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Started by upstream project "BIOFORMATS-test-repo" build number 2 originally caused by: Started by upstream project "Trigger" build number 3 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10 [BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins7097371517305799550.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_208_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] 00:56:13,180 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:56:13,182 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 00:56:13,182 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:56:13,184 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:56:13,184 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:56:13,184 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:56:13,184 |-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] 00:56:13,184 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:56:13,185 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:56:13,185 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:56:13,186 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:56:13,186 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:56:13,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:56:13,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:56:13,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:56:13,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:56:13,539 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:56:13,539 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:56:13,539 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:56:13,540 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:56:13,540 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 00:56:13,541 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 00:56:13,541 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 356 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-15 00:56:13,553] [main] java.version = 1.8.0_342 [testng] 00:56:13,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:56:13,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:13,614 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-15_00-56-13.log] [testng] 00:56:13,617 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-03-15 00:56:13,620] [main] testng.directory = /data [testng] [2024-03-15 00:56:13,621] [main] testng.configDirectory = /config [testng] [2024-03-15 00:56:13,640] [main] testng.multiplier = 1.0 [testng] [2024-03-15 00:56:13,640] [main] testng.in-memory = false [testng] [2024-03-15 00:56:13,640] [main] testng.allow-missing = false [testng] [2024-03-15 00:56:13,640] [main] user.language = en [testng] [2024-03-15 00:56:13,640] [main] user.country = ${user.country} [testng] [2024-03-15 00:56:13,641] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-03-15 00:56:17,649] [main] ---------------------------------------- [testng] [2024-03-15 00:56:17,649] [main] Total files: 46 [testng] [2024-03-15 00:56:17,650] [main] Scan time: 4.008 s (87 ms/file) [testng] [2024-03-15 00:56:17,650] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-15 00:56:44,163] [pool-1-thread-1] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] 00:56:44,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:56:44,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:44,164 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-15_00-56-44.log] [testng] 00:56:44,165 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5222ba74 - End of configuration. [testng] [2024-03-15 00:56:44,398] [pool-1-thread-12] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 00:56:44,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:56:44,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:44,399 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-15_00-56-44.log] [testng] 00:56:44,399 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11f72703 - End of configuration. [testng] [2024-03-15 00:56:48,311] [pool-1-thread-11] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] 00:56:48,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:56:48,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:48,312 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-15_00-56-48.log] [testng] 00:56:48,313 |-INFO in ch.qos.logback.core.sift.SiftProcessor@95ee397 - End of configuration. [testng] [2024-03-15 00:56:48,800] [pool-1-thread-10] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] 00:56:48,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:56:48,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:48,801 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-15_00-56-48.log] [testng] 00:56:48,802 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64313eaa - End of configuration. [testng] [2024-03-15 00:56:48,991] [pool-1-thread-9] Initializing /data/stephan/two sequences.vws: [testng] 00:56:48,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:56:48,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:48,992 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-15_00-56-48.log] [testng] 00:56:48,993 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20f2bc53 - End of configuration. [testng] [2024-03-15 00:56:49,232] [pool-1-thread-8] Initializing /data/samples/fibre.vws: [testng] 00:56:49,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:56:49,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:49,233 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-15_00-56-49.log] [testng] 00:56:49,233 |-INFO in ch.qos.logback.core.sift.SiftProcessor@526aeb4e - End of configuration. [testng] [2024-03-15 00:56:49,437] [pool-1-thread-7] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] 00:56:49,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:56:49,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:49,438 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-15_00-56-49.log] [testng] 00:56:49,438 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29aefc76 - End of configuration. [testng] [2024-03-15 00:56:49,675] [pool-1-thread-6] Initializing /data/imagesc-84715/not working.vws: [testng] 00:56:49,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:56:49,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:49,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-15_00-56-49.log] [testng] 00:56:49,677 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f1e340f - End of configuration. [testng] [2024-03-15 00:56:49,995] [pool-1-thread-5] Initializing /data/andreas/090811E1.vws: [testng] 00:56:49,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:56:49,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:49,996 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-15_00-56-49.log] [testng] 00:56:49,996 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2726fd38 - End of configuration. [testng] [2024-03-15 00:56:53,453] [pool-1-thread-4] Initializing /data/christian/080807epi/080807epi2.vws: [testng] 00:56:53,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:56:53,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:53,454 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-15_00-56-53.log] [testng] 00:56:53,455 |-INFO in ch.qos.logback.core.sift.SiftProcessor@480f3404 - End of configuration. [testng] [2024-03-15 00:56:53,624] [pool-1-thread-3] Initializing /data/imagesc-84715/working.vws: [testng] 00:56:53,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:56:53,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:53,625 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-15_00-56-53.log] [testng] 00:56:53,626 |-INFO in ch.qos.logback.core.sift.SiftProcessor@198a7fc - End of configuration. [testng] [2024-03-15 00:56:54,181] [pool-1-thread-2] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] 00:56:54,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:56:54,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:54,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-15_00-56-54.log] [testng] 00:56:54,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77450173 - End of configuration. [testng] [2024-03-15 00:56:57,628] [pool-1-thread-8] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] [2024-03-15 00:57:02,247] [pool-1-thread-11] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] [2024-03-15 00:57:02,480] [pool-1-thread-2] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] [2024-03-15 00:57:06,489] [pool-1-thread-4] Initializing /data/andreas/090812E4.vws: [testng] [2024-03-15 00:57:08,239] [pool-1-thread-10] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2024-03-15 00:57:10,044] [pool-1-thread-9] Initializing /data/gerhard/test.vws: [testng] [2024-03-15 00:57:10,342] [pool-1-thread-1] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] [2024-03-15 00:57:11,103] [pool-1-thread-6] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] [2024-03-15 00:57:12,649] [pool-1-thread-10] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] [2024-03-15 00:57:14,658] [pool-1-thread-3] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] [2024-03-15 00:57:16,311] [pool-1-thread-9] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] [2024-03-15 00:57:16,567] [pool-1-thread-1] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] [2024-03-15 00:57:18,719] [pool-1-thread-7] 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: 7 minutes 33 seconds Finished: SUCCESS