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Started by upstream project "BIOFORMATS-test-repo" build number 278 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins13870321475316334886.sh + '[' gatan-dm2 = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43846_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] 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] 10:34:19,264 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 10:34:19,266 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 10:34:19,266 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:34:19,267 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:34:19,268 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 10:34:19,268 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 10:34:19,269 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 10:34:19,269 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:34:19,269 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:34:19,270 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 10:34:19,270 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 10:34:19,270 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 10:34:19,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 10:34:19,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 10:34:19,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 10:34:19,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 10:34:19,485 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 10:34:19,485 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 10:34:19,485 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 10:34:19,486 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 10:34:19,486 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 10:34:19,487 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 10:34:19,487 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 218 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-03 10:34:19,497] [main] java.version = 11.0.16 [testng] 10:34:19,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 10:34:19,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:34:19,547 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-03_10-34-19.log] [testng] 10:34:19,548 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-12-03 10:34:19,551] [main] testng.directory = /data [testng] [2024-12-03 10:34:19,551] [main] testng.configDirectory = /config [testng] [2024-12-03 10:34:19,561] [main] testng.multiplier = 1.0 [testng] [2024-12-03 10:34:19,563] [main] testng.in-memory = false [testng] [2024-12-03 10:34:19,563] [main] testng.allow-missing = false [testng] [2024-12-03 10:34:19,563] [main] user.language = en [testng] [2024-12-03 10:34:19,563] [main] user.country = ${user.country} [testng] [2024-12-03 10:34:19,563] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-03 10:34:42,371] [main] ---------------------------------------- [testng] [2024-12-03 10:34:42,371] [main] Total files: 25 [testng] [2024-12-03 10:34:42,372] [main] Scan time: 22.808 s (912 ms/file) [testng] [2024-12-03 10:34:42,372] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 18 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-03 10:35:02,940] [pool-1-thread-1] Initializing /data/pang/DLMeD2E1_010500x03.dm2: [testng] 10:35:02,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:35:02,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:35:02,943 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-03_10-35-02.log] [testng] 10:35:02,943 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b022c4 - End of configuration. [testng] [2024-12-03 10:35:03,238] [pool-1-thread-12] Initializing /data/imagic/not read correctly/Abeta Moon.dm2: [testng] 10:35:03,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:35:03,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:35:03,239 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-03_10-35-03.log] [testng] 10:35:03,240 |-INFO in ch.qos.logback.core.sift.SiftProcessor@607cdbd2 - End of configuration. [testng] [2024-12-03 10:35:03,521] [pool-1-thread-11] Initializing /data/pang/screen capture of metadata/tem_dm_microscope_info.png: [testng] 10:35:03,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:35:03,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:35:03,522 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-03_10-35-03.log] [testng] 10:35:03,522 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b75f68c - End of configuration. [testng] [2024-12-03 10:35:03,582] [pool-1-thread-10] Initializing /data/pang/10500x-o4: [testng] 10:35:03,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:35:03,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:35:03,583 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-03_10-35-03.log] [testng] 10:35:03,584 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3728b78e - End of configuration. [testng] [2024-12-03 10:35:03,943] [pool-1-thread-9] Initializing /data/imagic/13008.dm2: [testng] 10:35:03,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:35:03,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:35:03,944 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-03_10-35-03.log] [testng] 10:35:03,944 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b37f52e - End of configuration. [testng] [2024-12-03 10:35:04,308] [pool-1-thread-8] Initializing /data/pang/grating025k.dm2: [testng] 10:35:04,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:35:04,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:35:04,309 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-03_10-35-04.log] [testng] 10:35:04,310 |-INFO in ch.qos.logback.core.sift.SiftProcessor@99aa2e8 - End of configuration. [testng] [2024-12-03 10:35:04,605] [pool-1-thread-7] Initializing /data/imagic/not read correctly/Abeta Moon_preview.png: [testng] 10:35:04,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:35:04,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:35:04,606 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-03_10-35-04.log] [testng] 10:35:04,606 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76110ba6 - End of configuration. [testng] [2024-12-03 10:35:04,661] [pool-1-thread-6] Initializing /data/pang/signed: [testng] 10:35:04,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:35:04,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:35:04,662 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-03_10-35-04.log] [testng] 10:35:04,663 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a2cce9f - End of configuration. [testng] [2024-12-03 10:35:04,971] [pool-1-thread-5] Initializing /data/imagic/Histiocyte in Skin Dermis.dm2: [testng] 10:35:04,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:35:04,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:35:04,972 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-03_10-35-04.log] [testng] 10:35:04,973 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6292a096 - End of configuration. [testng] [2024-12-03 10:35:05,264] [pool-1-thread-4] Initializing /data/pang/screen capture of metadata/tem_dm_keywords_info.png: [testng] 10:35:05,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:35:05,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:35:05,265 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-03_10-35-05.log] [testng] 10:35:05,266 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27442a3b - End of configuration. [testng] [2024-12-03 10:35:05,315] [pool-1-thread-3] Initializing /data/imagic/not read correctly/Zucchini.dm2: [testng] 10:35:05,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:35:05,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:35:05,316 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-03_10-35-05.log] [testng] 10:35:05,316 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2bc242f6 - End of configuration. [testng] [2024-12-03 10:35:05,599] [pool-1-thread-2] Initializing /data/imagic/TEM 10118.dm2: [testng] 10:35:05,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:35:05,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:35:05,600 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-03_10-35-05.log] [testng] 10:35:05,600 |-INFO in ch.qos.logback.core.sift.SiftProcessor@528b6fee - End of configuration. [testng] [2024-12-03 10:35:09,264] [pool-1-thread-7] Initializing /data/pang/unproc-auto: [testng] [2024-12-03 10:35:09,590] [pool-1-thread-4] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info2.png: [testng] [2024-12-03 10:35:09,663] [pool-1-thread-11] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info1.png: [testng] [2024-12-03 10:35:10,072] [pool-1-thread-8] Initializing /data/imagic/not read correctly/Zucchini_preview.png: [testng] [2024-12-03 10:35:10,149] [pool-1-thread-3] Initializing /data/imagic/1-1.dm2: [testng] [2024-12-03 10:35:10,704] [pool-1-thread-12] Initializing /data/pang/screen capture of metadata/tem_dm_general_info.png: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 954, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 57 seconds Finished: SUCCESS