurl3-gnutls:amd64 (7.67.0-2) ...
Setting up libpaper-utils (1.1.28+b1) ...
Setting up man-db (2.9.0-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxml-sax-perl (1.02+dfsg-1) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...

Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up gfortran (4:9.2.1-3.1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ...
Setting up libinput-bin (1.14.3-1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up tex-common (6.13) ...
update-language: texlive-base not installed and configured, doing nothing!
Setting up libegl-mesa0:amd64 (19.3.2-1) ...
Setting up doxygen (1.8.16-2) ...
Setting up libumfpack5:amd64 (1:5.6.0+dfsg-2) ...
Setting up libnet-smtp-ssl-perl (1.04-1) ...
Setting up libmodule-runtime-perl (0.016-1) ...
Setting up libmailtools-perl (2.21-1) ...
Setting up libxfixes3:amd64 (1:5.0.3-1) ...
Setting up libconfig-model-perl (2.138-1) ...
Setting up libxinerama1:amd64 (2:1.1.4-2) ...
Setting up libhdf5-dev (1.10.4+repack-10) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
Setting up libgraphicsmagick-q16-3 (1.4+really1.3.34+hg16181-1) ...
Setting up libxt6:amd64 (1:1.1.5-1+b3) ...
Setting up libxml-libxml-perl (2.0134+dfsg-1+b1) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up libcups2:amd64 (2.3.1-1) ...
Setting up xauth (1:1.0.10-1) ...
Setting up libegl1:amd64 (1.3.0-7) ...
Setting up cmake (3.15.4-1) ...
Setting up libgraphicsmagick++-q16-12 (1.4+really1.3.34+hg16181-1) ...
Setting up libxss1:amd64 (1:1.2.3-1) ...
Setting up libfontconfig1:amd64 (2.13.1-2+b1) ...
Setting up libstring-rewriteprefix-perl (0.007-2) ...
Setting up libpython3-stdlib:amd64 (3.7.5-3) ...
Setting up libinput10:amd64 (1.14.3-1) ...
Setting up python3.7 (3.7.6-1) ...
Setting up fontconfig (2.13.1-2+b1) ...
Regenerating fonts cache... done.
Setting up libxft2:amd64 (2.3.2-2) ...
Setting up libxmu6:amd64 (2:1.1.2-2+b3) ...
Setting up libxdamage1:amd64 (1:1.1.5-1) ...
Setting up libpython3-dev:amd64 (3.7.5-3) ...
Setting up libxi6:amd64 (2:1.7.9-1) ...
Setting up libmodule-implementation-perl (0.09-1) ...
Setting up libpackage-stash-perl (0.38-1) ...
Setting up libxtst6:amd64 (2:1.2.3-1) ...
Setting up po-debconf (1.0.21) ...
Setting up libtk8.6:amd64 (8.6.10-1) ...
Setting up libxcursor1:amd64 (1:1.2.0-2) ...
Setting up libpango-1.0-0:amd64 (1.42.4-8) ...
Setting up python3 (3.7.5-3) ...
Setting up libxaw7:amd64 (2:1.0.13-1+b2) ...
Setting up libmime-tools-perl (5.509-1) ...
Setting up python3.7-dev (3.7.6-1) ...
Setting up libcairo2:amd64 (1.16.0-4) ...
Setting up libclass-load-perl (0.25-1) ...
Setting up libgd3:amd64 (2.2.5-5.2) ...
Setting up texinfo (6.7.0.dfsg.2-5) ...
Running mktexlsr. This may take some time. ... done.
Setting up texlive-binaries (2019.20190605.51237-3) ...
update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
Setting up libpangoft2-1.0-0:amd64 (1.42.4-8) ...
Setting up libparams-validate-perl (1.29-3) ...
Setting up python3-lib2to3 (3.8.0-1) ...
Setting up texlive-base (2019.20191208-4) ...
tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps
tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg
tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper
tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/config/pdftexconfig.tex
Setting up libpangocairo-1.0-0:amd64 (1.42.4-8) ...
Setting up python3-distutils (3.8.0-1) ...
Setting up libglx-mesa0:amd64 (19.3.2-1) ...
Setting up libglx0:amd64 (1.3.0-7) ...
Setting up libfltk1.3:amd64 (1.3.4-10) ...
Setting up libgdiplus (6.0.4+dfsg-1) ...
Setting up libgl1:amd64 (1.3.0-7) ...
Setting up texlive-latex-base (2019.20191208-4) ...
Setting up python3-dev (3.7.5-3) ...
Setting up r-base-core (3.6.2-2) ...

Creating config file /etc/R/Renviron with new version
Setting up libgvc6 (2.42.2-3) ...
Setting up libgetopt-long-descriptive-perl (0.104-1) ...
Setting up libglx-dev:amd64 (1.3.0-7) ...
Setting up libglu1-mesa:amd64 (9.0.1-1) ...
Setting up gnuplot-nox (5.2.8+dfsg1-1) ...
update-alternatives: using /usr/bin/gnuplot-nox to provide /usr/bin/gnuplot (gnuplot) in auto mode
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Setting up libqt5widgets5:amd64 (5.12.5+dfsg-5) ...
Setting up libqt5help5:amd64 (5.12.5-2+b1) ...
Setting up libgl2ps1.4 (1.4.0+dfsg1-2) ...
Setting up libqt5printsupport5:amd64 (5.12.5+dfsg-5) ...
Setting up liboctave7:amd64 (5.1.0-4+b1) ...
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Setting up cme (1.030-1) ...
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Setting up octave (5.1.0-4+b1) ...
Setting up liboctave-dev (5.1.0-4+b1) ...
Setting up libmono-system-xml4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-configuration4.0-cil (5.18.0.240+dfsg-5) ...
Setting up liblwp-protocol-https-perl (6.07-2) ...
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Setting up openjdk-11-jre-headless:amd64 (11.0.6+10-1) ...
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Setting up libmono-system-core4.0-cil (5.18.0.240+dfsg-5) ...
Setting up dh-autoreconf (19) ...
Setting up default-jdk-headless (2:1.11-72) ...
Setting up ca-certificates-java (20190909) ...
head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GeoTrust_Primary_Certification_Authority.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem
Adding debian:Certigna.pem
Adding debian:Global_Chambersign_Root_-_2008.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:GlobalSign_Root_CA_-_R2.pem
Adding debian:GeoTrust_Global_CA.pem
Adding debian:Chambers_of_Commerce_Root_-_2008.pem
Adding debian:GlobalSign_Root_CA_-_R6.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:SecureTrust_CA.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:GeoTrust_Universal_CA.pem
Adding debian:TrustCor_ECA-1.pem
Adding debian:TrustCor_RootCert_CA-2.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:LuxTrust_Global_Root_2.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem
Adding debian:Izenpe.com.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Certinomis_-_Root_CA.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:E-Tugra_Certification_Authority.pem
Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
Adding debian:GeoTrust_Universal_CA_2.pem
Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
Adding debian:Cybertrust_Global_Root.pem
Adding debian:Hongkong_Post_Root_CA_1.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:thawte_Primary_Root_CA.pem
Adding debian:thawte_Primary_Root_CA_-_G3.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:AddTrust_External_Root.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:Taiwan_GRCA.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:thawte_Primary_Root_CA_-_G2.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:Secure_Global_CA.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:QuoVadis_Root_CA.pem
Adding debian:Deutsche_Telekom_Root_CA_2.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:Network_Solutions_Certificate_Authority.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:EE_Certification_Centre_Root_CA.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:Sonera_Class_2_Root_CA.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:Trustis_FPS_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:VeriSign_Universal_Root_Certification_Authority.pem
Adding debian:EC-ACC.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem
Adding debian:Certplus_Class_2_Primary_CA.pem
Adding debian:TrustCor_RootCert_CA-1.pem
Adding debian:ACCVRAIZ1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:DST_Root_CA_X3.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem
done.
Setting up libxml-parser-perl (2.46-1+b1) ...
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Setting up libmono-system-ldap-protocols4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-web-applicationservices4.0-cil (5.18.0.240+dfsg-5) ...
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Setting up libmono-system-configuration-install4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-numerics-vectors4.0-cil (5.18.0.240+dfsg-5) ...
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Setting up libmono-rabbitmq4.0-cil (5.18.0.240+dfsg-5) ...
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Setting up libmono-system-workflow-runtime4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-web-regularexpressions4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-microsoft-visualc10.0-cil (5.18.0.240+dfsg-5) ...
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Setting up libmono-microsoft-build-engine4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-reflection-context4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-posix4.0-cil (5.18.0.240+dfsg-5) ...
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update-alternatives: using /usr/bin/monodis to provide /usr/bin/cli-ildasm (cil-disassembler) in auto mode
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Setting up libmono-system-reactive-interfaces2.2-cil (5.18.0.240+dfsg-5) ...
Setting up libnunit-core-interfaces2.6.3-cil (2.6.4+dfsg-1) ...
* Installing 1 assembly from libnunit-core-interfaces2.6.3-cil into Mono
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Setting up libmono-debugger-soft4.0a-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-net-http4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-deployment4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-io-compression4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-runtime-serialization4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-xaml4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-relaxng4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-messaging4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-tasklets4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-threading-tasks-dataflow4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-management4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-webbrowser4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-runtime-serialization-formatters-soap4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-i18n-mideast4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-codecontracts4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-i18n-west4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-parallel4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-web-mobile4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-json4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-management4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-i18n-rare4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-i18n-other4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-reactive-core2.2-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-csharp4.0c-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-web-razor2.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-drawing4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-custommarshalers4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-sharpzip4.84-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-identitymodel4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-data-services-client4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-microsoft-csharp4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libnunit-framework2.6.3-cil (2.6.4+dfsg-1) ...
* Installing 1 assembly from libnunit-framework2.6.3-cil into Mono
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Setting up libmono-system-transactions4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-componentmodel-dataannotations4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-cscompmgd0.0-cil (5.18.0.240+dfsg-5) ...
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* Installing 1 assembly from libnunit-mocks2.6.3-cil into Mono
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* Installing 1 assembly from libnunit-core2.6.3-cil into Mono
Setting up libmono-messaging-rabbitmq4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-json-microsoft4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-ldap4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-system-io-compression-filesystem4.0-cil (5.18.0.240+dfsg-5) ...
Setting up libmono-i18n4.0-all (5.18.0.240+dfsg-5) ...
Setting up libmono-microsoft-build-tasks-v4.0-4.0-cil (5.18.0.240+dfsg-5) ...
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update-alternatives: using /usr/bin/mono-csc to provide /usr/bin/cli-csc (c-sharp-compiler) in auto mode
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[0mI: Building the package[0m
[0mI: Running cd /build/libsbml-5.17.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin" HOME="/nonexistent" dpkg-buildpackage -us -uc [0m
dpkg-buildpackage: info: source package libsbml
dpkg-buildpackage: info: source version 5.17.2+dfsg-3
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
dpkg-source: info: using options from libsbml-5.17.2+dfsg/debian/source/options: --extend-diff-ignore=(^|/)(src/sbml/validator/constraints/.*|src/bindings/csharp/csharp-files.*|src/sbml/extension/SBMLExtensionRegistry.*|src/sbml/packages/comp/validator/constraints/CompIdBase.cpp|src/bindings/java/java-files/org/sbml/libsbml/SBMLExtensionRegistry.java|src/sbml/xml/XMLErrorLog.cpp|docs/src/doxygen-config-common.txt)$
 fakeroot debian/rules clean
dh  clean --with python3,cli
dh: unable to load addon python3: Can't locate Debian/Debhelper/Sequence/python3.pm in @INC (you may need to install the Debian::Debhelper::Sequence::python3 module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at (eval 12) line 1.
BEGIN failed--compilation aborted at (eval 12) line 1.

make: *** [debian/rules:33: clean] Error 255
dpkg-buildpackage: error: fakeroot debian/rules clean subprocess returned exit status 2
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[0mI: removing directory /var/cache/pbuilder/build/2183 and its subdirectories[0m
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