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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/jenkins5108118655393585544.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_34530_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 test-automated: [testng] File leak detector installed [testng] 14:58:24,461 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 14:58:24,463 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 14:58:24,463 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:58:24,464 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:58:24,464 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 14:58:24,464 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 14:58:24,464 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 14:58:24,464 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:58:24,465 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:58:24,465 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 14:58:24,465 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 14:58:24,465 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 14:58:24,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 14:58:24,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 14:58:24,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 14:58:24,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 14:58:24,812 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 14:58:24,813 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 14:58:24,813 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 14:58:24,813 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 14:58:24,813 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 14:58:24,814 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 14:58:24,814 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 349 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-11 14:58:24,823] [main] java.version = 1.8.0_342 [testng] 14:58:24,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 14:58:24,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:58:24,870 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-11_14-58-24.log] [testng] 14:58:24,871 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-11 14:58:24,873] [main] testng.directory = /data [testng] [2024-10-11 14:58:24,873] [main] testng.configDirectory = /config [testng] [2024-10-11 14:58:24,884] [main] testng.multiplier = 1.0 [testng] [2024-10-11 14:58:24,884] [main] testng.in-memory = false [testng] [2024-10-11 14:58:24,884] [main] testng.allow-missing = false [testng] [2024-10-11 14:58:24,884] [main] user.language = en [testng] [2024-10-11 14:58:24,884] [main] user.country = ${user.country} [testng] [2024-10-11 14:58:24,884] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-11 15:00:18,439] [main] ---------------------------------------- [testng] [2024-10-11 15:00:18,439] [main] Total files: 68 [testng] [2024-10-11 15:00:18,439] [main] Scan time: 113.554 s (1669 ms/file) [testng] [2024-10-11 15:00:18,439] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 60 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-11 15:01:53,292] [pool-1-thread-1] Initializing /data/kay/Imaris503_test_Kay.ims: [testng] 15:01:53,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 15:01:53,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:01:53,294 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-11_15-01-53.log] [testng] 15:01:53,295 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a3d9e5b - End of configuration. [testng] [2024-10-11 15:01:55,154] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0011.ims: [testng] [2024-10-11 15:01:55,695] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0004.ims: [testng] [2024-10-11 15:01:56,183] [pool-1-thread-1] Initializing /data/generated/MF-2CH-Z-T.ims: [testng] [2024-10-11 15:01:56,714] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/SwimmingAlgae.ims: [testng] [2024-10-11 15:01:57,573] [pool-1-thread-1] Initializing /data/qa-17522/2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol.ims: [testng] [2024-10-11 15:02:02,336] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/R18Demo.ims: [testng] [2024-10-11 15:02:02,916] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/HeLaCell.ims: [testng] [2024-10-11 15:02:03,436] [pool-1-thread-1] Initializing /data/qa-17522/2016-12-14_08.43.34_Sample Prefix_WAINWRIGHT James_Protocol.ims: [testng] [2024-10-11 15:02:50,319] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/PyramidalCell.ims: [testng] [2024-10-11 15:02:50,843] [pool-1-thread-1] Initializing /data/public/davemason/TransFactors_2C_SRRF.ims: [testng] [2024-10-11 15:03:00,722] [pool-1-thread-1] Initializing /data/james/apoEcherry_IL10GFP_tfn647_1_R3D_D3D-Display Adjustment-Save-2011-7-5-1.ims: [testng] [2024-10-11 15:03:04,378] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal.ims: [testng] [2024-10-11 15:03:09,445] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal_IMS3.ims: [testng] [2024-10-11 15:03:16,980] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_IMS3.ims: [testng] [2024-10-11 15:03:19,127] [pool-1-thread-1] Initializing /data/public/davemason/TransFactors_2C_34Z_SRRF_IMS3.ims: [testng] [2024-10-11 15:03:34,988] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_10T_confocal.ims: [testng] [2024-10-11 15:03:36,177] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal.ims: [testng] [2024-10-11 15:03:41,832] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0012.ims: [testng] [2024-10-11 15:03:42,531] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_1T_confocal_IMS3.ims: [testng] [2024-10-11 15:03:44,712] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0006.ims: [testng] [2024-10-11 15:03:45,192] [pool-1-thread-1] Initializing /data/oliver/Stack2_float32Bit.ims: [testng] [2024-10-11 15:03:49,684] [pool-1-thread-1] Initializing /data/qa-4898/o383_1_457_CS_r1.ims: [testng] [2024-10-11 15:03:50,541] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0000.ims: [testng] [2024-10-11 15:03:51,151] [pool-1-thread-1] Initializing /data/qa-17515/Organoid=1.ims: [testng] [2024-10-11 15:04:06,251] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0005.ims: [testng] [2024-10-11 15:04:06,839] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0007.ims: [testng] [2024-10-11 15:04:07,378] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/PtK2Cell.ims: [testng] [2024-10-11 15:04:07,937] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0014.ims: [testng] [2024-10-11 15:04:08,545] [pool-1-thread-1] Initializing /data/gh-4193/24-5-9_RSV+AfumMscar+CFW_40x Stack_deconvolved.ims: [testng] [2024-10-11 15:04:23,252] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_deconvolved_IMS3.ims: [testng] [2024-10-11 15:04:26,086] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/retina.ims: [testng] [2024-10-11 15:04:27,392] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0003.ims: [testng] [2024-10-11 15:04:27,863] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_deconvolved.ims: [testng] [2024-10-11 15:04:33,965] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal.ims: [testng] [2024-10-11 15:04:38,522] [pool-1-thread-1] Initializing /data/oliver/Stack2_8Bit.ims: [testng] [2024-10-11 15:04:40,349] [pool-1-thread-1] Initializing /data/jake/p75Cherry M2 010-3~B.ims: [testng] [2024-10-11 15:11:00,082] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal_IMS3.ims: [testng] [2024-10-11 15:11:05,992] [pool-1-thread-1] Initializing /data/jcb/fig 6B GFP-AP-2d.ims: [testng] [2024-10-11 15:11:16,047] [pool-1-thread-1] Initializing /data/public/eliana/retina_large.ims: [testng] [2024-10-11 15:11:20,088] [pool-1-thread-1] Initializing /data/public/eliana/2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol.ims: [testng] [2024-10-11 15:11:24,111] [pool-1-thread-1] Initializing /data/qa-17839/Fusion_2048_2048_50_1_Acquire.ims: [testng] [2024-10-11 15:11:32,683] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/PlantCell.ims: [testng] [2024-10-11 15:11:34,152] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0009.ims: [testng] [2024-10-11 15:11:34,700] [pool-1-thread-1] Initializing /data/chris/supMovie3.ims: [testng] [2024-10-11 15:11:40,749] [pool-1-thread-1] Initializing /data/public/davemason/TransFactors_2C_SRRF_IMS3.ims: [testng] [2024-10-11 15:11:53,616] [pool-1-thread-1] Initializing /data/niko/imaris-testfile_5x5x5.ims: [testng] [2024-10-11 15:11:53,948] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0010.ims: [testng] [2024-10-11 15:11:54,441] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0002.ims: [testng] [2024-10-11 15:11:54,813] [pool-1-thread-1] Initializing /data/qa-17839/Fusion _Stack.ims: [testng] [2024-10-11 15:12:07,968] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0013.ims: [testng] [2024-10-11 15:12:08,447] [pool-1-thread-1] Initializing /data/generated/mri-stack-original.ims: [testng] [2024-10-11 15:12:08,713] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0008.ims: [testng] [2024-10-11 15:12:09,162] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_1T_confocal.ims: [testng] [2024-10-11 15:12:10,500] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0001.ims: [testng] [2024-10-11 15:12:11,049] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0015.ims: [testng] [2024-10-11 15:12:11,651] [pool-1-thread-1] Initializing /data/public/davemason/TransFactors_2C_34Z_SRRF.ims: [testng] [2024-10-11 15:12:31,994] [pool-1-thread-1] Initializing /data/oliver/Stack2_u16Bit.ims: [testng] [2024-10-11 15:12:34,197] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_10T_confocal_IMS3.ims: [testng] [2024-10-11 15:12:37,174] [pool-1-thread-1] Initializing /data/qa-8019/wrong_num_dimensions.ims: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3180, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 14 minutes 19 seconds Finished: SUCCESS