Started by upstream project "BIOFORMATS-test-repo" build number 213
originally caused by:
Started by upstream project "Trigger" build number 240
originally caused by:
Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2
[BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins9676153603318561921.sh
+ '[' tillvision = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_33838_merge_ci -v /uod/idr/repos/curated/tillvision:/data -v /uod/idr-scratch/merge-ci/curated/tillvision:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12
Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml
[echo] isSnapshot = true
init-title:
[echo] ----------=========== bio-formats-testing-framework ===========----------
init-timestamp:
init:
copy-resources:
compile:
[resolver:resolve] Resolving artifacts
compile-tests:
[resolver:resolve] Resolving artifacts
[javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test
[javac] warning: [options] bootstrap class path not set in conjunction with -source 8
[javac] 1 warning
test-automated:
[testng] WARNING: An illegal reflective access operation has occurred
[testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket
[testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener
[testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
[testng] WARNING: All illegal access operations will be denied in a future release
[testng] File leak detector installed
[testng] 06:54:01,346 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 06:54:01,348 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service.
[testng] 06:54:01,348 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 06:54:01,349 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 06:54:01,349 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 06:54:01,350 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 06:54:01,350 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 06:54:01,350 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 06:54:01,350 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 06:54:01,351 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 06:54:01,351 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 06:54:01,351 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 06:54:01,524 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 06:54:01,524 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 06:54:01,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 06:54:01,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 06:54:01,554 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 06:54:01,554 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 06:54:01,554 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 06:54:01,554 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 06:54:01,554 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration.
[testng] 06:54:01,555 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point
[testng] 06:54:01,555 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 205 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-08 06:54:01,564] [main] java.version = 11.0.16
[testng] 06:54:01,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 06:54:01,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:54:01,611 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-08_06-54-01.log]
[testng] 06:54:01,613 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration.
[testng] [2024-10-08 06:54:01,615] [main] testng.directory = /data
[testng] [2024-10-08 06:54:01,615] [main] testng.configDirectory = /config
[testng] [2024-10-08 06:54:01,625] [main] testng.multiplier = 1.0
[testng] [2024-10-08 06:54:01,627] [main] testng.in-memory = false
[testng] [2024-10-08 06:54:01,627] [main] testng.allow-missing = false
[testng] [2024-10-08 06:54:01,627] [main] user.language = en
[testng] [2024-10-08 06:54:01,627] [main] user.country = ${user.country}
[testng] [2024-10-08 06:54:01,627] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-10-08 06:54:13,107] [main] ----------------------------------------
[testng] [2024-10-08 06:54:13,107] [main] Total files: 46
[testng] [2024-10-08 06:54:13,107] [main] Scan time: 11.48 s (249 ms/file)
[testng] [2024-10-08 06:54:13,108] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 25 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-08 06:55:00,337] [pool-1-thread-1] Initializing /data/imagesc-84715/working.vws:
[testng] 06:55:00,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 06:55:00,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:55:00,340 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-08_06-55-00.log]
[testng] 06:55:00,340 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26f33d2b - End of configuration.
[testng] [2024-10-08 06:55:01,222] [pool-1-thread-12] Initializing /data/andreas/090812E4.vws:
[testng] 06:55:01,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 06:55:01,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:55:01,223 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-08_06-55-01.log]
[testng] 06:55:01,224 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d6b7360 - End of configuration.
[testng] [2024-10-08 06:55:03,251] [pool-1-thread-11] Initializing /data/andreas/090811E1.vws:
[testng] 06:55:03,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 06:55:03,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:55:03,252 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-08_06-55-03.log]
[testng] 06:55:03,253 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e1e360c - End of configuration.
[testng] [2024-10-08 06:55:09,887] [pool-1-thread-10] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws:
[testng] 06:55:09,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 06:55:09,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:55:09,889 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-08_06-55-09.log]
[testng] 06:55:09,889 |-INFO in ch.qos.logback.core.sift.SiftProcessor@525738bb - End of configuration.
[testng] [2024-10-08 06:55:10,752] [pool-1-thread-9] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws:
[testng] 06:55:10,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 06:55:10,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:55:10,753 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-08_06-55-10.log]
[testng] 06:55:10,753 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7426236b - End of configuration.
[testng] [2024-10-08 06:55:11,610] [pool-1-thread-8] Initializing /data/samples/fibre.vws:
[testng] 06:55:11,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 06:55:11,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:55:11,612 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-08_06-55-11.log]
[testng] 06:55:11,612 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d515d6a - End of configuration.
[testng] [2024-10-08 06:55:12,138] [pool-1-thread-7] Initializing /data/ian/working_tillvision_vws/20120322.vws:
[testng] 06:55:12,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 06:55:12,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:55:12,139 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-08_06-55-12.log]
[testng] 06:55:12,139 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a3941ab - End of configuration.
[testng] [2024-10-08 06:55:15,958] [pool-1-thread-6] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws:
[testng] 06:55:15,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 06:55:15,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:55:15,960 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-08_06-55-15.log]
[testng] 06:55:15,960 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e7485a5 - End of configuration.
[testng] [2024-10-08 06:55:16,707] [pool-1-thread-5] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif:
[testng] 06:55:16,708 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 06:55:16,708 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:55:16,708 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-08_06-55-16.log]
[testng] 06:55:16,709 |-INFO in ch.qos.logback.core.sift.SiftProcessor@288236f3 - End of configuration.
[testng] [2024-10-08 06:55:18,695] [pool-1-thread-4] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws:
[testng] 06:55:18,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 06:55:18,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:55:18,696 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-08_06-55-18.log]
[testng] 06:55:18,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68084013 - End of configuration.
[testng] [2024-10-08 06:55:20,038] [pool-1-thread-3] Initializing /data/imagesc-84715/not working.vws:
[testng] 06:55:20,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 06:55:20,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:55:20,039 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-08_06-55-20.log]
[testng] 06:55:20,039 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ec3a828 - End of configuration.
[testng] [2024-10-08 06:55:20,894] [pool-1-thread-2] Initializing /data/ian/non_working_tillvision_vws/20120404.vws:
[testng] 06:55:20,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 06:55:20,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:55:20,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-08_06-55-20.log]
[testng] 06:55:20,895 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a20652f - End of configuration.
[testng] [2024-10-08 06:55:32,981] [pool-1-thread-8] Initializing /data/christian/080807ionophore/080807ionophore3.vws:
[testng] [2024-10-08 06:55:36,244] [pool-1-thread-5] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif:
[testng] [2024-10-08 06:55:48,250] [pool-1-thread-5] Initializing /data/gerhard/test.vws:
[testng] [2024-10-08 06:55:55,645] [pool-1-thread-3] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws:
[testng] [2024-10-08 06:55:56,961] [pool-1-thread-8] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif:
[testng] [2024-10-08 06:56:00,199] [pool-1-thread-5] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws:
[testng] [2024-10-08 06:56:05,180] [pool-1-thread-9] Initializing /data/stephan/two sequences.vws:
[testng] [2024-10-08 06:56:06,036] [pool-1-thread-1] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif:
[testng] [2024-10-08 06:56:08,004] [pool-1-thread-8] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws:
[testng] [2024-10-08 06:56:13,845] [pool-1-thread-10] Initializing /data/christian/080807epi/080807epi2.vws:
[testng] [2024-10-08 06:56:15,075] [pool-1-thread-1] Initializing /data/venu/060310/drug addition _BAM.vws:
[testng] [2024-10-08 06:56:27,858] [pool-1-thread-5] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws:
[testng] [2024-10-08 06:56:31,060] [pool-1-thread-6] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws:
time="2024-10-08T06:01:38Z" level=error msg="error waiting for container: unexpected EOF"
Build step 'Execute shell' marked build as failure
Finished: FAILURE