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Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins3758742033873831840.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_44271_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=1 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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 11:11:11,406 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:11:11,407 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 11:11:11,407 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:11:11,408 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:11:11,408 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:11:11,409 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:11:11,409 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:11:11,409 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:11:11,409 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:11:11,410 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:11:11,410 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:11:11,411 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:11:11,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:11:11,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:11:11,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:11:11,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:11:11,592 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:11:11,592 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:11:11,593 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:11:11,593 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:11:11,593 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 11:11:11,594 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 11:11:11,594 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 185 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-05 11:11:11,603] [main] java.version = 21 [testng] 11:11:11,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:11:11,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:11:11,645 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-05_11-11-11.log] [testng] 11:11:11,646 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-12-05 11:11:11,648] [main] testng.directory = /data [testng] [2024-12-05 11:11:11,648] [main] testng.configDirectory = /config [testng] [2024-12-05 11:11:11,656] [main] testng.multiplier = 1.0 [testng] [2024-12-05 11:11:11,657] [main] testng.in-memory = false [testng] [2024-12-05 11:11:11,657] [main] testng.allow-missing = false [testng] [2024-12-05 11:11:11,657] [main] user.language = en [testng] [2024-12-05 11:11:11,657] [main] user.country = ${user.country} [testng] [2024-12-05 11:11:11,657] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-05 11:11:16,002] [main] ---------------------------------------- [testng] [2024-12-05 11:11:16,003] [main] Total files: 73 [testng] [2024-12-05 11:11:16,003] [main] Scan time: 4.345 s (59 ms/file) [testng] [2024-12-05 11:11:16,003] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 63 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-05 11:11:25,586] [pool-1-thread-1] Initializing /data/public/eliana/2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol.ims: [testng] 11:11:25,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:11:25,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:11:25,587 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-05_11-11-25.log] [testng] 11:11:25,588 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d38e6f9 - End of configuration. [testng] [2024-12-05 11:11:28,014] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/retina.ims: [testng] [2024-12-05 11:11:29,445] [pool-1-thread-1] Initializing /data/public/bitplane/lz4/croppedRetinaLz4.ims: [testng] [2024-12-05 11:11:30,009] [pool-1-thread-1] Initializing /data/oliver/Stack2_u16Bit.ims: [testng] [2024-12-05 11:11:31,935] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0014.ims: [testng] [2024-12-05 11:11:32,266] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/PlantCell.ims: [testng] [2024-12-05 11:11:33,867] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal.ims: [testng] [2024-12-05 11:11:37,128] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0010.ims: [testng] [2024-12-05 11:11:37,436] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_deconvolved.ims: [testng] [2024-12-05 11:11:40,087] [pool-1-thread-1] Initializing /data/qa-4898/o383_1_457_CS_r1.ims: [testng] [2024-12-05 11:11:41,341] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_10T_confocal_IMS3.ims: [testng] [2024-12-05 11:11:43,574] [pool-1-thread-1] Initializing /data/qa-17515/Organoid=1.ims: [testng] [2024-12-05 11:11:54,553] [pool-1-thread-1] Initializing /data/qa-17522/2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol.ims: [testng] [2024-12-05 11:11:56,196] [pool-1-thread-1] Initializing /data/niko/imaris-testfile_5x5x5.ims: [testng] [2024-12-05 11:11:56,496] [pool-1-thread-1] Initializing /data/qa-8019/wrong_num_dimensions.ims: [testng] [2024-12-05 11:11:57,302] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/SwimmingAlgae.ims: [testng] [2024-12-05 11:11:58,015] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_IMS3.ims: [testng] [2024-12-05 11:11:59,708] [pool-1-thread-1] Initializing /data/qa-17839/Fusion _Stack.ims: [testng] [2024-12-05 11:12:17,932] [pool-1-thread-1] Initializing /data/oliver/Stack2_8Bit.ims: [testng] [2024-12-05 11:12:19,090] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0005.ims: [testng] [2024-12-05 11:12:19,349] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0001.ims: [testng] [2024-12-05 11:12:19,610] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0015.ims: [testng] [2024-12-05 11:12:19,862] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/HeLaCell.ims: [testng] [2024-12-05 11:12:20,332] [pool-1-thread-1] Initializing /data/generated/mri-stack-original.ims: [testng] [2024-12-05 11:12:20,557] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0004.ims: [testng] [2024-12-05 11:12:20,818] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0008.ims: [testng] [2024-12-05 11:12:21,072] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0011.ims: [testng] [2024-12-05 11:12:21,324] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/PtK2Cell.ims: [testng] [2024-12-05 11:12:22,100] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0003.ims: [testng] [2024-12-05 11:12:22,367] [pool-1-thread-1] Initializing /data/generated/MF-2CH-Z-T.ims: [testng] [2024-12-05 11:12:22,590] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal.ims: [testng] [2024-12-05 11:12:25,605] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal_IMS3.ims: [testng] [2024-12-05 11:12:30,962] [pool-1-thread-1] Initializing /data/oliver/Stack2_float32Bit.ims: [testng] [2024-12-05 11:12:33,921] [pool-1-thread-1] Initializing /data/gh-4193/24-5-9_RSV+AfumMscar+CFW_40x Stack_deconvolved.ims: [testng] [2024-12-05 11:12:47,366] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0012.ims: [testng] [2024-12-05 11:12:47,631] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_1T_confocal.ims: [testng] [2024-12-05 11:12:48,347] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_deconvolved_IMS3.ims: [testng] [2024-12-05 11:12:49,992] [pool-1-thread-1] Initializing /data/chris/supMovie3.ims: [testng] [2024-12-05 11:12:54,295] [pool-1-thread-1] Initializing /data/jcb/fig 6B GFP-AP-2d.ims: [testng] [2024-12-05 11:13:01,291] [pool-1-thread-1] Initializing /data/public/davemason/TransFactors_2C_34Z_SRRF.ims: [testng] [2024-12-05 11:13:32,600] [pool-1-thread-1] Initializing /data/public/davemason/TransFactors_2C_SRRF_IMS3.ims: [testng] [2024-12-05 11:13:43,811] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0000.ims: [testng] [2024-12-05 11:13:44,054] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/PyramidalCell.ims: [testng] [2024-12-05 11:13:44,534] [pool-1-thread-1] Initializing /data/public/eliana/retina_large.ims: [testng] [2024-12-05 11:13:50,996] [pool-1-thread-1] Initializing /data/qa-17522/2016-12-14_08.43.34_Sample Prefix_WAINWRIGHT James_Protocol.ims: [testng] [2024-12-05 11:14:32,342] [pool-1-thread-1] Initializing /data/public/davemason/TransFactors_2C_SRRF.ims: [testng] [2024-12-05 11:14:38,699] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0007.ims: [testng] [2024-12-05 11:14:38,957] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0009.ims: [testng] [2024-12-05 11:14:39,204] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/R18Demo.ims: [testng] [2024-12-05 11:14:39,655] [pool-1-thread-1] Initializing /data/james/apoEcherry_IL10GFP_tfn647_1_R3D_D3D-Display Adjustment-Save-2011-7-5-1.ims: [testng] [2024-12-05 11:14:43,141] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0013.ims: [testng] [2024-12-05 11:14:43,397] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0002.ims: [testng] [2024-12-05 11:14:43,647] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_1T_confocal_IMS3.ims: [testng] [2024-12-05 11:14:45,385] [pool-1-thread-1] Initializing /data/public/davemason/TransFactors_2C_34Z_SRRF_IMS3.ims: [testng] [2024-12-05 11:14:59,579] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0006.ims: [testng] [2024-12-05 11:14:59,842] [pool-1-thread-1] Initializing /data/kay/Imaris503_test_Kay.ims: [testng] [2024-12-05 11:15:00,300] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_10T_confocal.ims: [testng] [2024-12-05 11:15:01,037] [pool-1-thread-1] Initializing /data/public/bitplane/lz4/croppedCDM3DLz4.ims: [testng] [2024-12-05 11:15:01,654] [pool-1-thread-1] Initializing /data/jake/p75Cherry M2 010-3~B.ims: [testng] [2024-12-05 11:17:14,925] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal.ims: [testng] [2024-12-05 11:17:17,698] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal_IMS3.ims: [testng] [2024-12-05 11:17:22,185] [pool-1-thread-1] Initializing /data/public/bitplane/performance/performanceTestImage.ims: [testng] [2024-12-05 11:17:26,520] [pool-1-thread-1] Initializing /data/qa-17839/Fusion_2048_2048_50_1_Acquire.ims: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3339, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 6 minutes 22 seconds Finished: SUCCESS