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Started by upstream project "BIOFORMATS-test-repo" build number 20 originally caused by: Started by upstream project "Trigger" build number 23 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins13370787107194593178.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_2549_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] 02:16:27,889 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:16:27,891 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 02:16:27,891 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:16:27,892 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:16:27,892 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:16:27,892 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:16:27,893 |-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] 02:16:27,893 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:16:27,893 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:16:27,894 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:16:27,894 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:16:27,894 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:16:28,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:16:28,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:16:28,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:16:28,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:16:28,139 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:16:28,140 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:16:28,140 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:16:28,141 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:16:28,141 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 02:16:28,142 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 02:16:28,142 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 249 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-02 02:16:28,153] [main] java.version = 11.0.16 [testng] 02:16:28,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:16:28,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:28,207 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-02_02-16-28.log] [testng] 02:16:28,208 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-04-02 02:16:28,211] [main] testng.directory = /data [testng] [2024-04-02 02:16:28,211] [main] testng.configDirectory = /config [testng] [2024-04-02 02:16:28,222] [main] testng.multiplier = 1.0 [testng] [2024-04-02 02:16:28,223] [main] testng.in-memory = false [testng] [2024-04-02 02:16:28,224] [main] testng.allow-missing = false [testng] [2024-04-02 02:16:28,224] [main] user.language = en [testng] [2024-04-02 02:16:28,224] [main] user.country = ${user.country} [testng] [2024-04-02 02:16:28,224] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-02 02:16:36,105] [main] ---------------------------------------- [testng] [2024-04-02 02:16:36,105] [main] Total files: 67 [testng] [2024-04-02 02:16:36,105] [main] Scan time: 7.881 s (117 ms/file) [testng] [2024-04-02 02:16:36,105] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-02 02:16:59,618] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_IMS3.ims: [testng] 02:16:59,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:16:59,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:59,622 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-02_02-16-59.log] [testng] 02:16:59,623 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29a3689f - End of configuration. [testng] [2024-04-02 02:16:59,666] [pool-1-thread-12] Initializing /data/generated/10-31_E_t0001.ims: [testng] 02:16:59,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:16:59,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:59,668 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-02_02-16-59.log] [testng] 02:16:59,669 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23e81448 - End of configuration. [testng] [2024-04-02 02:16:59,690] [pool-1-thread-11] Initializing /data/jake/p75Cherry M2 010-3~B.ims: [testng] 02:16:59,690 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:16:59,690 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:59,691 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-02_02-16-59.log] [testng] 02:16:59,691 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76f8d5e9 - End of configuration. [testng] [2024-04-02 02:16:59,749] [pool-1-thread-10] Initializing /data/generated/10-31_E_t0013.ims: [testng] 02:16:59,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:16:59,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:59,750 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-02_02-16-59.log] [testng] 02:16:59,750 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58be81e3 - End of configuration. [testng] [2024-04-02 02:16:59,765] [pool-1-thread-9] Initializing /data/james/apoEcherry_IL10GFP_tfn647_1_R3D_D3D-Display Adjustment-Save-2011-7-5-1.ims: [testng] 02:16:59,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:16:59,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:59,766 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-02_02-16-59.log] [testng] 02:16:59,766 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6922ebcd - End of configuration. [testng] [2024-04-02 02:16:59,907] [pool-1-thread-8] Initializing /data/generated/10-31_E_t0000.ims: [testng] 02:16:59,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:16:59,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:59,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-02_02-16-59.log] [testng] 02:16:59,908 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2bfc8709 - End of configuration. [testng] [2024-04-02 02:16:59,923] [pool-1-thread-7] Initializing /data/jason/imaris_5_5_demoimages/HeLaCell.ims: [testng] 02:16:59,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:16:59,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:59,924 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-02_02-16-59.log] [testng] 02:16:59,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ad3d9db - End of configuration. [testng] [2024-04-02 02:16:59,981] [pool-1-thread-6] Initializing /data/public/davemason/TransFactors_2C_34Z_SRRF_IMS3.ims: [testng] 02:16:59,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:16:59,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:59,983 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-02_02-16-59.log] [testng] 02:16:59,983 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bb6c5fd - End of configuration. [testng] [2024-04-02 02:17:00,047] [pool-1-thread-5] Initializing /data/jason/imaris_5_5_demoimages/PlantCell.ims: [testng] 02:17:00,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:17:00,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:00,049 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-02_02-17-00.log] [testng] 02:17:00,049 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3dbf1ca5 - End of configuration. [testng] [2024-04-02 02:17:00,152] [pool-1-thread-4] Initializing /data/niko/imaris-testfile_5x5x5.ims: [testng] 02:17:00,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:17:00,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:00,154 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-02_02-17-00.log] [testng] 02:17:00,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5aa6b09d - End of configuration. [testng] [2024-04-02 02:17:00,182] [pool-1-thread-3] Initializing /data/qa-17839/Fusion _Stack.ims: [testng] 02:17:00,183 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:17:00,183 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:00,184 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-02_02-17-00.log] [testng] 02:17:00,185 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b4bd3f1 - End of configuration. [testng] [2024-04-02 02:17:00,249] [pool-1-thread-2] Initializing /data/public/eliana/retina_large.ims: [testng] 02:17:00,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:17:00,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:00,251 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-02_02-17-00.log] [testng] 02:17:00,253 |-INFO in ch.qos.logback.core.sift.SiftProcessor@635a98bc - End of configuration. [testng] [2024-04-02 02:17:01,880] [pool-1-thread-4] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal_IMS3.ims: [testng] [2024-04-02 02:17:01,905] [pool-1-thread-12] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal.ims: [testng] [2024-04-02 02:17:01,943] [pool-1-thread-10] Initializing /data/generated/10-31_E_t0006.ims: [testng] [2024-04-02 02:17:01,956] [pool-1-thread-8] Initializing /data/generated/mri-stack-original.ims: [testng] [2024-04-02 02:17:01,972] [pool-1-thread-7] Initializing /data/qa-8019/wrong_num_dimensions.ims: [testng] [2024-04-02 02:17:02,383] [pool-1-thread-8] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal.ims: [testng] [2024-04-02 02:17:02,590] [pool-1-thread-5] Initializing /data/public/davemason/TransFactors_2C_SRRF_IMS3.ims: [testng] [2024-04-02 02:17:02,624] [pool-1-thread-10] Initializing /data/public/davemason/Convallaria_3C_10T_confocal.ims: [testng] [2024-04-02 02:17:03,181] [pool-1-thread-7] Initializing /data/generated/10-31_E_t0009.ims: [testng] [2024-04-02 02:17:03,513] [pool-1-thread-9] Initializing /data/public/davemason/Convallaria_3C_1T_confocal_IMS3.ims: [testng] [2024-04-02 02:17:03,555] [pool-1-thread-1] Initializing /data/oliver/Stack2_float32Bit.ims: [testng] [2024-04-02 02:17:03,755] [pool-1-thread-7] Initializing /data/generated/10-31_E_t0002.ims: [testng] [2024-04-02 02:17:04,007] [pool-1-thread-10] Initializing /data/qa-17522/2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol.ims: BUILD SUCCESSFUL Total time: 2 minutes 27 seconds Finished: SUCCESS