[Debian-med-packaging] Bug#795586: libfreecontact-perl: FTBFS: Can't load '/tmp/buildd/libfreecontact-perl-0.08/blib/arch/auto/FreeContact/FreeContact.so
Andreas Tille
tille at debian.org
Sat Aug 15 14:02:37 UTC 2015
Hi Perl team,
I admit I have no idea how to fix this. It somehow smells like a gcc-5
issue but I'm not sure.
Any hint would be welcome
Andreas.
On Sat, Aug 15, 2015 at 02:12:07PM +0100, Chris Lamb wrote:
> Source: libfreecontact-perl
> Version: 0.08-2
> Severity: serious
> Justification: fails to build from source
>
> Dear Maintainer,
>
> libfreecontact-perl fails to build from source on unstable/amd64:
>
> [..]
> Failed 3/3 subtests
>
> # Failed test 'use FreeContact;'
> # at t/02test.t line 6.
> # Tried to use 'FreeContact'.
> # Error: Can't load
> '/tmp/buildd/libfreecontact-perl-0.08/blib/arch/auto/FreeContact/FreeContact.so'
> for module FreeContact:
> /tmp/buildd/libfreecontact-perl-0.08/blib/arch/auto/FreeContact/FreeContact.so:
> undefined symbol:
> _ZN11freecontact9predictor3runERKNS_5ali_tERKSt6vectorIdSaIdEEdddtddbdbbdilPSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessISF_ESaISt4pairIKSF_dEEE
> at /usr/lib/x86_64-linux-gnu/perl/5.20/DynaLoader.pm line 187.
> # at t/02test.t line 6.
> # Compilation failed in require at t/02test.t line 6.
> # BEGIN failed--compilation aborted at t/02test.t line 6.
> Can't locate object method "_new" via package "FreeContact::Predictor"
> at /tmp/buildd/libfreecontact-perl-0.08/blib/lib/FreeContact.pm line
> 50.
> # Looks like you planned 10 tests but ran 1.
>
> [..]
>
> The full build log is attached or can be viewed here:
>
> https://reproducible.debian.net/rbuild/unstable/amd64/libfreecontact-perl_0.08-2.rbuild.log.gz
>
>
> Regards,
>
> --
> ,''`.
> : :' : Chris Lamb
> `. `'` lamby at debian.org / chris-lamb.co.uk
> `-
> Starting to build libfreecontact-perl/unstable on 2015-08-10 19:26
> The jenkins build log is/was available at https://jenkins.debian.net/job/reproducible_builder_zeta/25426/console
> Reading package lists...
> Building dependency tree...
> Reading state information...
> NOTICE: 'libfreecontact-perl' packaging is maintained in the 'Git' version control system at:
> git://anonscm.debian.org/debian-med/libfreecontact-perl.git
> Need to get 63.2 kB of source archives.
> Get:1 http://ftp.de.debian.org/debian/ unstable/main libfreecontact-perl 0.08-2 (dsc) [2079 B]
> Get:2 http://ftp.de.debian.org/debian/ unstable/main libfreecontact-perl 0.08-2 (tar) [58.7 kB]
> Get:3 http://ftp.de.debian.org/debian/ unstable/main libfreecontact-perl 0.08-2 (diff) [2477 B]
> Fetched 63.2 kB in 0s (274 kB/s)
> Download complete and in download only mode
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Format: 3.0 (quilt)
> Source: libfreecontact-perl
> Binary: libfreecontact-perl
> Architecture: any
> Version: 0.08-2
> Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
> Uploaders: Laszlo Kajan <lkajan at rostlab.org>
> Homepage: http://rostlab.org/
> Standards-Version: 3.9.4
> Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/libfreecontact-perl.git
> Vcs-Git: git://anonscm.debian.org/debian-med/libfreecontact-perl.git
> Build-Depends: debhelper (>= 9.0.0), libextutils-xspp-perl, libfreecontact0-dev (>= 1.0.21-1~), perl
> Package-List:
> libfreecontact-perl deb perl extra
> Checksums-Sha1:
> dea098c8025b42e79227265dd74252ceedbfa007 58672 libfreecontact-perl_0.08.orig.tar.gz
> acb37c09d3a6e3d667f12c7832761c0045b084a1 2477 libfreecontact-perl_0.08-2.debian.tar.gz
> Checksums-Sha256:
> 7386762985b9e36ec13379948528f1f18e49cf799ba5436a46aa60e9cb041911 58672 libfreecontact-perl_0.08.orig.tar.gz
> d0ecf233da20d826c6e4efb465c3d837e1bbf48d7dbc59cb6117424d5969fe46 2477 libfreecontact-perl_0.08-2.debian.tar.gz
> Files:
> 798e25cfc3954e027d208f62dd3fe6ea 58672 libfreecontact-perl_0.08.orig.tar.gz
> 93cde55bc0aa93b788d6a9e1c08efdcb 2477 libfreecontact-perl_0.08-2.debian.tar.gz
>
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> + sudo timeout -k 12.1h 12h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/tmp.jbuDJd2yb8/pbuilderrc_0kfa --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult b1 --logfile b1/build.log libfreecontact-perl_0.08-2.dsc
> W: /root/.pbuilderrc does not exist
> I: Logging to b1/build.log
> I: using fakeroot in build.
> I: pbuilder: network access will be disabled during build
> I: Current time: Mon Aug 10 07:26:09 GMT+12 2015
> I: pbuilder-time-stamp: 1439234769
> I: Building the build Environment
> I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
> I: creating local configuration
> I: copying local configuration
> I: mounting /proc filesystem
> I: mounting /run/shm filesystem
> I: mounting /dev/pts filesystem
> I: Mounting /dev/shm
> I: Mounting /sys
> I: policy-rc.d already exists
> I: Installing the build-deps
> -> Attempting to satisfy build-dependencies
> -> Creating pbuilder-satisfydepends-dummy package
> Package: pbuilder-satisfydepends-dummy
> Version: 0.invalid.0
> Architecture: amd64
> Maintainer: Debian Pbuilder Team <pbuilder-maint at 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 (>= 9.0.0), libextutils-xspp-perl, libfreecontact0-dev (>= 1.0.21-1~), perl
> dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
> Selecting previously unselected package pbuilder-satisfydepends-dummy.
> (Reading database ... 20247 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 libextutils-xspp-perl; however:
> Package libextutils-xspp-perl is not installed.
> pbuilder-satisfydepends-dummy depends on libfreecontact0-dev (>= 1.0.21-1~); however:
> Package libfreecontact0-dev 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...
> The following NEW packages will be installed:
> libblas-common{a} libblas3{a} libextutils-xspp-perl{a} libfreecontact0{a}
> libfreecontact0-dev{a} libgfortran3{a} liblapack3{a}
> 0 packages upgraded, 7 newly installed, 0 to remove and 0 not upgraded.
> Need to get 2648 kB of archives. After unpacking 9062 kB will be used.
> Writing extended state information...
> Get: 1 http://ftp.de.debian.org/debian/ unstable/main libgfortran3 amd64 5.2.1-15 [253 kB]
> Get: 2 http://ftp.de.debian.org/debian/ unstable/main libblas-common amd64 1.2.20110419-10 [8496 B]
> Get: 3 http://ftp.de.debian.org/debian/ unstable/main libblas3 amd64 1.2.20110419-10 [167 kB]
> Get: 4 http://ftp.de.debian.org/debian/ unstable/main liblapack3 amd64 3.5.0-4 [1852 kB]
> Get: 5 http://ftp.de.debian.org/debian/ unstable/main libfreecontact0 amd64 1.0.21-3+b1 [85.9 kB]
> Get: 6 http://ftp.de.debian.org/debian/ unstable/main libextutils-xspp-perl all 0.1800-2 [191 kB]
> Get: 7 http://ftp.de.debian.org/debian/ unstable/main libfreecontact0-dev amd64 1.0.21-3+b1 [90.6 kB]
> Fetched 2648 kB in 0s (12.2 MB/s)
> debconf: delaying package configuration, since apt-utils is not installed
> Selecting previously unselected package libgfortran3:amd64.
> (Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 20247 files and directories currently installed.)
> Preparing to unpack .../libgfortran3_5.2.1-15_amd64.deb ...
> Unpacking libgfortran3:amd64 (5.2.1-15) ...
> Selecting previously unselected package libblas-common.
> Preparing to unpack .../libblas-common_1.2.20110419-10_amd64.deb ...
> Unpacking libblas-common (1.2.20110419-10) ...
> Selecting previously unselected package libblas3.
> Preparing to unpack .../libblas3_1.2.20110419-10_amd64.deb ...
> Unpacking libblas3 (1.2.20110419-10) ...
> Selecting previously unselected package liblapack3.
> Preparing to unpack .../liblapack3_3.5.0-4_amd64.deb ...
> Unpacking liblapack3 (3.5.0-4) ...
> Selecting previously unselected package libfreecontact0.
> Preparing to unpack .../libfreecontact0_1.0.21-3+b1_amd64.deb ...
> Unpacking libfreecontact0 (1.0.21-3+b1) ...
> Selecting previously unselected package libextutils-xspp-perl.
> Preparing to unpack .../libextutils-xspp-perl_0.1800-2_all.deb ...
> Unpacking libextutils-xspp-perl (0.1800-2) ...
> Selecting previously unselected package libfreecontact0-dev.
> Preparing to unpack .../libfreecontact0-dev_1.0.21-3+b1_amd64.deb ...
> Unpacking libfreecontact0-dev (1.0.21-3+b1) ...
> Processing triggers for man-db (2.7.0.2-5) ...
> Setting up libgfortran3:amd64 (5.2.1-15) ...
> Setting up libblas-common (1.2.20110419-10) ...
> Setting up libblas3 (1.2.20110419-10) ...
> update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
> Setting up liblapack3 (3.5.0-4) ...
> update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
> Setting up libfreecontact0 (1.0.21-3+b1) ...
> Setting up libextutils-xspp-perl (0.1800-2) ...
> Setting up libfreecontact0-dev (1.0.21-3+b1) ...
> Processing triggers for libc-bin (2.19-19) ...
> Reading package lists...
> Building dependency tree...
> Reading state information...
> Reading extended state information...
> Initializing package states...
> Writing extended state information...
> Building tag database...
> -> Finished parsing the build-deps
> Reading package lists...
> Building dependency tree...
> Reading state information...
> fakeroot is already the newest version.
> 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
> I: Copying source file
> I: copying [libfreecontact-perl_0.08-2.dsc]
> I: copying [./libfreecontact-perl_0.08.orig.tar.gz]
> I: copying [./libfreecontact-perl_0.08-2.debian.tar.gz]
> I: Extracting source
> gpgv: keyblock resource `/tmp/buildd/.gnupg/trustedkeys.gpg': file open error
> gpgv: Signature made Sat Sep 28 08:55:17 2013 GMT+12 using RSA key ID 9A0C52FA
> gpgv: Can't check signature: public key not found
> dpkg-source: warning: failed to verify signature on ./libfreecontact-perl_0.08-2.dsc
> dpkg-source: info: extracting libfreecontact-perl in libfreecontact-perl-0.08
> dpkg-source: info: unpacking libfreecontact-perl_0.08.orig.tar.gz
> dpkg-source: info: unpacking libfreecontact-perl_0.08-2.debian.tar.gz
> I: Building the package
> I: Running cd tmp/buildd/*/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" dpkg-buildpackage -us -uc -b -rfakeroot
> dpkg-buildpackage: source package libfreecontact-perl
> dpkg-buildpackage: source version 0.08-2
> dpkg-buildpackage: source distribution unstable
> dpkg-buildpackage: source changed by Laszlo Kajan <lkajan at rostlab.org>
> dpkg-source --before-build libfreecontact-perl-0.08
> dpkg-buildpackage: host architecture amd64
> fakeroot debian/rules clean
> dh clean --parallel
> dh_testdir -O--parallel
> debian/rules override_dh_auto_clean
> make[1]: Entering directory '/tmp/buildd/libfreecontact-perl-0.08'
> rm -f Makefile.old
> dh_auto_clean
> make[1]: Leaving directory '/tmp/buildd/libfreecontact-perl-0.08'
> dh_clean -O--parallel
> debian/rules build
> dh build --parallel
> dh_testdir -O--parallel
> debian/rules override_dh_auto_configure
> make[1]: Entering directory '/tmp/buildd/libfreecontact-perl-0.08'
> dh_auto_configure -- OPTIMIZE="-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security" LD="'cc' -Wl,-z,relro"
> perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro" "OPTIMIZE=-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "LD='cc' -Wl,-z,relro"
> Checking if your kit is complete...
> Looks good
> Generating a Unix-style Makefile
> Writing Makefile for FreeContact
> Writing MYMETA.yml and MYMETA.json
> make[1]: Leaving directory '/tmp/buildd/libfreecontact-perl-0.08'
> dh_auto_build -O--parallel
> make -j23
> make[1]: Entering directory '/tmp/buildd/libfreecontact-perl-0.08'
> /usr/bin/perl /usr/share/perl/5.20/ExtUtils/xsubpp -C++ -hiertype -noprototypes -typemap /usr/share/perl/5.20/ExtUtils/typemap -typemap perlobject.map -typemap typemap -typemap typemap FreeContact.xs > FreeContact.xsc && mv FreeContact.xsc FreeContact.c
> Running Mkbootstrap for FreeContact ()
> chmod 644 FreeContact.bs
> cp lib/FreeContact.pm blib/lib/FreeContact.pm
> AutoSplitting blib/lib/FreeContact.pm (blib/lib/auto/FreeContact)
> g++ -c -I. -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DVERSION=\"0.08\" -DXS_VERSION=\"0.08\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.20/CORE" FreeContact.c
> rm -f blib/arch/auto/FreeContact/FreeContact.so
> 'cc' -Wl,-z,relro -shared -L/usr/local/lib -fstack-protector FreeContact.o -o blib/arch/auto/FreeContact/FreeContact.so \
> -lfreecontact \
>
> chmod 755 blib/arch/auto/FreeContact/FreeContact.so
> /usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- FreeContact.bs blib/arch/auto/FreeContact/FreeContact.bs 644
> Manifying blib/man3/FreeContact.3pm
> make[1]: Leaving directory '/tmp/buildd/libfreecontact-perl-0.08'
> dh_auto_test -O--parallel
> make -j23 test TEST_VERBOSE=1
> make[1]: Entering directory '/tmp/buildd/libfreecontact-perl-0.08'
> Running Mkbootstrap for FreeContact ()
> chmod 644 FreeContact.bs
> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t
>
> # Failed test 'use FreeContact;'
> # at t/01FreeContact.t line 9.
> # Tried to use 'FreeContact'.
> # Error: Can't load '/tmp/buildd/libfreecontact-perl-0.08/blib/arch/auto/FreeContact/FreeContact.so' for module FreeContact: /tmp/buildd/libfreecontact-perl-0.08/blib/arch/auto/FreeContact/FreeContact.so: undefined symbol: _ZN11freecontact9predictor3runERKNS_5ali_tERKSt6vectorIdSaIdEEdddtddbdbbdilPSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessISF_ESaISt4pairIKSF_dEEE at /usr/lib/x86_64-linux-gnu/perl/5.20/DynaLoader.pm line 187.
> # at t/01FreeContact.t line 9.
> # Compilation failed in require at t/01FreeContact.t line 9.
> # BEGIN failed--compilation aborted at t/01FreeContact.t line 9.
>
> # Failed test 'FreeContact->can(...)'
> # at t/01FreeContact.t line 17.
> # FreeContact->can('get_ps_evfold') failed
> # FreeContact->can('get_ps_psicov') failed
> # FreeContact->can('get_ps_psicov_sd') failed
>
> # Failed test 'FreeContact::Predictor->can(...)'
> # at t/01FreeContact.t line 18.
> # FreeContact::Predictor->can('_get_seq_weights') failed
> # FreeContact::Predictor->can('_run') failed
> # Looks like you failed 3 tests of 3.
> t/01FreeContact.t ..
> 1..3
> not ok 1 - use FreeContact;
> not ok 2 - FreeContact->can(...)
> not ok 3 - FreeContact::Predictor->can(...)
> Dubious, test returned 3 (wstat 768, 0x300)
> Failed 3/3 subtests
>
> # Failed test 'use FreeContact;'
> # at t/02test.t line 6.
> # Tried to use 'FreeContact'.
> # Error: Can't load '/tmp/buildd/libfreecontact-perl-0.08/blib/arch/auto/FreeContact/FreeContact.so' for module FreeContact: /tmp/buildd/libfreecontact-perl-0.08/blib/arch/auto/FreeContact/FreeContact.so: undefined symbol: _ZN11freecontact9predictor3runERKNS_5ali_tERKSt6vectorIdSaIdEEdddtddbdbbdilPSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessISF_ESaISt4pairIKSF_dEEE at /usr/lib/x86_64-linux-gnu/perl/5.20/DynaLoader.pm line 187.
> # at t/02test.t line 6.
> # Compilation failed in require at t/02test.t line 6.
> # BEGIN failed--compilation aborted at t/02test.t line 6.
> Can't locate object method "_new" via package "FreeContact::Predictor" at /tmp/buildd/libfreecontact-perl-0.08/blib/lib/FreeContact.pm line 50.
> # Looks like you planned 10 tests but ran 1.
> # Looks like you failed 1 test of 1 run.
> # Looks like your test exited with 255 just after 1.
> t/02test.t .........
> 1..10
> not ok 1 - use FreeContact;
> Dubious, test returned 255 (wstat 65280, 0xff00)
> Failed 10/10 subtests
>
> Test Summary Report
> -------------------
> t/01FreeContact.t (Wstat: 768 Tests: 3 Failed: 3)
> Failed tests: 1-3
> Non-zero exit status: 3
> t/02test.t (Wstat: 65280 Tests: 1 Failed: 1)
> Failed test: 1
> Non-zero exit status: 255
> Parse errors: Bad plan. You planned 10 tests but ran 1.
> Files=2, Tests=4, 0 wallclock secs ( 0.04 usr 0.01 sys + 0.11 cusr 0.03 csys = 0.19 CPU)
> Result: FAIL
> Failed 2/2 test programs. 4/4 subtests failed.
> Makefile:992: recipe for target 'test_dynamic' failed
> make[1]: *** [test_dynamic] Error 255
> make[1]: Leaving directory '/tmp/buildd/libfreecontact-perl-0.08'
> dh_auto_test: make -j23 test TEST_VERBOSE=1 returned exit code 2
> debian/rules:30: recipe for target 'build' failed
> make: *** [build] Error 2
> dpkg-buildpackage: error: debian/rules build gave error exit status 2
> E: Failed autobuilding of package
> I: unmounting /sys filesystem
> I: unmounting /dev/shm filesystem
> I: unmounting dev/pts filesystem
> I: unmounting run/shm filesystem
> I: unmounting proc filesystem
> I: cleaning the build env
> I: removing directory /var/cache/pbuilder/build//15954 and its subdirectories
> Warning: No second build log
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