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Started by upstream project "BIOFORMATS-test-repo" build number 309 originally caused by: Started by upstream project "Trigger" build number 331 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins11948016823562762371.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_49000_merge_ci -v /uod/idr/repos/curated/imaris:/data -v /uod/idr-scratch/merge-ci/curated/imaris:/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] 03:09:39,334 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:09:39,335 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 03:09:39,335 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:09:39,336 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:09:39,336 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:09:39,336 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:09:39,337 |-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] 03:09:39,337 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:09:39,337 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:09:39,338 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:09:39,338 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:09:39,338 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:09:39,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:09:39,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:09:39,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:09:39,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:09:39,518 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:09:39,518 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:09:39,518 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:09:39,519 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:09:39,519 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 03:09:39,520 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 03:09:39,520 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 183 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-05 03:09:39,528] [main] java.version = 17.0.2 [testng] 03:09:39,531 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:09:39,531 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:09:39,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-05_03-09-39.log] [testng] 03:09:39,571 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2025-01-05 03:09:39,572] [main] testng.directory = /data [testng] [2025-01-05 03:09:39,573] [main] testng.configDirectory = /config [testng] [2025-01-05 03:09:39,581] [main] testng.multiplier = 1.0 [testng] [2025-01-05 03:09:39,582] [main] testng.in-memory = false [testng] [2025-01-05 03:09:39,582] [main] testng.allow-missing = false [testng] [2025-01-05 03:09:39,582] [main] user.language = en [testng] [2025-01-05 03:09:39,582] [main] user.country = ${user.country} [testng] [2025-01-05 03:09:39,582] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-05 03:10:04,508] [main] ---------------------------------------- [testng] [2025-01-05 03:10:04,509] [main] Total files: 73 [testng] [2025-01-05 03:10:04,509] [main] Scan time: 24.926 s (341 ms/file) [testng] [2025-01-05 03:10:04,509] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 63 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-05 03:10:40,016] [pool-1-thread-1] Initializing /data/jake/p75Cherry M2 010-3~B.ims: [testng] 03:10:40,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:10:40,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:40,018 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-05_03-10-40.log] [testng] 03:10:40,018 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12f208cb - End of configuration. [testng] [2025-01-05 03:10:40,513] [pool-1-thread-12] Initializing /data/jcb/fig 6B GFP-AP-2d.ims: [testng] 03:10:40,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:10:40,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:40,520 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-05_03-10-40.log] [testng] 03:10:40,521 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6716dd6e - End of configuration. [testng] [2025-01-05 03:10:40,738] [pool-1-thread-11] Initializing /data/jason/imaris_5_5_demoimages/PyramidalCell.ims: [testng] 03:10:40,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:10:40,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:40,739 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-05_03-10-40.log] [testng] 03:10:40,740 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66fa26cd - End of configuration. [testng] [2025-01-05 03:10:40,977] [pool-1-thread-10] Initializing /data/jason/imaris_5_5_demoimages/HeLaCell.ims: [testng] 03:10:40,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:10:40,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:40,978 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-05_03-10-40.log] [testng] 03:10:40,978 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69c4af42 - End of configuration. [testng] [2025-01-05 03:10:41,219] [pool-1-thread-9] Initializing /data/qa-17839/Fusion_2048_2048_50_1_Acquire.ims: [testng] 03:10:41,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:10:41,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:41,220 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-05_03-10-41.log] [testng] 03:10:41,220 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5736b6cc - End of configuration. [testng] [2025-01-05 03:10:41,474] [pool-1-thread-8] Initializing /data/oliver/Stack2_float32Bit.ims: [testng] 03:10:41,475 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:10:41,475 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:41,475 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-05_03-10-41.log] [testng] 03:10:41,476 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68c1838a - End of configuration. [testng] [2025-01-05 03:10:41,752] [pool-1-thread-7] Initializing /data/generated/10-31_E_t0006.ims: [testng] 03:10:41,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:10:41,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:41,753 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-05_03-10-41.log] [testng] 03:10:41,754 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60828ecf - End of configuration. [testng] [2025-01-05 03:10:41,903] [pool-1-thread-6] Initializing /data/generated/10-31_E_t0015.ims: [testng] 03:10:41,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:10:41,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:41,904 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-05_03-10-41.log] [testng] 03:10:41,904 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cc62335 - End of configuration. [testng] [2025-01-05 03:10:42,064] [pool-1-thread-5] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal.ims: [testng] 03:10:42,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:10:42,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:42,065 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-05_03-10-42.log] [testng] 03:10:42,065 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5670a367 - End of configuration. [testng] [2025-01-05 03:10:42,330] [pool-1-thread-4] Initializing /data/public/davemason/TransFactors_2C_34Z_SRRF_IMS3.ims: [testng] 03:10:42,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:10:42,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:42,331 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-05_03-10-42.log] [testng] 03:10:42,332 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61d7a5c9 - End of configuration. [testng] [2025-01-05 03:10:42,609] [pool-1-thread-3] Initializing /data/qa-17522/2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol.ims: [testng] 03:10:42,609 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:10:42,609 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:42,610 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-05_03-10-42.log] [testng] 03:10:42,610 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d4a2f79 - End of configuration. [testng] [2025-01-05 03:10:43,032] [pool-1-thread-2] Initializing /data/public/eliana/2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol.ims: [testng] 03:10:43,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:10:43,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:43,033 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-05_03-10-43.log] [testng] 03:10:43,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cd086a3 - End of configuration. BUILD SUCCESSFUL Total time: 3 minutes 4 seconds Finished: SUCCESS