[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_arm64_27 #3497
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Fri Feb 3 07:55:54 UTC 2017
https://jenkins.debian.net/job/reproducible_builder_arm64_27/3497/------------------------------------------
[...truncated 557.52 KB...]
[ 88%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o
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[ 90%] Building CXX object CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o
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[ 91%] Building CXX object CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o
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[ 93%] Building CXX object CMakeFiles/tvc.dir/Util/OptArgs.cpp.o
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[ 94%] Building CXX object CMakeFiles/tvc.dir/realignment/Realigner.cpp.o
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[ 95%] Building C object CMakeFiles/tvc.dir/file-io/ion_util.c.o
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[ 97%] Building C object CMakeFiles/tvc.dir/file-io/ion_error.c.o
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[ 98%] Building CXX object CMakeFiles/tvc.dir/IonVersion.cpp.o
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[100%] Linking CXX executable tvc
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+make[3]: Leaving directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
[100%] Built target tvc
-make[2]: Leaving directory '/build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu'
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+make[2]: Leaving directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
+/usr/bin/cmake -E cmake_progress_start /build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu/CMakeFiles 0
+make[1]: Leaving directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
dh_auto_test -O--parallel
make -j8 test ARGS\+=-j8
-make[1]: Entering directory '/build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu'
+make[1]: Entering directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
Running tests...
/usr/bin/ctest --force-new-ctest-process -j8
-Test project /build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu
+Test project /build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu
Start 1: tvc_call
Start 2: tvc_test_1_thread_sse_off
Start 3: tvc_test_4_threads_sse_off_with_parameter_file
@@ -833,19 +850,19 @@
Start 6: tvcutils_validate_bed_call
Start 7: tvcutils_unify_vcf_call
Start 8: tvcassembly_call
-1/8 Test #8: tvcassembly_call ................................. Passed 0.02 sec
-2/8 Test #4: tvcutils_call .................................... Passed 0.21 sec
-3/8 Test #5: tvcutils_prepare_hotspots_call ................... Passed 0.20 sec
-4/8 Test #6: tvcutils_validate_bed_call ....................... Passed 0.16 sec
-5/8 Test #7: tvcutils_unify_vcf_call .......................... Passed 0.14 sec
-6/8 Test #1: tvc_call ......................................... Passed 0.34 sec
-7/8 Test #2: tvc_test_1_thread_sse_off ........................ Passed 3.42 sec
-8/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 3.55 sec
+1/8 Test #4: tvcutils_call .................................... Passed 0.26 sec
+2/8 Test #5: tvcutils_prepare_hotspots_call ................... Passed 0.25 sec
+3/8 Test #8: tvcassembly_call ................................. Passed 0.22 sec
+4/8 Test #6: tvcutils_validate_bed_call ....................... Passed 0.24 sec
+5/8 Test #7: tvcutils_unify_vcf_call .......................... Passed 0.23 sec
+6/8 Test #1: tvc_call ......................................... Passed 0.28 sec
+7/8 Test #2: tvc_test_1_thread_sse_off ........................ Passed 2.27 sec
+8/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 2.68 sec
100% tests passed, 0 tests failed out of 8
-Total Test time (real) = 3.56 sec
-make[1]: Leaving directory '/build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu'
+Total Test time (real) = 2.70 sec
+make[1]: Leaving directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary
dh binary --parallel
@@ -853,79 +870,79 @@
dh_testroot -O--parallel
dh_prep -O--parallel
dh_auto_install -O--parallel
- make -j8 install DESTDIR=/build/1st/tvc-5.0.3\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no
-make[1]: Entering directory '/build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu'
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+ make -j8 install DESTDIR=/build/tvc-5.0.3\+dfsg/2nd/debian/tvc AM_UPDATE_INFO_DIR=no
+make[1]: Entering directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
+/usr/bin/cmake -H/build/tvc-5.0.3+dfsg/2nd -B/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
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make -f CMakeFiles/Makefile2 all
-make[2]: Entering directory '/build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu'
+make[2]: Entering directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend
make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend
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-make[3]: Entering directory '/build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu'
-cd /build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/1st/tvc-5.0.3+dfsg /build/1st/tvc-5.0.3+dfsg /build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu /build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu /build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color=
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-cd /build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/1st/tvc-5.0.3+dfsg /build/1st/tvc-5.0.3+dfsg /build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu /build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu /build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color=
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+cd /build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+dfsg/2nd /build/tvc-5.0.3+dfsg/2nd /build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu /build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu /build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color=
+make[3]: Entering directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
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+make[3]: Leaving directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build
-make[3]: Entering directory '/build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu'
+make[3]: Entering directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
make[3]: Nothing to be done for 'CMakeFiles/tvcassembly.dir/build'.
-make[3]: Leaving directory '/build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu'
-make[3]: Leaving directory '/build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu'
+make[3]: Leaving directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
+make[3]: Leaving directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build
[ 9%] Built target tvcassembly
-make[3]: Entering directory '/build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu'
+make[3]: Entering directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
make[3]: Nothing to be done for 'CMakeFiles/tvcutils.dir/build'.
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+make[3]: Leaving directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
[ 33%] Built target tvcutils
-make[3]: Leaving directory '/build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu'
+make[3]: Leaving directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build
-make[3]: Entering directory '/build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu'
+make[3]: Entering directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
make[3]: Nothing to be done for 'CMakeFiles/tvc.dir/build'.
-make[3]: Leaving directory '/build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu'
+make[3]: Leaving directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
[100%] Built target tvc
-make[2]: Leaving directory '/build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu'
-/usr/bin/cmake -E cmake_progress_start /build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0
+make[2]: Leaving directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
+/usr/bin/cmake -E cmake_progress_start /build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu/CMakeFiles 0
make -f CMakeFiles/Makefile2 preinstall
-make[2]: Entering directory '/build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu'
+make[2]: Entering directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
make[2]: Nothing to be done for 'preinstall'.
-make[2]: Leaving directory '/build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu'
+make[2]: Leaving directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/bin/tvc
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/bin/tvcassembly
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/bin/tvcutils
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/bin/variant_caller_pipeline.py
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/pluginMedia
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/sse
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/sse/motifset.txt
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/examples
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/examples/example1
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai
--- Installing: /build/1st/tvc-5.0.3+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed
-make[1]: Leaving directory '/build/1st/tvc-5.0.3+dfsg/obj-aarch64-linux-gnu'
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/bin/tvc
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/bin/tvcassembly
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/bin/tvcutils
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/bin/variant_caller_pipeline.py
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/pluginMedia
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/sse
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/sse/motifset.txt
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/examples
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/examples/example1
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/examples/example1/reference.dict
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/examples/example1/test.bam
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/examples/example1/test_original.bed
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/examples/example1/test.bed
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/examples/example1/expected
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/examples/example1/reference.fasta
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai
+-- Installing: /build/tvc-5.0.3+dfsg/2nd/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed
+make[1]: Leaving directory '/build/tvc-5.0.3+dfsg/2nd/obj-aarch64-linux-gnu'
dh_installdocs -O--parallel
dh_installchangelogs -O--parallel
dh_perl -O--parallel
@@ -950,15 +967,17 @@
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../tvc_5.0.3+dfsg-1_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
- dpkg-source --after-build tvc-5.0.3+dfsg
+ dpkg-source --after-build 2nd
dpkg-buildpackage: info: binary-only upload (no source included)
I: copying local configuration
+I: user script /srv/workspace/pbuilder/11002/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/11002/tmp/hooks/B01_cleanup finished
I: unmounting /dev/shm filesystem
I: unmounting dev/pts filesystem
I: unmounting run/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
-I: removing directory /srv/workspace/pbuilder/22431 and its subdirectories
-I: Current time: Thu Feb 2 19:48:30 -12 2017
-I: pbuilder-time-stamp: 1486108110
+I: removing directory /srv/workspace/pbuilder/11002 and its subdirectories
+I: Current time: Fri Mar 9 04:17:53 +14 2018
+I: pbuilder-time-stamp: 1520518673
Compressing the 2nd log...
/var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/arm64/tvc_5.0.3+dfsg-1.diff:
gzip: /var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/arm64/tvc_5.0.3+dfsg-1.diff.gz: No space left on device
Starting cleanup.
/srv/reproducible-results/rbuild-debian-aCIcL1U4/tmp.AT6zgLIdIa: 89.4% -- replaced with /srv/reproducible-results/rbuild-debian-aCIcL1U4/tmp.AT6zgLIdIa.gz
INFO: Starting at 2017-02-03 07:55:53.486665
CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/experimental/arm64/tvc_5.0.3+dfsg-1_arm64.buildinfo
CRITICAL: https://tests.reproducible-builds.org/debian/experimental/arm64/tvc didn't produce a buildlog, even though it has been built.
CRITICAL: https://tests.reproducible-builds.org/debian/experimental/arm64/tvc is unreproducible, but without diffoscope output.
INFO: Finished at 2017-02-03 07:55:53.781068, took: 0:00:00.294425
All cleanup done.
Fri 3 Feb 07:55:54 UTC 2017 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-KcMXhe1p, which will now be removed.
Build step 'Execute shell' marked build as failure
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