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Started by upstream project "BIOFORMATS-test-repo" build number 3 originally caused by: Started by upstream project "Trigger" build number 4 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/jenkins17900859283068050520.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_372_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] 01:01:46,047 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:01:46,050 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:01:46,050 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:01:46,051 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:01:46,053 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:01:46,053 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:01:46,054 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 3 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:01:46,054 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:01:46,054 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:01:46,055 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:01:46,056 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:01:46,056 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:01:46,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:01:46,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:01:46,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:01:46,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:01:46,281 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:01:46,281 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:01:46,282 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:01:46,282 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:01:46,282 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:01:46,283 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:01:46,283 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 229 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-16 01:01:46,293] [main] java.version = 11.0.16 [testng] 01:01:46,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:01:46,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:01:46,341 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-16_01-01-46.log] [testng] 01:01:46,342 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-03-16 01:01:46,345] [main] testng.directory = /data [testng] [2024-03-16 01:01:46,345] [main] testng.configDirectory = /config [testng] [2024-03-16 01:01:46,355] [main] testng.multiplier = 1.0 [testng] [2024-03-16 01:01:46,356] [main] testng.in-memory = false [testng] [2024-03-16 01:01:46,356] [main] testng.allow-missing = false [testng] [2024-03-16 01:01:46,356] [main] user.language = en [testng] [2024-03-16 01:01:46,356] [main] user.country = ${user.country} [testng] [2024-03-16 01:01:46,357] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-16 01:01:48,265] [main] ---------------------------------------- [testng] [2024-03-16 01:01:48,265] [main] Total files: 46 [testng] [2024-03-16 01:01:48,266] [main] Scan time: 1.908 s (41 ms/file) [testng] [2024-03-16 01:01:48,266] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-16 01:02:04,720] [pool-1-thread-1] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] 01:02:04,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:02:04,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:04,723 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-16_01-02-04.log] [testng] 01:02:04,723 |-INFO in ch.qos.logback.core.sift.SiftProcessor@794d7321 - End of configuration. [testng] [2024-03-16 01:02:04,843] [pool-1-thread-12] Initializing /data/imagesc-84715/not working.vws: [testng] 01:02:04,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:02:04,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:04,844 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-16_01-02-04.log] [testng] 01:02:04,844 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47d2d0cc - End of configuration. [testng] [2024-03-16 01:02:05,034] [pool-1-thread-11] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] 01:02:05,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:02:05,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:05,035 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-16_01-02-05.log] [testng] 01:02:05,035 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a88d2bc - End of configuration. [testng] [2024-03-16 01:02:05,121] [pool-1-thread-10] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] 01:02:05,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:02:05,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:05,122 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-16_01-02-05.log] [testng] 01:02:05,122 |-INFO in ch.qos.logback.core.sift.SiftProcessor@beb22b - End of configuration. [testng] [2024-03-16 01:02:05,293] [pool-1-thread-9] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] 01:02:05,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:02:05,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:05,294 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-16_01-02-05.log] [testng] 01:02:05,294 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9fedd6a - End of configuration. [testng] [2024-03-16 01:02:05,333] [pool-1-thread-8] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 01:02:05,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:02:05,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:05,334 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-16_01-02-05.log] [testng] 01:02:05,334 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63eee6d - End of configuration. [testng] [2024-03-16 01:02:05,805] [pool-1-thread-7] Initializing /data/gerhard/test.vws: [testng] 01:02:05,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:02:05,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:05,806 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-16_01-02-05.log] [testng] 01:02:05,807 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33b3a914 - End of configuration. [testng] [2024-03-16 01:02:05,959] [pool-1-thread-6] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] 01:02:05,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:02:05,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:05,961 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-16_01-02-05.log] [testng] 01:02:05,961 |-INFO in ch.qos.logback.core.sift.SiftProcessor@376902e6 - End of configuration. [testng] [2024-03-16 01:02:06,675] [pool-1-thread-5] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 01:02:06,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:02:06,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:06,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-16_01-02-06.log] [testng] 01:02:06,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53fe7d6 - End of configuration. [testng] [2024-03-16 01:02:09,795] [pool-1-thread-4] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] 01:02:09,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:02:09,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:09,796 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-16_01-02-09.log] [testng] 01:02:09,797 |-INFO in ch.qos.logback.core.sift.SiftProcessor@191d818a - End of configuration. [testng] [2024-03-16 01:02:09,927] [pool-1-thread-3] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] 01:02:09,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:02:09,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:09,928 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-16_01-02-09.log] [testng] 01:02:09,928 |-INFO in ch.qos.logback.core.sift.SiftProcessor@323d77ff - End of configuration. [testng] [2024-03-16 01:02:10,083] [pool-1-thread-2] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] 01:02:10,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:02:10,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:10,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-16_01-02-10.log] [testng] 01:02:10,084 |-INFO in ch.qos.logback.core.sift.SiftProcessor@515407a2 - End of configuration. [testng] [2024-03-16 01:02:14,141] [pool-1-thread-2] Initializing /data/samples/fibre.vws: [testng] [2024-03-16 01:02:14,335] [pool-1-thread-3] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] [2024-03-16 01:02:14,658] [pool-1-thread-8] Initializing /data/stephan/two sequences.vws: [testng] [2024-03-16 01:02:14,862] [pool-1-thread-7] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2024-03-16 01:02:18,994] [pool-1-thread-2] Initializing /data/andreas/090811E1.vws: [testng] [2024-03-16 01:02:22,582] [pool-1-thread-7] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] [2024-03-16 01:02:23,605] [pool-1-thread-10] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] [2024-03-16 01:02:27,880] [pool-1-thread-9] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] [2024-03-16 01:02:28,032] [pool-1-thread-11] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] [2024-03-16 01:02:29,493] [pool-1-thread-12] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [2024-03-16 01:02:30,131] [pool-1-thread-1] Initializing /data/christian/080807epi/080807epi2.vws: [testng] [2024-03-16 01:02:31,235] [pool-1-thread-3] Initializing /data/imagesc-84715/working.vws: [testng] [2024-03-16 01:02:31,801] [pool-1-thread-4] Initializing /data/andreas/090812E4.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 8 seconds Finished: SUCCESS