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Started by upstream project "BIOFORMATS-test-repo" build number 269 originally caused by: Started by upstream project "Trigger" build number 292 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins12309427311123247810.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42506_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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 01:42:06,722 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:42:06,723 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 01:42:06,723 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:42:06,724 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:42:06,725 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:42:06,725 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:42:06,726 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:42:06,726 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:42:06,726 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:42:06,727 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:42:06,727 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:42:06,727 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:42:06,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:42:06,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:42:06,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:42:06,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:42:06,932 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:42:06,932 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:42:06,932 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:42:06,933 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:42:06,933 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 01:42:06,934 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 01:42:06,934 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 208 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-27 01:42:06,943] [main] java.version = 17.0.2 [testng] 01:42:06,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:42:06,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:42:06,987 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-27_01-42-06.log] [testng] 01:42:06,989 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-27 01:42:06,991] [main] testng.directory = /data [testng] [2024-11-27 01:42:06,991] [main] testng.configDirectory = /config [testng] [2024-11-27 01:42:07,000] [main] testng.multiplier = 1.0 [testng] [2024-11-27 01:42:07,001] [main] testng.in-memory = false [testng] [2024-11-27 01:42:07,001] [main] testng.allow-missing = false [testng] [2024-11-27 01:42:07,001] [main] user.language = en [testng] [2024-11-27 01:42:07,001] [main] user.country = ${user.country} [testng] [2024-11-27 01:42:07,001] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-27 01:42:21,873] [main] ---------------------------------------- [testng] [2024-11-27 01:42:21,873] [main] Total files: 46 [testng] [2024-11-27 01:42:21,873] [main] Scan time: 14.871 s (323 ms/file) [testng] [2024-11-27 01:42:21,873] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-27 01:43:24,401] [pool-1-thread-1] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] 01:43:24,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:43:24,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:24,403 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-27_01-43-24.log] [testng] 01:43:24,403 |-INFO in ch.qos.logback.core.sift.SiftProcessor@faae294 - End of configuration. [testng] [2024-11-27 01:43:25,228] [pool-1-thread-12] Initializing /data/gerhard/test.vws: [testng] 01:43:25,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:43:25,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:25,229 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-27_01-43-25.log] [testng] 01:43:25,230 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30eed605 - End of configuration. [testng] [2024-11-27 01:43:26,065] [pool-1-thread-11] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 01:43:26,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:43:26,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:26,066 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-27_01-43-26.log] [testng] 01:43:26,067 |-INFO in ch.qos.logback.core.sift.SiftProcessor@307e1263 - End of configuration. [testng] [2024-11-27 01:43:28,377] [pool-1-thread-10] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 01:43:28,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:43:28,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:28,378 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-27_01-43-28.log] [testng] 01:43:28,378 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72871f54 - End of configuration. [testng] [2024-11-27 01:43:34,998] [pool-1-thread-9] Initializing /data/samples/fibre.vws: [testng] 01:43:34,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:43:34,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:34,998 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-27_01-43-34.log] [testng] 01:43:34,999 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ff8a022 - End of configuration. [testng] [2024-11-27 01:43:35,622] [pool-1-thread-8] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] 01:43:35,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:43:35,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:35,623 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-27_01-43-35.log] [testng] 01:43:35,623 |-INFO in ch.qos.logback.core.sift.SiftProcessor@eb989b - End of configuration. [testng] [2024-11-27 01:43:37,392] [pool-1-thread-7] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] 01:43:37,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:43:37,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:37,393 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-27_01-43-37.log] [testng] 01:43:37,394 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1298b0d1 - End of configuration. [testng] [2024-11-27 01:43:38,281] [pool-1-thread-6] Initializing /data/christian/080807epi/080807epi2.vws: [testng] 01:43:38,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:43:38,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:38,282 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-27_01-43-38.log] [testng] 01:43:38,282 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49bcfe18 - End of configuration. [testng] [2024-11-27 01:43:39,094] [pool-1-thread-5] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] 01:43:39,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:43:39,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:39,095 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-27_01-43-39.log] [testng] 01:43:39,096 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18c500a3 - End of configuration. [testng] [2024-11-27 01:43:41,282] [pool-1-thread-4] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] 01:43:41,283 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:43:41,283 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:41,283 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-27_01-43-41.log] [testng] 01:43:41,284 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2750c33 - End of configuration. [testng] [2024-11-27 01:43:42,190] [pool-1-thread-3] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] 01:43:42,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:43:42,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:42,191 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-27_01-43-42.log] [testng] 01:43:42,191 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5503af77 - End of configuration. [testng] [2024-11-27 01:43:43,079] [pool-1-thread-2] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] 01:43:43,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:43:43,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:43,080 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-27_01-43-43.log] [testng] 01:43:43,080 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45d02c99 - End of configuration. [testng] [2024-11-27 01:43:56,015] [pool-1-thread-9] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [2024-11-27 01:43:57,774] [pool-1-thread-12] Initializing /data/imagesc-84715/not working.vws: [testng] [2024-11-27 01:44:01,099] [pool-1-thread-11] Initializing /data/andreas/090811E1.vws: [testng] [2024-11-27 01:44:23,769] [pool-1-thread-6] Initializing /data/imagesc-84715/working.vws: [testng] [2024-11-27 01:44:25,234] [pool-1-thread-4] Initializing /data/stephan/two sequences.vws: [testng] [2024-11-27 01:44:34,965] [pool-1-thread-7] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] [2024-11-27 01:44:36,282] [pool-1-thread-1] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2024-11-27 01:44:39,230] [pool-1-thread-2] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] [2024-11-27 01:44:46,663] [pool-1-thread-12] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] [2024-11-27 01:44:58,744] [pool-1-thread-2] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] [2024-11-27 01:44:59,779] [pool-1-thread-1] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] [2024-11-27 01:45:02,576] [pool-1-thread-9] Initializing /data/andreas/090812E4.vws: [testng] [2024-11-27 01:45:16,288] [pool-1-thread-6] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1325, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 22 minutes 0 seconds Finished: SUCCESS