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Started by upstream project "BIOFORMATS-test-repo" build number 263 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10 [BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins8819973947522733520.sh + '[' gatan-dm2 = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41515_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 16:41:40,556 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 16:41:40,558 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 16:41:40,558 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 16:41:40,559 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 16:41:40,559 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 16:41:40,559 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 16:41:40,560 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 16:41:40,560 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 16:41:40,560 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 16:41:40,561 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 16:41:40,561 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 16:41:40,561 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 16:41:40,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 16:41:40,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 16:41:40,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 16:41:40,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 16:41:40,744 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 16:41:40,745 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 16:41:40,745 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 16:41:40,745 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 16:41:40,745 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 16:41:40,746 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 16:41:40,746 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 186 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-21 16:41:40,755] [main] java.version = 21 [testng] 16:41:40,758 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 16:41:40,758 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:41:40,804 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-21_16-41-40.log] [testng] 16:41:40,805 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-11-21 16:41:40,806] [main] testng.directory = /data [testng] [2024-11-21 16:41:40,807] [main] testng.configDirectory = /config [testng] [2024-11-21 16:41:40,815] [main] testng.multiplier = 1.0 [testng] [2024-11-21 16:41:40,816] [main] testng.in-memory = false [testng] [2024-11-21 16:41:40,816] [main] testng.allow-missing = false [testng] [2024-11-21 16:41:40,816] [main] user.language = en [testng] [2024-11-21 16:41:40,816] [main] user.country = ${user.country} [testng] [2024-11-21 16:41:40,816] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-21 16:42:10,540] [main] ---------------------------------------- [testng] [2024-11-21 16:42:10,541] [main] Total files: 25 [testng] [2024-11-21 16:42:10,541] [main] Scan time: 29.724 s (1188 ms/file) [testng] [2024-11-21 16:42:10,541] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 18 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-21 16:42:44,353] [pool-1-thread-1] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info2.png: [testng] 16:42:44,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 16:42:44,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:42:44,354 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-21_16-42-44.log] [testng] 16:42:44,355 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b4c812d - End of configuration. [testng] [2024-11-21 16:42:44,436] [pool-1-thread-12] Initializing /data/imagic/TEM 10118.dm2: [testng] 16:42:44,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 16:42:44,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:42:44,437 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-21_16-42-44.log] [testng] 16:42:44,438 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56a5a589 - End of configuration. [testng] [2024-11-21 16:42:44,867] [pool-1-thread-11] Initializing /data/imagic/not read correctly/Abeta Moon.dm2: [testng] 16:42:44,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 16:42:44,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:42:44,869 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-21_16-42-44.log] [testng] 16:42:44,869 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56b43735 - End of configuration. [testng] [2024-11-21 16:42:45,383] [pool-1-thread-10] Initializing /data/pang/unproc-auto: [testng] 16:42:45,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 16:42:45,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:42:45,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-21_16-42-45.log] [testng] 16:42:45,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c0d4ea3 - End of configuration. [testng] [2024-11-21 16:42:45,915] [pool-1-thread-9] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info1.png: [testng] 16:42:45,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 16:42:45,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:42:45,916 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-21_16-42-45.log] [testng] 16:42:45,917 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17de64cd - End of configuration. [testng] [2024-11-21 16:42:46,001] [pool-1-thread-8] Initializing /data/imagic/1-1.dm2: [testng] 16:42:46,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 16:42:46,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:42:46,002 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-21_16-42-46.log] [testng] 16:42:46,003 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6eaaaea6 - End of configuration. [testng] [2024-11-21 16:42:46,525] [pool-1-thread-7] Initializing /data/imagic/not read correctly/Abeta Moon_preview.png: [testng] 16:42:46,525 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 16:42:46,525 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:42:46,526 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-21_16-42-46.log] [testng] 16:42:46,526 |-INFO in ch.qos.logback.core.sift.SiftProcessor@571ac318 - End of configuration. [testng] [2024-11-21 16:42:46,626] [pool-1-thread-6] Initializing /data/pang/signed: [testng] 16:42:46,627 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 16:42:46,627 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:42:46,627 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-21_16-42-46.log] [testng] 16:42:46,628 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58d15b70 - End of configuration. [testng] [2024-11-21 16:42:47,202] [pool-1-thread-5] Initializing /data/imagic/Histiocyte in Skin Dermis.dm2: [testng] 16:42:47,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 16:42:47,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:42:47,203 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-21_16-42-47.log] [testng] 16:42:47,203 |-INFO in ch.qos.logback.core.sift.SiftProcessor@565bb2cc - End of configuration. [testng] [2024-11-21 16:42:47,635] [pool-1-thread-4] Initializing /data/pang/10500x-o4: [testng] 16:42:47,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 16:42:47,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:42:47,636 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-21_16-42-47.log] [testng] 16:42:47,636 |-INFO in ch.qos.logback.core.sift.SiftProcessor@605b712d - End of configuration. [testng] [2024-11-21 16:42:48,148] [pool-1-thread-3] Initializing /data/imagic/not read correctly/Zucchini_preview.png: [testng] 16:42:48,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 16:42:48,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:42:48,149 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-21_16-42-48.log] [testng] 16:42:48,150 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79170391 - End of configuration. [testng] [2024-11-21 16:42:48,225] [pool-1-thread-2] Initializing /data/pang/screen capture of metadata/tem_dm_keywords_info.png: [testng] 16:42:48,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 16:42:48,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:42:48,226 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-21_16-42-48.log] [testng] 16:42:48,226 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59e7a2e6 - End of configuration. [testng] [2024-11-21 16:42:51,998] [pool-1-thread-7] Initializing /data/imagic/13008.dm2: [testng] [2024-11-21 16:42:52,466] [pool-1-thread-9] Initializing /data/imagic/not read correctly/Zucchini.dm2: [testng] [2024-11-21 16:42:52,984] [pool-1-thread-3] Initializing /data/pang/screen capture of metadata/tem_dm_microscope_info.png: [testng] [2024-11-21 16:42:53,071] [pool-1-thread-2] Initializing /data/pang/DLMeD2E1_010500x03.dm2: [testng] [2024-11-21 16:42:53,553] [pool-1-thread-1] Initializing /data/pang/grating025k.dm2: [testng] [2024-11-21 16:42:54,686] [pool-1-thread-5] 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: 1 minute 21 seconds Finished: SUCCESS