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Started by upstream project "BIOFORMATS-test-repo" build number 129 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins3541546207366608975.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_20219_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 -Duser.language=fr -Duser.country=FR 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 test-automated: [testng] File leak detector installed [testng] 14:08:29,421 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 14:08:29,423 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 14:08:29,423 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:08:29,425 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:08:29,425 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 14:08:29,425 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 14:08:29,425 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 14:08:29,425 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:08:29,426 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:08:29,426 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 14:08:29,426 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 14:08:29,427 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 14:08:29,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 14:08:29,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 14:08:29,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 14:08:29,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 14:08:29,715 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 14:08:29,715 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 14:08:29,715 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 14:08:29,715 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 14:08:29,716 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 14:08:29,716 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 14:08:29,717 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 291 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-22 14:08:29,727] [main] java.version = 1.8.0_342 [testng] 14:08:29,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 14:08:29,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:08:29,778 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-22_14-08-29.log] [testng] 14:08:29,780 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-22 14:08:29,782] [main] testng.directory = /data [testng] [2024-07-22 14:08:29,783] [main] testng.configDirectory = /config [testng] [2024-07-22 14:08:29,797] [main] testng.multiplier = 1.0 [testng] [2024-07-22 14:08:29,798] [main] testng.in-memory = false [testng] [2024-07-22 14:08:29,798] [main] testng.allow-missing = false [testng] [2024-07-22 14:08:29,798] [main] user.language = fr [testng] [2024-07-22 14:08:29,798] [main] user.country = FR [testng] [2024-07-22 14:08:29,798] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-22 14:08:31,724] [main] ---------------------------------------- [testng] [2024-07-22 14:08:31,724] [main] Total files: 46 [testng] [2024-07-22 14:08:31,724] [main] Scan time: 1.926 s (41 ms/file) [testng] [2024-07-22 14:08:31,724] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-22 14:08:50,813] [pool-1-thread-1] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] 14:08:50,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 14:08:50,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:08:50,815 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-22_14-08-50.log] [testng] 14:08:50,816 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6eb4f209 - End of configuration. [testng] [2024-07-22 14:08:50,950] [pool-1-thread-12] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 14:08:50,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 14:08:50,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:08:50,952 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-22_14-08-50.log] [testng] 14:08:50,952 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29da072c - End of configuration. [testng] [2024-07-22 14:08:54,602] [pool-1-thread-11] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] 14:08:54,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 14:08:54,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:08:54,604 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-22_14-08-54.log] [testng] 14:08:54,604 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11f72703 - End of configuration. [testng] [2024-07-22 14:08:54,640] [pool-1-thread-10] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] 14:08:54,640 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 14:08:54,640 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:08:54,640 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-22_14-08-54.log] [testng] 14:08:54,641 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2424e7d2 - End of configuration. [testng] [2024-07-22 14:08:54,659] [pool-1-thread-9] Initializing /data/stephan/two sequences.vws: [testng] 14:08:54,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 14:08:54,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:08:54,660 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-22_14-08-54.log] [testng] 14:08:54,660 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e88b79e - End of configuration. [testng] [2024-07-22 14:08:54,677] [pool-1-thread-8] Initializing /data/samples/fibre.vws: [testng] 14:08:54,678 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 14:08:54,678 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:08:54,678 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-22_14-08-54.log] [testng] 14:08:54,679 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52d1470c - End of configuration. [testng] [2024-07-22 14:08:54,705] [pool-1-thread-7] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] 14:08:54,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 14:08:54,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:08:54,706 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-22_14-08-54.log] [testng] 14:08:54,707 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a6f4a9 - End of configuration. [testng] [2024-07-22 14:08:54,747] [pool-1-thread-6] Initializing /data/imagesc-84715/not working.vws: [testng] 14:08:54,747 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 14:08:54,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:08:54,748 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-22_14-08-54.log] [testng] 14:08:54,748 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29aefc76 - End of configuration. [testng] [2024-07-22 14:08:54,924] [pool-1-thread-5] Initializing /data/andreas/090811E1.vws: [testng] 14:08:54,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 14:08:54,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:08:54,925 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-22_14-08-54.log] [testng] 14:08:54,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f1e340f - End of configuration. [testng] [2024-07-22 14:08:57,718] [pool-1-thread-4] Initializing /data/christian/080807epi/080807epi2.vws: [testng] 14:08:57,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 14:08:57,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:08:57,719 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-22_14-08-57.log] [testng] 14:08:57,719 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2726fd38 - End of configuration. [testng] [2024-07-22 14:08:57,814] [pool-1-thread-3] Initializing /data/imagesc-84715/working.vws: [testng] 14:08:57,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 14:08:57,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:08:57,815 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-22_14-08-57.log] [testng] 14:08:57,815 |-INFO in ch.qos.logback.core.sift.SiftProcessor@480f3404 - End of configuration. [testng] [2024-07-22 14:08:58,374] [pool-1-thread-2] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] 14:08:58,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 14:08:58,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:08:58,375 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-22_14-08-58.log] [testng] 14:08:58,376 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1447741e - End of configuration. [testng] [2024-07-22 14:08:59,734] [pool-1-thread-8] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] [2024-07-22 14:09:03,279] [pool-1-thread-2] Initializing /data/andreas/090812E4.vws: [testng] [2024-07-22 14:09:04,238] [pool-1-thread-11] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] [2024-07-22 14:09:04,879] [pool-1-thread-10] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] [2024-07-22 14:09:05,205] [pool-1-thread-9] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2024-07-22 14:09:05,429] [pool-1-thread-4] Initializing /data/gerhard/test.vws: [testng] [2024-07-22 14:09:05,789] [pool-1-thread-9] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] [2024-07-22 14:09:06,672] [pool-1-thread-10] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] [2024-07-22 14:09:06,683] [pool-1-thread-7] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] [2024-07-22 14:09:08,319] [pool-1-thread-9] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] [2024-07-22 14:09:08,490] [pool-1-thread-1] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] [2024-07-22 14:09:08,708] [pool-1-thread-6] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] [2024-07-22 14:09:09,051] [pool-1-thread-4] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1325, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 6 minutes 8 seconds Finished: SUCCESS