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Started by upstream project "BIOFORMATS-test-repo" build number 71 originally caused by: Started by upstream project "Trigger" build number 79 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins2361428076636418252.sh + '[' gatan-dm2 = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_10700_merge_ci -v /uod/idr/repos/curated/gatan-dm2:/data -v /uod/idr-scratch/merge-ci/curated/gatan-dm2:/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] 04:13:17,222 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 04:13:17,223 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 04:13:17,223 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:13:17,224 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:13:17,224 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:13:17,225 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:13:17,225 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 04:13:17,225 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:13:17,226 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:13:17,226 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:13:17,227 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:13:17,227 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:13:17,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:13:17,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:13:17,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:13:17,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:13:17,418 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:13:17,418 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:13:17,418 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:13:17,419 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:13:17,419 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 04:13:17,419 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 04:13:17,419 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 193 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-22 04:13:17,428] [main] java.version = 17.0.2 [testng] 04:13:17,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:13:17,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:13:17,470 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-22_04-13-17.log] [testng] 04:13:17,471 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-05-22 04:13:17,473] [main] testng.directory = /data [testng] [2024-05-22 04:13:17,474] [main] testng.configDirectory = /config [testng] [2024-05-22 04:13:17,482] [main] testng.multiplier = 1.0 [testng] [2024-05-22 04:13:17,483] [main] testng.in-memory = false [testng] [2024-05-22 04:13:17,483] [main] testng.allow-missing = false [testng] [2024-05-22 04:13:17,483] [main] user.language = en [testng] [2024-05-22 04:13:17,483] [main] user.country = ${user.country} [testng] [2024-05-22 04:13:17,483] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-22 04:13:18,292] [main] ---------------------------------------- [testng] [2024-05-22 04:13:18,292] [main] Total files: 25 [testng] [2024-05-22 04:13:18,292] [main] Scan time: 0.809 s (32 ms/file) [testng] [2024-05-22 04:13:18,292] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 18 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-22 04:13:19,460] [pool-1-thread-1] Initializing /data/pang/screen capture of metadata/tem_dm_microscope_info.png: [testng] 04:13:19,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:13:19,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:13:19,463 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-22_04-13-19.log] [testng] 04:13:19,464 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1dc5ddf2 - End of configuration. [testng] [2024-05-22 04:13:19,478] [pool-1-thread-12] Initializing /data/imagic/13008.dm2: [testng] 04:13:19,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:13:19,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:13:19,479 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-22_04-13-19.log] [testng] 04:13:19,479 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26469cc2 - End of configuration. [testng] [2024-05-22 04:13:19,498] [pool-1-thread-11] Initializing /data/pang/screen capture of metadata/tem_dm_keywords_info.png: [testng] 04:13:19,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:13:19,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:13:19,499 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-22_04-13-19.log] [testng] 04:13:19,500 |-INFO in ch.qos.logback.core.sift.SiftProcessor@757a484 - End of configuration. [testng] [2024-05-22 04:13:19,504] [pool-1-thread-10] Initializing /data/imagic/not read correctly/Zucchini_preview.png: [testng] 04:13:19,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:13:19,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:13:19,505 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-22_04-13-19.log] [testng] 04:13:19,505 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d2225ef - End of configuration. [testng] [2024-05-22 04:13:19,510] [pool-1-thread-9] Initializing /data/imagic/not read correctly/Zucchini.dm2: [testng] 04:13:19,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:13:19,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:13:19,511 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-22_04-13-19.log] [testng] 04:13:19,511 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a0aa7bb - End of configuration. [testng] [2024-05-22 04:13:19,522] [pool-1-thread-8] Initializing /data/imagic/Histiocyte in Skin Dermis.dm2: [testng] 04:13:19,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:13:19,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:13:19,523 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-22_04-13-19.log] [testng] 04:13:19,524 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2dbb17 - End of configuration. [testng] [2024-05-22 04:13:19,535] [pool-1-thread-7] Initializing /data/pang/screen capture of metadata/tem_dm_general_info.png: [testng] 04:13:19,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:13:19,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:13:19,536 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-22_04-13-19.log] [testng] 04:13:19,537 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d95a2bd - End of configuration. [testng] [2024-05-22 04:13:19,541] [pool-1-thread-6] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info1.png: [testng] 04:13:19,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:13:19,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:13:19,543 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-22_04-13-19.log] [testng] 04:13:19,543 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7aede80f - End of configuration. [testng] [2024-05-22 04:13:19,548] [pool-1-thread-5] Initializing /data/imagic/1-1.dm2: [testng] 04:13:19,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:13:19,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:13:19,549 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-22_04-13-19.log] [testng] 04:13:19,550 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ef7ee08 - End of configuration. [testng] [2024-05-22 04:13:19,563] [pool-1-thread-4] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info2.png: [testng] 04:13:19,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:13:19,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:13:19,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-22_04-13-19.log] [testng] 04:13:19,565 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6091627b - End of configuration. [testng] [2024-05-22 04:13:19,568] [pool-1-thread-3] Initializing /data/imagic/not read correctly/Abeta Moon_preview.png: [testng] 04:13:19,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:13:19,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:13:19,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-22_04-13-19.log] [testng] 04:13:19,569 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43b32c40 - End of configuration. [testng] [2024-05-22 04:13:19,590] [pool-1-thread-2] Initializing /data/imagic/not read correctly/Abeta Moon.dm2: [testng] 04:13:19,590 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:13:19,590 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:13:19,591 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-22_04-13-19.log] [testng] 04:13:19,592 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29fa9e9e - End of configuration. [testng] [2024-05-22 04:13:20,899] [pool-1-thread-2] Initializing /data/pang/10500x-o4: [testng] [2024-05-22 04:13:20,910] [pool-1-thread-11] Initializing /data/pang/signed: [testng] [2024-05-22 04:13:20,918] [pool-1-thread-7] Initializing /data/pang/grating025k.dm2: [testng] [2024-05-22 04:13:20,925] [pool-1-thread-6] Initializing /data/pang/unproc-auto: [testng] [2024-05-22 04:13:20,932] [pool-1-thread-4] Initializing /data/pang/DLMeD2E1_010500x03.dm2: [testng] [2024-05-22 04:13:20,942] [pool-1-thread-1] Initializing /data/imagic/TEM 10118.dm2: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 954, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 8 seconds Finished: SUCCESS