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Started by upstream project "BIOFORMATS-test-repo" build number 217 originally caused by: Started by upstream project "Trigger" build number 244 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins11276622478468263462.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_34441_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] 04:02:24,684 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 04:02:24,685 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 04:02:24,685 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:02:24,686 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:02:24,687 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:02:24,687 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:02:24,687 |-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] 04:02:24,687 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:02:24,687 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:02:24,688 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:02:24,688 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:02:24,688 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:02:24,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:02:24,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:02:24,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:02:24,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:02:24,952 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:02:24,952 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:02:24,952 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:02:24,953 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:02:24,953 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 04:02:24,954 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 04:02:24,954 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 267 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-11 04:02:24,964] [main] java.version = 1.8.0_342 [testng] 04:02:24,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:02:24,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:25,014 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-11_04-02-24.log] [testng] 04:02:25,015 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-11 04:02:25,017] [main] testng.directory = /data [testng] [2024-10-11 04:02:25,018] [main] testng.configDirectory = /config [testng] [2024-10-11 04:02:25,030] [main] testng.multiplier = 1.0 [testng] [2024-10-11 04:02:25,030] [main] testng.in-memory = false [testng] [2024-10-11 04:02:25,030] [main] testng.allow-missing = false [testng] [2024-10-11 04:02:25,030] [main] user.language = en [testng] [2024-10-11 04:02:25,030] [main] user.country = ${user.country} [testng] [2024-10-11 04:02:25,030] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-11 04:03:11,148] [main] ---------------------------------------- [testng] [2024-10-11 04:03:11,149] [main] Total files: 46 [testng] [2024-10-11 04:03:11,149] [main] Scan time: 46.118 s (1002 ms/file) [testng] [2024-10-11 04:03:11,149] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-11 04:04:57,421] [pool-1-thread-1] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] 04:04:57,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:04:57,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:57,423 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-11_04-04-57.log] [testng] 04:04:57,424 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c97744 - End of configuration. [testng] [2024-10-11 04:05:00,856] [pool-1-thread-12] Initializing /data/gerhard/test.vws: [testng] 04:05:00,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:05:00,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:05:00,857 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-11_04-05-00.log] [testng] 04:05:00,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@334b5e63 - End of configuration. [testng] [2024-10-11 04:05:01,770] [pool-1-thread-11] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] 04:05:01,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:05:01,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:05:01,771 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-11_04-05-01.log] [testng] 04:05:01,771 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f6e9b83 - End of configuration. [testng] [2024-10-11 04:05:04,402] [pool-1-thread-10] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] 04:05:04,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:05:04,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:05:04,404 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-11_04-05-04.log] [testng] 04:05:04,404 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33c1d8f1 - End of configuration. [testng] [2024-10-11 04:05:07,078] [pool-1-thread-9] Initializing /data/samples/fibre.vws: [testng] 04:05:07,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:05:07,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:05:07,079 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-11_04-05-07.log] [testng] 04:05:07,079 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f9e35e4 - End of configuration. [testng] [2024-10-11 04:05:08,110] [pool-1-thread-8] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] 04:05:08,111 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:05:08,111 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:05:08,112 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-11_04-05-08.log] [testng] 04:05:08,112 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70e4536f - End of configuration. [testng] [2024-10-11 04:05:10,263] [pool-1-thread-7] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] 04:05:10,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:05:10,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:05:10,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-11_04-05-10.log] [testng] 04:05:10,264 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37f851ab - End of configuration. [testng] [2024-10-11 04:05:11,941] [pool-1-thread-6] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] 04:05:11,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:05:11,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:05:11,941 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-11_04-05-11.log] [testng] 04:05:11,942 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d834c - End of configuration. [testng] [2024-10-11 04:05:13,459] [pool-1-thread-5] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] 04:05:13,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:05:13,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:05:13,460 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-11_04-05-13.log] [testng] 04:05:13,460 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12796489 - End of configuration. [testng] [2024-10-11 04:05:18,675] [pool-1-thread-4] Initializing /data/andreas/090812E4.vws: [testng] 04:05:18,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:05:18,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:05:18,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-11_04-05-18.log] [testng] 04:05:18,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a37209a - End of configuration. [testng] [2024-10-11 04:05:22,035] [pool-1-thread-3] Initializing /data/imagesc-84715/not working.vws: [testng] 04:05:22,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:05:22,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:05:22,036 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-11_04-05-22.log] [testng] 04:05:22,036 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7582e5a1 - End of configuration. [testng] [2024-10-11 04:05:23,296] [pool-1-thread-2] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 04:05:23,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:05:23,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:05:23,297 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-11_04-05-23.log] [testng] 04:05:23,298 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f44e52f - End of configuration. [testng] [2024-10-11 04:05:37,190] [pool-1-thread-9] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] [2024-10-11 04:05:42,812] [pool-1-thread-12] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] [2024-10-11 04:05:44,767] [pool-1-thread-11] Initializing /data/imagesc-84715/working.vws: [testng] [2024-10-11 04:05:46,427] [pool-1-thread-2] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] [2024-10-11 04:05:47,659] [pool-1-thread-1] Initializing /data/andreas/090811E1.vws: [testng] [2024-10-11 04:06:19,646] [pool-1-thread-3] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] [2024-10-11 04:06:24,420] [pool-1-thread-6] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] [2024-10-11 04:06:32,675] [pool-1-thread-7] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] [2024-10-11 04:06:39,152] [pool-1-thread-8] Initializing /data/stephan/two sequences.vws: [testng] [2024-10-11 04:06:47,285] [pool-1-thread-6] Initializing /data/christian/080807epi/080807epi2.vws: [testng] [2024-10-11 04:07:03,330] [pool-1-thread-3] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] [2024-10-11 04:07:04,871] [pool-1-thread-2] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] [2024-10-11 04:07:07,422] [pool-1-thread-12] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1325, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 39 minutes 50 seconds Finished: SUCCESS