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Started by upstream project "BIOFORMATS-test-repo" build number 134 originally caused by: Started by upstream project "Trigger" build number 154 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins10356341244155486345.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_21082_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] 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] 02:11:08,376 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:11:08,378 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 02:11:08,378 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:11:08,379 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:11:08,379 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:11:08,380 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:11:08,380 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:11:08,380 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:11:08,380 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:11:08,381 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:11:08,381 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:11:08,382 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:11:08,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:11:08,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:11:08,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:11:08,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:11:08,582 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:11:08,582 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:11:08,582 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:11:08,583 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:11:08,583 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 02:11:08,584 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 02:11:08,584 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 204 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-27 02:11:08,592] [main] java.version = 11.0.16 [testng] 02:11:08,595 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:11:08,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:08,638 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-27_02-11-08.log] [testng] 02:11:08,639 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-27 02:11:08,641] [main] testng.directory = /data [testng] [2024-07-27 02:11:08,642] [main] testng.configDirectory = /config [testng] [2024-07-27 02:11:08,651] [main] testng.multiplier = 1.0 [testng] [2024-07-27 02:11:08,653] [main] testng.in-memory = false [testng] [2024-07-27 02:11:08,653] [main] testng.allow-missing = false [testng] [2024-07-27 02:11:08,653] [main] user.language = en [testng] [2024-07-27 02:11:08,653] [main] user.country = ${user.country} [testng] [2024-07-27 02:11:08,653] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-27 02:11:18,462] [main] ---------------------------------------- [testng] [2024-07-27 02:11:18,462] [main] Total files: 68 [testng] [2024-07-27 02:11:18,462] [main] Scan time: 9.808 s (144 ms/file) [testng] [2024-07-27 02:11:18,462] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 60 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-27 02:11:50,367] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/retina.ims: [testng] 02:11:50,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:11:50,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:50,370 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-27_02-11-50.log] [testng] 02:11:50,370 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a3634fd - End of configuration. [testng] [2024-07-27 02:11:50,405] [pool-1-thread-12] Initializing /data/jason/imaris_5_5_demoimages/PyramidalCell.ims: [testng] 02:11:50,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:11:50,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:50,406 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-27_02-11-50.log] [testng] 02:11:50,407 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70bc7e53 - End of configuration. [testng] [2024-07-27 02:11:50,429] [pool-1-thread-11] Initializing /data/generated/10-31_E_t0006.ims: [testng] 02:11:50,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:11:50,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:50,430 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-27_02-11-50.log] [testng] 02:11:50,431 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e2e12b0 - End of configuration. [testng] [2024-07-27 02:11:50,446] [pool-1-thread-10] Initializing /data/generated/MF-2CH-Z-T.ims: [testng] 02:11:50,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:11:50,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:50,447 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-27_02-11-50.log] [testng] 02:11:50,447 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56496f00 - End of configuration. [testng] [2024-07-27 02:11:50,459] [pool-1-thread-9] Initializing /data/generated/10-31_E_t0005.ims: [testng] 02:11:50,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:11:50,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:50,460 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-27_02-11-50.log] [testng] 02:11:50,460 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5731f6ae - End of configuration. [testng] [2024-07-27 02:11:50,474] [pool-1-thread-8] Initializing /data/jason/imaris_5_5_demoimages/HeLaCell.ims: [testng] 02:11:50,475 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:11:50,475 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:50,475 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-27_02-11-50.log] [testng] 02:11:50,476 |-INFO in ch.qos.logback.core.sift.SiftProcessor@433e0777 - End of configuration. [testng] [2024-07-27 02:11:50,525] [pool-1-thread-7] Initializing /data/generated/10-31_E_t0009.ims: [testng] 02:11:50,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:11:50,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:50,526 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-27_02-11-50.log] [testng] 02:11:50,527 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31a3382c - End of configuration. [testng] [2024-07-27 02:11:50,538] [pool-1-thread-6] Initializing /data/qa-17839/Fusion_2048_2048_50_1_Acquire.ims: [testng] 02:11:50,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:11:50,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:50,539 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-27_02-11-50.log] [testng] 02:11:50,539 |-INFO in ch.qos.logback.core.sift.SiftProcessor@174efbe9 - End of configuration. [testng] [2024-07-27 02:11:50,595] [pool-1-thread-5] Initializing /data/public/davemason/Convallaria_3C_10T_confocal.ims: [testng] 02:11:50,595 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:11:50,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:50,596 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-27_02-11-50.log] [testng] 02:11:50,596 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ecf03aa - End of configuration. [testng] [2024-07-27 02:11:50,620] [pool-1-thread-4] Initializing /data/generated/10-31_E_t0002.ims: [testng] 02:11:50,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:11:50,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:50,621 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-27_02-11-50.log] [testng] 02:11:50,622 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ea50118 - End of configuration. [testng] [2024-07-27 02:11:50,635] [pool-1-thread-3] Initializing /data/generated/10-31_E_t0012.ims: [testng] 02:11:50,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:11:50,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:50,636 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-27_02-11-50.log] [testng] 02:11:50,636 |-INFO in ch.qos.logback.core.sift.SiftProcessor@82720cd - End of configuration. [testng] [2024-07-27 02:11:50,648] [pool-1-thread-2] Initializing /data/qa-4898/o383_1_457_CS_r1.ims: [testng] 02:11:50,649 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:11:50,649 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:50,650 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-27_02-11-50.log] [testng] 02:11:50,650 |-INFO in ch.qos.logback.core.sift.SiftProcessor@155560c3 - End of configuration. [testng] [2024-07-27 02:11:52,381] [pool-1-thread-10] Initializing /data/generated/10-31_E_t0010.ims: [testng] [2024-07-27 02:11:52,391] [pool-1-thread-8] Initializing /data/generated/10-31_E_t0008.ims: [testng] [2024-07-27 02:11:52,401] [pool-1-thread-7] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal_IMS3.ims: [testng] [2024-07-27 02:11:52,427] [pool-1-thread-3] Initializing /data/generated/10-31_E_t0000.ims: [testng] [2024-07-27 02:11:52,439] [pool-1-thread-11] Initializing /data/public/davemason/TransFactors_2C_34Z_SRRF_IMS3.ims: [testng] [2024-07-27 02:11:52,461] [pool-1-thread-4] Initializing /data/generated/10-31_E_t0014.ims: [testng] [2024-07-27 02:11:52,472] [pool-1-thread-9] Initializing /data/generated/10-31_E_t0013.ims: [testng] [2024-07-27 02:11:52,495] [pool-1-thread-12] Initializing /data/jcb/fig 6B GFP-AP-2d.ims: [testng] [2024-07-27 02:11:52,546] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal.ims: [testng] [2024-07-27 02:11:52,582] [pool-1-thread-2] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_deconvolved.ims: [testng] [2024-07-27 02:11:52,713] [pool-1-thread-5] Initializing /data/gh-4193/24-5-9_RSV+AfumMscar+CFW_40x Stack_deconvolved.ims: [testng] [2024-07-27 02:11:52,907] [pool-1-thread-9] Initializing /data/qa-17522/2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol.ims: [testng] [2024-07-27 02:11:52,938] [pool-1-thread-10] Initializing /data/jason/imaris_5_5_demoimages/SwimmingAlgae.ims: [testng] [2024-07-27 02:11:53,007] [pool-1-thread-8] Initializing /data/generated/10-31_E_t0003.ims: [testng] [2024-07-27 02:11:53,019] [pool-1-thread-4] Initializing /data/generated/10-31_E_t0007.ims: [testng] [2024-07-27 02:11:53,122] [pool-1-thread-3] Initializing /data/public/davemason/Convallaria_3C_1T_confocal_IMS3.ims: [testng] [2024-07-27 02:11:53,328] [pool-1-thread-8] Initializing /data/chris/supMovie3.ims: [testng] [2024-07-27 02:11:53,360] [pool-1-thread-4] Initializing /data/generated/10-31_E_t0001.ims: [testng] [2024-07-27 02:11:53,677] [pool-1-thread-4] Initializing /data/james/apoEcherry_IL10GFP_tfn647_1_R3D_D3D-Display Adjustment-Save-2011-7-5-1.ims: [testng] [2024-07-27 02:11:53,728] [pool-1-thread-10] Initializing /data/jake/p75Cherry M2 010-3~B.ims: [testng] [2024-07-27 02:11:54,746] [pool-1-thread-2] Initializing /data/public/davemason/Convallaria_3C_10T_confocal_IMS3.ims: BUILD SUCCESSFUL Total time: 1 minute 39 seconds Finished: SUCCESS