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Started by upstream project "BIOFORMATS-test-repo" build number 222 originally caused by: Started by upstream project "Trigger" build number 249 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/jenkins10101016309325569422.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35305_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] 13:56:22,636 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 13:56:22,638 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 13:56:22,638 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:56:22,638 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:56:22,639 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 13:56:22,639 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 13:56:22,639 |-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] 13:56:22,639 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:56:22,640 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:56:22,640 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 13:56:22,641 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 13:56:22,641 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 13:56:22,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 13:56:22,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 13:56:22,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 13:56:22,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 13:56:22,822 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 13:56:22,822 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 13:56:22,822 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 13:56:22,823 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 13:56:22,823 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 13:56:22,824 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 13:56:22,824 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 184 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-16 13:56:22,832] [main] java.version = 17.0.2 [testng] 13:56:22,835 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 13:56:22,835 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:56:22,874 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-16_13-56-22.log] [testng] 13:56:22,875 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-16 13:56:22,877] [main] testng.directory = /data [testng] [2024-10-16 13:56:22,877] [main] testng.configDirectory = /config [testng] [2024-10-16 13:56:22,885] [main] testng.multiplier = 1.0 [testng] [2024-10-16 13:56:22,886] [main] testng.in-memory = false [testng] [2024-10-16 13:56:22,886] [main] testng.allow-missing = false [testng] [2024-10-16 13:56:22,886] [main] user.language = en [testng] [2024-10-16 13:56:22,886] [main] user.country = ${user.country} [testng] [2024-10-16 13:56:22,886] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-16 14:01:07,409] [main] ---------------------------------------- [testng] [2024-10-16 14:01:07,410] [main] Total files: 68 [testng] [2024-10-16 14:01:07,410] [main] Scan time: 284.523 s (4184 ms/file) [testng] [2024-10-16 14:01:07,410] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 60 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-16 14:06:27,518] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_1T_confocal_IMS3.ims: [testng] 14:06:27,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 14:06:27,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:06:27,520 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-16_14-06-27.log] [testng] 14:06:27,520 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ede88be - End of configuration. [testng] [2024-10-16 14:06:31,562] [pool-1-thread-12] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_deconvolved.ims: [testng] 14:06:31,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 14:06:31,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:06:31,566 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-16_14-06-31.log] [testng] 14:06:31,567 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53df713e - End of configuration. [testng] [2024-10-16 14:06:36,633] [pool-1-thread-11] Initializing /data/public/davemason/TransFactors_2C_SRRF_IMS3.ims: [testng] 14:06:36,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 14:06:36,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:06:36,634 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-16_14-06-36.log] [testng] 14:06:36,635 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45be539d - End of configuration. [testng] [2024-10-16 14:06:42,247] [pool-1-thread-10] Initializing /data/oliver/Stack2_u16Bit.ims: [testng] 14:06:42,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 14:06:42,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:06:42,248 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-16_14-06-42.log] [testng] 14:06:42,248 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c24bcc9 - End of configuration. [testng] [2024-10-16 14:06:48,508] [pool-1-thread-9] Initializing /data/jason/imaris_5_5_demoimages/retina.ims: [testng] 14:06:48,508 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 14:06:48,508 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:06:48,509 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-16_14-06-48.log] [testng] 14:06:48,509 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fba052b - End of configuration. [testng] [2024-10-16 14:06:54,413] [pool-1-thread-8] Initializing /data/jcb/fig 6B GFP-AP-2d.ims: [testng] 14:06:54,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 14:06:54,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:06:54,414 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-16_14-06-54.log] [testng] 14:06:54,415 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c958b50 - End of configuration. [testng] [2024-10-16 14:06:58,784] [pool-1-thread-7] Initializing /data/public/eliana/retina_large.ims: [testng] 14:06:58,784 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 14:06:58,784 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:06:58,785 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-16_14-06-58.log] [testng] 14:06:58,786 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d1801fe - End of configuration. [testng] [2024-10-16 14:07:03,966] [pool-1-thread-6] Initializing /data/niko/imaris-testfile_5x5x5.ims: [testng] 14:07:03,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 14:07:03,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:03,967 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-16_14-07-03.log] [testng] 14:07:03,967 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c277aef - End of configuration. [testng] [2024-10-16 14:07:08,607] [pool-1-thread-5] Initializing /data/qa-17839/Fusion_2048_2048_50_1_Acquire.ims: [testng] 14:07:08,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 14:07:08,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:08,607 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-16_14-07-08.log] [testng] 14:07:08,608 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d964030 - End of configuration. [testng] [2024-10-16 14:07:15,481] [pool-1-thread-4] Initializing /data/generated/10-31_E_t0004.ims: [testng] 14:07:15,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 14:07:15,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:15,481 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-16_14-07-15.log] [testng] 14:07:15,482 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e4af835 - End of configuration. [testng] [2024-10-16 14:07:18,320] [pool-1-thread-3] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal.ims: [testng] 14:07:18,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 14:07:18,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:18,321 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-16_14-07-18.log] [testng] 14:07:18,321 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5264c10c - End of configuration. [testng] [2024-10-16 14:07:24,587] [pool-1-thread-2] Initializing /data/generated/10-31_E_t0005.ims: [testng] 14:07:24,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 14:07:24,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:24,588 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-16_14-07-24.log] [testng] 14:07:24,589 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69c4af42 - End of configuration. BUILD SUCCESSFUL Total time: 17 minutes 9 seconds Finished: SUCCESS