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Started by upstream project "BIOFORMATS-test-repo" build number 45 originally caused by: Started by upstream project "Trigger" build number 52 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins2695375207559374754.sh + '[' gatan-dm2 = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_6436_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 test-automated: [testng] File leak detector installed [testng] 01:46:20,293 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:46:20,295 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:46:20,295 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:46:20,296 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:46:20,297 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:46:20,297 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:46:20,297 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:46:20,297 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:46:20,298 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:46:20,298 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:46:20,298 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:46:20,298 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:46:20,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:46:20,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:46:20,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:46:20,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:46:20,631 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:46:20,631 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:46:20,632 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:46:20,633 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:46:20,633 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:46:20,634 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:46:20,635 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 336 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-26 01:46:20,653] [main] java.version = 1.8.0_342 [testng] 01:46:20,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:46:20,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:20,744 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-26_01-46-20.log] [testng] 01:46:20,747 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-26 01:46:20,752] [main] testng.directory = /data [testng] [2024-04-26 01:46:20,753] [main] testng.configDirectory = /config [testng] [2024-04-26 01:46:20,779] [main] testng.multiplier = 1.0 [testng] [2024-04-26 01:46:20,780] [main] testng.in-memory = false [testng] [2024-04-26 01:46:20,781] [main] testng.allow-missing = false [testng] [2024-04-26 01:46:20,781] [main] user.language = en [testng] [2024-04-26 01:46:20,781] [main] user.country = ${user.country} [testng] [2024-04-26 01:46:20,781] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-26 01:46:22,363] [main] ---------------------------------------- [testng] [2024-04-26 01:46:22,363] [main] Total files: 25 [testng] [2024-04-26 01:46:22,363] [main] Scan time: 1.582 s (63 ms/file) [testng] [2024-04-26 01:46:22,363] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 18 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-26 01:46:24,560] [pool-1-thread-1] Initializing /data/pang/screen capture of metadata/tem_dm_microscope_info.png: [testng] 01:46:24,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:46:24,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:24,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-26_01-46-24.log] [testng] 01:46:24,565 |-INFO in ch.qos.logback.core.sift.SiftProcessor@721a65f5 - End of configuration. [testng] [2024-04-26 01:46:24,605] [pool-1-thread-12] Initializing /data/imagic/not read correctly/Abeta Moon_preview.png: [testng] 01:46:24,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:46:24,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:24,613 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-26_01-46-24.log] [testng] 01:46:24,613 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51a5eb63 - End of configuration. [testng] [2024-04-26 01:46:24,644] [pool-1-thread-10] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info2.png: [testng] 01:46:24,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:46:24,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:24,645 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-26_01-46-24.log] [testng] 01:46:24,646 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20b03cdd - End of configuration. [testng] [2024-04-26 01:46:24,667] [pool-1-thread-8] Initializing /data/pang/10500x-o4: [testng] 01:46:24,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:46:24,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:24,669 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-26_01-46-24.log] [testng] 01:46:24,669 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2656b5fb - End of configuration. [testng] [2024-04-26 01:46:24,757] [pool-1-thread-11] Initializing /data/imagic/not read correctly/Zucchini.dm2: [testng] 01:46:24,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:46:24,758 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:24,758 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-26_01-46-24.log] [testng] 01:46:24,759 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5da0ca2a - End of configuration. [testng] [2024-04-26 01:46:24,807] [pool-1-thread-9] Initializing /data/pang/signed: [testng] 01:46:24,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:46:24,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:24,808 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-26_01-46-24.log] [testng] 01:46:24,808 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f531603 - End of configuration. [testng] [2024-04-26 01:46:24,842] [pool-1-thread-6] Initializing /data/imagic/not read correctly/Zucchini_preview.png: [testng] 01:46:24,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:46:24,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:24,844 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-26_01-46-24.log] [testng] 01:46:24,844 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e781352 - End of configuration. [testng] [2024-04-26 01:46:24,854] [pool-1-thread-7] Initializing /data/pang/grating025k.dm2: [testng] 01:46:24,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:46:24,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:24,858 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-26_01-46-24.log] [testng] 01:46:24,858 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e454c7d - End of configuration. [testng] [2024-04-26 01:46:24,917] [pool-1-thread-5] Initializing /data/imagic/Histiocyte in Skin Dermis.dm2: [testng] 01:46:24,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:46:24,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:24,918 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-26_01-46-24.log] [testng] 01:46:24,919 |-INFO in ch.qos.logback.core.sift.SiftProcessor@764b946a - End of configuration. [testng] [2024-04-26 01:46:24,941] [pool-1-thread-4] Initializing /data/imagic/TEM 10118.dm2: [testng] 01:46:24,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:46:24,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:24,943 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-26_01-46-24.log] [testng] 01:46:24,943 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75c32d19 - End of configuration. [testng] [2024-04-26 01:46:24,973] [pool-1-thread-3] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info1.png: [testng] 01:46:24,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:46:24,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:24,977 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-26_01-46-24.log] [testng] 01:46:24,986 |-INFO in ch.qos.logback.core.sift.SiftProcessor@149155a6 - End of configuration. [testng] [2024-04-26 01:46:25,001] [pool-1-thread-2] Initializing /data/pang/unproc-auto: [testng] 01:46:25,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:46:25,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:46:25,002 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-26_01-46-25.log] [testng] 01:46:25,002 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15ed8700 - End of configuration. [testng] [2024-04-26 01:46:27,838] [pool-1-thread-3] Initializing /data/pang/screen capture of metadata/tem_dm_general_info.png: [testng] [2024-04-26 01:46:27,841] [pool-1-thread-2] Initializing /data/imagic/not read correctly/Abeta Moon.dm2: [testng] [2024-04-26 01:46:27,851] [pool-1-thread-7] Initializing /data/pang/DLMeD2E1_010500x03.dm2: [testng] [2024-04-26 01:46:27,866] [pool-1-thread-5] Initializing /data/imagic/1-1.dm2: [testng] [2024-04-26 01:46:27,890] [pool-1-thread-4] Initializing /data/imagic/13008.dm2: [testng] [2024-04-26 01:46:27,901] [pool-1-thread-8] Initializing /data/pang/screen capture of metadata/tem_dm_keywords_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: 12 seconds Finished: SUCCESS