[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_armhf_28 #4719
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Wed Jun 15 08:56:24 UTC 2016
See <https://jenkins.debian.net/job/reproducible_builder_armhf_28/4719/>
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./Installation.tex:558: Warning: Undefined label: 'sec:is_working'
./Installation.tex:561: Warning: '_' occurring outside math mode
./Installation.tex:609: Warning: Suppressing nested a element
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HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right.
Run, run, again...
Exclude comment 'comment'
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./Installation.tex:255: Warning: Suppressing nested a element
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./Installation.tex:317: Warning: Suppressing nested a element
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./Installation.tex:540: Warning: Suppressing nested a element
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./Installation.tex:561: Warning: '_' occurring outside math mode
./Installation.tex:609: Warning: Suppressing nested a element
./Installation.tex:609: Warning: Suppressing nested a element
Fixpoint reached in 2 step(s)
hevea -fix -text Installation.tex
Exclude comment 'comment'
./Installation.tex:55: Warning: tt_mode is an empty style
./Installation.tex:61: Warning: No date given
./Installation.tex:430: Warning: '_' occurring outside math mode
./Installation.tex:535: Warning: '_' occurring outside math mode
./Installation.tex:561: Warning: '_' occurring outside math mode
HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right.
Run, run, again...
Exclude comment 'comment'
./Installation.tex:55: Warning: tt_mode is an empty style
./Installation.tex:61: Warning: No date given
./Installation.tex:430: Warning: '_' occurring outside math mode
./Installation.tex:535: Warning: '_' occurring outside math mode
./Installation.tex:561: Warning: '_' occurring outside math mode
Fixpoint reached in 2 step(s)
make[3]: Leaving directory '/build/python-biopython-1.67+dfsg/Doc/install'
make[2]: Leaving directory '/build/python-biopython-1.67+dfsg/Doc'
make[1]: Leaving directory '/build/python-biopython-1.67+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/python-biopython-1.67+dfsg'
debian/rules:125: warning: overriding recipe for target 'override_dh_auto_clean'
debian/rules:59: warning: ignoring old recipe for target 'override_dh_auto_clean'
mkdir -p Tests_avoid
for avoid in PAML_tools EmbossPhylipNew MSAProbs_tool NACCESS_tool PopGen_DFDist PopGen_FDist PopGen_GenePop PopGen_GenePop_EasyController PopGen_SimCoal XXmotif_tool BWA_tool raxml_tool BioSQL_MySQLdb BioSQL_psycopg2 phyml_tool samtools_tool \
; do \
mv Tests/test_${avoid}.py Tests_avoid ; \
done
# For the doc package we need a clean testsuite without all the remaining files. So keep a clean copy here
mkdir -p debian/tmp_tests
cp -a Tests debian/tmp_tests
# remove duplicated file
rm -f debian/tmp_tests/Tests/Quality/example.fastq.gz
# We also keep the tests we need to avoid for later inspection
cp -a Tests_avoid debian/tmp_tests
# in the Debian package dialign it is not needed to set DIALIGN2_DIR but the test is verifying this dir
# to run the EMBOSS test test_Emboss also requires to have the environment variable EMBOSS_ROOT set
LC_ALL=C.UTF-8 dh_auto_test -- --test --system=custom \
--test-args='set -e; \
mkdir -p {build_dir}/home; \
mkdir -p {build_dir}/Doc/examples; \
cp -a Doc/Tutorial.tex {build_dir}/Doc; \
cp -a Doc/Tutorial {build_dir}/Doc; \
cp -a Doc/examples {build_dir}/Doc; \
cp -a Tests {build_dir}; \
cd {build_dir}/Tests; \
env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline'
pybuild --test -i python{version} -p 2.7 --test --system=custom "--test-args=set -e; \\\
mkdir -p {build_dir}/home; \\\
mkdir -p {build_dir}/Doc/examples; \\\
cp -a Doc/Tutorial.tex {build_dir}/Doc; \\\
cp -a Doc/Tutorial {build_dir}/Doc; \\\
cp -a Doc/examples {build_dir}/Doc; \\\
cp -a Tests {build_dir}; \\\
cd {build_dir}/Tests; \\\
env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline"
I: pybuild base:184: set -e; \
mkdir -p /build/python-biopython-1.67+dfsg/.pybuild/pythonX.Y_2.7/build/home; \
mkdir -p /build/python-biopython-1.67+dfsg/.pybuild/pythonX.Y_2.7/build/Doc/examples; \
cp -a Doc/Tutorial.tex /build/python-biopython-1.67+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \
cp -a Doc/Tutorial /build/python-biopython-1.67+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \
cp -a Doc/examples /build/python-biopython-1.67+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \
cp -a Tests /build/python-biopython-1.67+dfsg/.pybuild/pythonX.Y_2.7/build; \
cd /build/python-biopython-1.67+dfsg/.pybuild/pythonX.Y_2.7/build/Tests; \
env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/build/python-biopython-1.67+dfsg/.pybuild/pythonX.Y_2.7/build/home python2.7 run_tests.py --offline
test_Ace ... ok
test_AlignIO ... ok
test_AlignIO_ClustalIO ... ok
test_AlignIO_EmbossIO ... ok
test_AlignIO_FastaIO ... ok
test_AlignIO_PhylipIO ... ok
test_AlignIO_convert ... ok
test_AlignInfo ... ok
test_Application ... ok
test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
test_BioSQL_sqlite3 ... ok
test_CAPS ... ok
test_CelFile ... ok
test_Chi2 ... ok
test_ClustalOmega_tool ... ok
test_Clustalw_tool ... ok
test_Cluster ... ok
test_CodonTable ... ok
test_CodonUsage ... ok
test_ColorSpiral ... ok
test_Compass ... ok
test_Consensus ... ok
test_Crystal ... ok
test_DSSP_tool ... ok
test_Dialign_tool ... ok
test_DocSQL ... ok
test_EMBL_unittest ... ok
test_Emboss ... ok
test_EmbossPrimer ... ok
test_Entrez ... ok
test_Entrez_online ... skipping. internet not available
test_Enzyme ... ok
test_FSSP ... ok
test_Fasttree_tool ... ok
test_File ... ok
test_GACrossover ... ok
test_GAMutation ... ok
test_GAOrganism ... ok
test_GAQueens ... ok
test_GARepair ... ok
test_GASelection ... ok
test_GenBank ... ok
test_GenBank_unittest ... ok
test_GenomeDiagram ... ok
test_GraphicsBitmaps ... ok
test_GraphicsChromosome ... ok
test_GraphicsDistribution ... ok
test_GraphicsGeneral ... ok
test_HMMCasino ... ok
test_HMMGeneral ... ok
test_KDTree ... ok
test_KEGG ... ok
test_KEGG_online ... skipping. internet not available
test_KGML_graphics ... ok
test_KGML_graphics_online ... skipping. internet not available
test_KGML_nographics ... ok
test_KeyWList ... ok
test_Location ... ok
test_LogisticRegression ... ok
test_MMCIF ... ok
test_Mafft_tool ... ok
test_MarkovModel ... ok
test_Medline ... ok
test_Muscle_tool ... ok
test_NCBITextParser ... ok
test_NCBIXML ... ok
test_NCBI_BLAST_tools ... ok
test_NCBI_qblast ... skipping. internet not available
test_NNExclusiveOr ... ok
test_NNGene ... ok
test_NNGeneral ... ok
test_NaiveBayes ... ok
test_Nexus ... ok
test_PAML_baseml ... ok
test_PAML_codeml ... ok
test_PAML_yn00 ... ok
test_PDB ... /srv/reproducible-results/rbuild-debian-y0PQRuot/tmp.PJYyhNUK3A: 47.7% -- replaced with /srv/reproducible-results/rbuild-debian-y0PQRuot/tmp.PJYyhNUK3A.gz
INFO: Starting at 2016-06-15 08:56:20.448838
INFO: Finished at 2016-06-15 08:56:20.651547, took: 0:00:00.202721
Wed Jun 15 08:56:21 UTC 2016 - https://jenkins.debian.net/job/reproducible_builder_armhf_28/4719/console got remote error with exit code 143 from opi2a-armhf-rb.debian.net for build #1 for python-biopython on testing/armhf
FATAL: null
java.lang.NullPointerException
at hudson.plugins.build_timeout.BuildTimeoutWrapper$EnvironmentImpl.tearDown(BuildTimeoutWrapper.java:199)
at hudson.model.Build$BuildExecution.doRun(Build.java:173)
at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:534)
at hudson.model.Run.execute(Run.java:1738)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
at hudson.model.ResourceController.execute(ResourceController.java:98)
at hudson.model.Executor.run(Executor.java:410)
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