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Started by upstream project "BIOFORMATS-test-repo" build number 307 originally caused by: Started by upstream project "Trigger" build number 329 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins15894680745117423545.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_48627_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 test-automated: [testng] File leak detector installed [testng] 01:36:37,811 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:36:37,813 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 01:36:37,813 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:36:37,814 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:36:37,814 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:36:37,814 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:36:37,815 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:36:37,815 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:36:37,815 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:36:37,815 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:36:37,816 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:36:37,816 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:36:38,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:36:38,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:36:38,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:36:38,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:36:38,112 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:36:38,112 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:36:38,112 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:36:38,113 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:36:38,113 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 01:36:38,114 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 01:36:38,114 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 299 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-03 01:36:38,124] [main] java.version = 1.8.0_342 [testng] 01:36:38,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:36:38,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:38,174 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-03_01-36-38.log] [testng] 01:36:38,176 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2025-01-03 01:36:38,178] [main] testng.directory = /data [testng] [2025-01-03 01:36:38,178] [main] testng.configDirectory = /config [testng] [2025-01-03 01:36:38,191] [main] testng.multiplier = 1.0 [testng] [2025-01-03 01:36:38,191] [main] testng.in-memory = false [testng] [2025-01-03 01:36:38,191] [main] testng.allow-missing = false [testng] [2025-01-03 01:36:38,191] [main] user.language = en [testng] [2025-01-03 01:36:38,191] [main] user.country = ${user.country} [testng] [2025-01-03 01:36:38,191] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-01-03 01:36:53,576] [main] ---------------------------------------- [testng] [2025-01-03 01:36:53,576] [main] Total files: 46 [testng] [2025-01-03 01:36:53,576] [main] Scan time: 15.384 s (334 ms/file) [testng] [2025-01-03 01:36:53,576] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-03 01:37:41,279] [pool-1-thread-1] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] 01:37:41,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:37:41,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:41,281 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-03_01-37-41.log] [testng] 01:37:41,281 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57923066 - End of configuration. [testng] [2025-01-03 01:37:42,538] [pool-1-thread-12] Initializing /data/andreas/090812E4.vws: [testng] 01:37:42,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:37:42,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:42,540 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-03_01-37-42.log] [testng] 01:37:42,540 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c316226 - End of configuration. [testng] [2025-01-03 01:37:44,862] [pool-1-thread-11] Initializing /data/stephan/two sequences.vws: [testng] 01:37:44,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:37:44,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:44,864 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-03_01-37-44.log] [testng] 01:37:44,864 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67d3010e - End of configuration. [testng] [2025-01-03 01:37:45,383] [pool-1-thread-10] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] 01:37:45,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:37:45,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:45,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-03_01-37-45.log] [testng] 01:37:45,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@511a0739 - End of configuration. [testng] [2025-01-03 01:37:46,084] [pool-1-thread-9] Initializing /data/imagesc-84715/working.vws: [testng] 01:37:46,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:37:46,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:46,085 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-03_01-37-46.log] [testng] 01:37:46,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3815d3df - End of configuration. [testng] [2025-01-03 01:37:46,900] [pool-1-thread-8] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] 01:37:46,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:37:46,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:46,901 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-03_01-37-46.log] [testng] 01:37:46,902 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18804381 - End of configuration. [testng] [2025-01-03 01:37:47,407] [pool-1-thread-7] Initializing /data/imagesc-84715/not working.vws: [testng] 01:37:47,407 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:37:47,407 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:47,408 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-03_01-37-47.log] [testng] 01:37:47,408 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b777a4a - End of configuration. [testng] [2025-01-03 01:37:48,308] [pool-1-thread-6] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] 01:37:48,308 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:37:48,308 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:48,309 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-03_01-37-48.log] [testng] 01:37:48,309 |-INFO in ch.qos.logback.core.sift.SiftProcessor@364dc88b - End of configuration. [testng] [2025-01-03 01:37:49,130] [pool-1-thread-5] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] 01:37:49,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:37:49,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:49,131 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-03_01-37-49.log] [testng] 01:37:49,131 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ea802bb - End of configuration. [testng] [2025-01-03 01:37:49,628] [pool-1-thread-4] Initializing /data/gerhard/test.vws: [testng] 01:37:49,628 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:37:49,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:49,629 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-03_01-37-49.log] [testng] 01:37:49,630 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fac60c5 - End of configuration. [testng] [2025-01-03 01:37:50,072] [pool-1-thread-3] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] 01:37:50,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:37:50,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:50,072 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-03_01-37-50.log] [testng] 01:37:50,073 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d42c481 - End of configuration. [testng] [2025-01-03 01:37:50,516] [pool-1-thread-2] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] 01:37:50,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:37:50,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:50,517 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-03_01-37-50.log] [testng] 01:37:50,517 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ff6460e - End of configuration. [testng] [2025-01-03 01:38:02,561] [pool-1-thread-4] Initializing /data/christian/080807epi/080807epi2.vws: [testng] [2025-01-03 01:38:04,195] [pool-1-thread-1] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] [2025-01-03 01:38:15,612] [pool-1-thread-5] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] [2025-01-03 01:38:20,107] [pool-1-thread-1] Initializing /data/samples/fibre.vws: [testng] [2025-01-03 01:38:24,385] [pool-1-thread-7] Initializing /data/andreas/090811E1.vws: [testng] [2025-01-03 01:38:33,307] [pool-1-thread-1] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] [2025-01-03 01:38:36,328] [pool-1-thread-4] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] [2025-01-03 01:38:37,796] [pool-1-thread-3] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] [2025-01-03 01:38:39,338] [pool-1-thread-6] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] [2025-01-03 01:38:43,478] [pool-1-thread-8] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] [2025-01-03 01:38:45,735] [pool-1-thread-9] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] [2025-01-03 01:38:46,305] [pool-1-thread-10] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] [2025-01-03 01:38:46,834] [pool-1-thread-11] 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: 18 minutes 9 seconds Finished: SUCCESS