[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_amd64_5 #42059

Sat May 28 10:37:00 UTC 2016

See <https://jenkins.debian.net/job/reproducible_builder_amd64_5/42059/>

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[...truncated 438 lines...]
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for C compiler vendor... gnu
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checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for cc_r... gcc
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking for a BSD-compatible install... /usr/bin/install -c
checking how to run the C preprocessor... gcc -E
checking for C compiler vendor... (cached) gnu
checking for gcc option to accept ISO C99... none needed
checking for gcc option to accept ISO Standard C... (cached) none needed
checking for ranlib... ranlib
checking for ar... /usr/bin/ar
checking whether ln -s works... yes
checking whether you have a GNU make... yes, you do; and we assume you will use it!
checking for gcc option to produce PIC... -fPIC
checking whether C compiler accepts -msse2... yes
checking whether C compiler accepts -msse2 -msse3... yes
checking compiler support for sse2 cast functions... yes
checking whether SSE2 is supported... yes
checking whether _MM_SET_FLUSH_ZERO_MODE is supported... yes
configure: Activating Intel/AMD SSE optimized DP implementation
checking compiler support --start-group... yes
checking for gzip... /bin/gzip
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checking for _LARGEFILE_SOURCE value needed for large files... no
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configure: creating ./config.status
config.status: creating src/Makefile
config.status: creating src/impl_sse/Makefile
config.status: creating testsuite/Makefile
config.status: creating rmark/Makefile
config.status: creating documentation/Makefile
config.status: creating documentation/manpages/Makefile
config.status: creating documentation/userguide/Makefile
config.status: creating hmmer/documentation/Makefile
config.status: creating hmmer/documentation/man/Makefile
config.status: creating hmmer/documentation/userguide/Makefile
config.status: creating hmmer/src/Makefile
config.status: creating hmmer/testsuite/Makefile
config.status: creating hmmer/profmark/Makefile
config.status: creating hmmer/src/impl_sse/Makefile
config.status: creating hmmer/libdivsufsort/Makefile
config.status: creating hmmer/Makefile
config.status: creating easel/miniapps/Makefile
config.status: creating easel/testsuite/Makefile
config.status: creating easel/Makefile
config.status: creating easel/documentation/Makefile
config.status: creating Makefile
config.status: creating src/config.h
config.status: creating hmmer/src/p7_config.h
config.status: creating hmmer/libdivsufsort/divsufsort.h
config.status: creating easel/esl_config.h
config.status: linking hmmer/src/impl_sse to hmmer/src/impl
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking

INFERNAL configuration:

     compiler:             gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -msse2 -msse3 -pthread -fPIC
     linker:               -Wl,-z,relro
     libraries:              
     DP implementation:    sse

   dh_auto_build
	make -j1
make[1]: Entering directory '/build/infernal-1.1.1'
     SUBDIR easel
make[2]: Entering directory '/build/infernal-1.1.1/easel'
     CC easel.o
     CC esl_alphabet.o
     CC esl_buffer.o
     CC esl_cluster.o
     CC esl_dirichlet.o
     CC esl_distance.o
     CC esl_dmatrix.o
     CC esl_exponential.o
     CC esl_fileparser.o
     CC esl_gamma.o
     CC esl_getopts.o
     CC esl_gev.o
     CC esl_gumbel.o
     CC esl_histogram.o
     CC esl_hmm.o
     CC esl_hyperexp.o
     CC esl_keyhash.o
     CC esl_mem.o
     CC esl_minimizer.o
     CC esl_mixgev.o
     CC esl_mpi.o
     CC esl_msa.o
     CC esl_msacluster.o
     CC esl_msafile.o
     CC esl_msafile2.o
     CC esl_msafile_a2m.o
     CC esl_msafile_afa.o
     CC esl_msafile_clustal.o
     CC esl_msafile_phylip.o
     CC esl_msafile_psiblast.o
     CC esl_msafile_selex.o
     CC esl_msafile_stockholm.o
     CC esl_msashuffle.o
     CC esl_msaweight.o
     CC esl_normal.o
     CC esl_paml.o
     CC esl_random.o
     CC esl_randomseq.o
     CC esl_ratematrix.o
     CC esl_recorder.o
     CC esl_regexp.o
     CC esl_rootfinder.o
     CC esl_scorematrix.o
     CC esl_sq.o
     CC esl_sqio.o
     CC esl_sqio_ascii.o
     CC esl_sqio_ncbi.o
     CC esl_sse.o
     CC esl_ssi.o
     CC esl_stack.o
     CC esl_stats.o
     CC esl_stopwatch.o
     CC esl_stretchexp.o
     CC esl_threads.o
     CC esl_tree.o
     CC esl_vectorops.o
     CC esl_vmx.o
     CC esl_weibull.o
     CC esl_workqueue.o
     CC esl_wuss.o
     AR libeasel.a
     SUBDIR miniapps
make[3]: Entering directory '/build/infernal-1.1.1/easel/miniapps'
     CC esl-afetch.o
     GEN esl-afetch
     CC esl-alimanip.o
     GEN esl-alimanip
     CC esl-alimap.o
     GEN esl-alimap
     CC esl-alimask.o
     GEN esl-alimask
     CC esl-alimerge.o
     GEN esl-alimerge
     CC esl-alipid.o
     GEN esl-alipid
     CC esl-alistat.o
     GEN esl-alistat
     CC esl-cluster.o
     GEN esl-cluster
     CC esl-compalign.o
     GEN esl-compalign
     CC esl-compstruct.o
     GEN esl-compstruct
     CC esl-construct.o
     GEN esl-construct
     CC esl-histplot.o
     GEN esl-histplot
     CC esl-mask.o
     GEN esl-mask
     CC esl-reformat.o
     GEN esl-reformat
     CC esl-selectn.o
     GEN esl-selectn
     CC esl-seqrange.o
     GEN esl-seqrange
     CC esl-seqstat.o
     GEN esl-seqstat
     CC esl-sfetch.o
     GEN esl-sfetch
     CC esl-shuffle.o
     GEN esl-shuffle
     CC esl-ssdraw.o
/srv/reproducible-results/rbuild-debian-XxrSHXaV/tmp.OYpt2FUtdu:	 40.2% -- replaced with /srv/reproducible-results/rbuild-debian-XxrSHXaV/tmp.OYpt2FUtdu.gz
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)
INFO: Starting at 2016-05-28 10:37:00.136980
INFO: Finished at 2016-05-28 10:37:00.229146, took: 0:00:00.092177
INFO: Starting at 2016-05-28 10:37:00.608706