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Started by upstream project "BIOFORMATS-test-repo" build number 107 originally caused by: Started by upstream project "Trigger" build number 119 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins1578083552983477989.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_16611_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] 01:45:54,612 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:45:54,613 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:45:54,613 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:45:54,614 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:45:54,615 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:45:54,615 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:45:54,615 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:45:54,615 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:45:54,616 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:45:54,617 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:45:54,617 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:45:54,617 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:45:54,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:45:54,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:45:54,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:45:54,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:45:54,814 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:45:54,814 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:45:54,814 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:45:54,814 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:45:54,814 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:45:54,815 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:45:54,815 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 199 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-30 01:45:54,824] [main] java.version = 17.0.2 [testng] 01:45:54,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:45:54,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:54,869 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-30_01-45-54.log] [testng] 01:45:54,870 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-30 01:45:54,873] [main] testng.directory = /data [testng] [2024-06-30 01:45:54,873] [main] testng.configDirectory = /config [testng] [2024-06-30 01:45:54,881] [main] testng.multiplier = 1.0 [testng] [2024-06-30 01:45:54,882] [main] testng.in-memory = false [testng] [2024-06-30 01:45:54,882] [main] testng.allow-missing = false [testng] [2024-06-30 01:45:54,882] [main] user.language = en [testng] [2024-06-30 01:45:54,882] [main] user.country = ${user.country} [testng] [2024-06-30 01:45:54,882] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-30 01:45:56,385] [main] ---------------------------------------- [testng] [2024-06-30 01:45:56,385] [main] Total files: 46 [testng] [2024-06-30 01:45:56,385] [main] Scan time: 1.502 s (32 ms/file) [testng] [2024-06-30 01:45:56,385] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-30 01:46:12,582] [pool-1-thread-1] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] 01:46:12,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:46:12,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:12,584 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-30_01-46-12.log] [testng] 01:46:12,585 |-INFO in ch.qos.logback.core.sift.SiftProcessor@118ace2d - End of configuration. [testng] [2024-06-30 01:46:12,672] [pool-1-thread-12] Initializing /data/andreas/090812E4.vws: [testng] 01:46:12,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:46:12,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:12,673 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-30_01-46-12.log] [testng] 01:46:12,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64bb41cf - End of configuration. [testng] [2024-06-30 01:46:13,544] [pool-1-thread-11] Initializing /data/imagesc-84715/working.vws: [testng] 01:46:13,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:46:13,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:13,545 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-30_01-46-13.log] [testng] 01:46:13,545 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33263f65 - End of configuration. [testng] [2024-06-30 01:46:13,924] [pool-1-thread-10] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] 01:46:13,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:46:13,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:13,925 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-30_01-46-13.log] [testng] 01:46:13,926 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7fccf415 - End of configuration. [testng] [2024-06-30 01:46:14,143] [pool-1-thread-9] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] 01:46:14,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:46:14,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:14,144 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-30_01-46-14.log] [testng] 01:46:14,144 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c05f47a - End of configuration. [testng] [2024-06-30 01:46:14,155] [pool-1-thread-8] Initializing /data/andreas/090811E1.vws: [testng] 01:46:14,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:46:14,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:14,156 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-30_01-46-14.log] [testng] 01:46:14,156 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39455cc8 - End of configuration. [testng] [2024-06-30 01:46:17,318] [pool-1-thread-7] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] 01:46:17,318 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:46:17,318 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:17,319 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-30_01-46-17.log] [testng] 01:46:17,319 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14a5bd6b - End of configuration. [testng] [2024-06-30 01:46:17,333] [pool-1-thread-6] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] 01:46:17,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:46:17,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:17,334 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-30_01-46-17.log] [testng] 01:46:17,335 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a7a40ff - End of configuration. [testng] [2024-06-30 01:46:18,812] [pool-1-thread-5] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] 01:46:18,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:46:18,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:18,814 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-30_01-46-18.log] [testng] 01:46:18,814 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7667eb9e - End of configuration. [testng] [2024-06-30 01:46:21,959] [pool-1-thread-4] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] 01:46:21,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:46:21,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:21,960 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-30_01-46-21.log] [testng] 01:46:21,960 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bf3f847 - End of configuration. [testng] [2024-06-30 01:46:22,559] [pool-1-thread-3] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] 01:46:22,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:46:22,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:22,560 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-30_01-46-22.log] [testng] 01:46:22,560 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2eccac63 - End of configuration. [testng] [2024-06-30 01:46:22,572] [pool-1-thread-2] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 01:46:22,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:46:22,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:22,572 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-30_01-46-22.log] [testng] 01:46:22,573 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c0015ab - End of configuration. [testng] [2024-06-30 01:46:27,792] [pool-1-thread-3] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] [2024-06-30 01:46:27,826] [pool-1-thread-7] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2024-06-30 01:46:27,853] [pool-1-thread-9] Initializing /data/imagesc-84715/not working.vws: [testng] [2024-06-30 01:46:28,255] [pool-1-thread-1] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] [2024-06-30 01:46:28,393] [pool-1-thread-7] Initializing /data/samples/fibre.vws: [testng] [2024-06-30 01:46:28,431] [pool-1-thread-3] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] [2024-06-30 01:46:28,775] [pool-1-thread-1] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] [2024-06-30 01:46:28,828] [pool-1-thread-7] Initializing /data/christian/080807epi/080807epi2.vws: [testng] [2024-06-30 01:46:30,241] [pool-1-thread-10] Initializing /data/gerhard/test.vws: [testng] [2024-06-30 01:46:30,347] [pool-1-thread-7] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] [2024-06-30 01:46:30,834] [pool-1-thread-7] Initializing /data/stephan/two sequences.vws: [testng] [2024-06-30 01:46:31,074] [pool-1-thread-3] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] [2024-06-30 01:46:31,920] [pool-1-thread-9] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1325, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 5 minutes 8 seconds Finished: SUCCESS