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Started by upstream project "BIOFORMATS-test-repo" build number 7 originally caused by: Started by upstream project "Trigger" build number 10 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins2558026263025270066.sh + '[' gatan-dm2 = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_1021_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 00:53:03,633 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:53:03,635 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 00:53:03,635 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:53:03,636 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:53:03,636 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:53:03,637 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:53:03,637 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:53:03,637 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:53:03,637 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:53:03,638 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:53:03,638 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:53:03,639 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:53:03,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:53:03,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:53:03,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:53:03,835 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:53:03,842 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:53:03,842 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:53:03,842 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:53:03,843 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:53:03,843 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 00:53:03,843 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 00:53:03,844 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 207 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-21 00:53:03,853] [main] java.version = 21 [testng] 00:53:03,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:53:03,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:03,901 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-21_00-53-03.log] [testng] 00:53:03,903 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-03-21 00:53:03,904] [main] testng.directory = /data [testng] [2024-03-21 00:53:03,904] [main] testng.configDirectory = /config [testng] [2024-03-21 00:53:03,913] [main] testng.multiplier = 1.0 [testng] [2024-03-21 00:53:03,914] [main] testng.in-memory = false [testng] [2024-03-21 00:53:03,914] [main] testng.allow-missing = false [testng] [2024-03-21 00:53:03,914] [main] user.language = en [testng] [2024-03-21 00:53:03,914] [main] user.country = ${user.country} [testng] [2024-03-21 00:53:03,914] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-21 00:53:05,480] [main] ---------------------------------------- [testng] [2024-03-21 00:53:05,480] [main] Total files: 25 [testng] [2024-03-21 00:53:05,480] [main] Scan time: 1.566 s (62 ms/file) [testng] [2024-03-21 00:53:05,480] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 18 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-21 00:53:06,964] [pool-1-thread-1] Initializing /data/pang/screen capture of metadata/tem_dm_keywords_info.png: [testng] 00:53:06,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:53:06,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:06,966 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-21_00-53-06.log] [testng] 00:53:06,966 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41d05c1f - End of configuration. [testng] [2024-03-21 00:53:06,976] [pool-1-thread-12] Initializing /data/imagic/not read correctly/Abeta Moon_preview.png: [testng] 00:53:06,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:53:06,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:06,977 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-21_00-53-06.log] [testng] 00:53:06,978 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c5b9214 - End of configuration. [testng] [2024-03-21 00:53:06,982] [pool-1-thread-11] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info1.png: [testng] 00:53:06,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:53:06,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:06,983 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-21_00-53-06.log] [testng] 00:53:06,983 |-INFO in ch.qos.logback.core.sift.SiftProcessor@aff64f1 - End of configuration. [testng] [2024-03-21 00:53:06,988] [pool-1-thread-10] Initializing /data/pang/unproc-auto: [testng] 00:53:06,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:53:06,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:06,989 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-21_00-53-06.log] [testng] 00:53:06,989 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bfadff2 - End of configuration. [testng] [2024-03-21 00:53:07,012] [pool-1-thread-9] Initializing /data/pang/DLMeD2E1_010500x03.dm2: [testng] 00:53:07,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:53:07,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:07,013 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-21_00-53-07.log] [testng] 00:53:07,013 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7989283e - End of configuration. [testng] [2024-03-21 00:53:07,032] [pool-1-thread-8] Initializing /data/imagic/TEM 10118.dm2: [testng] 00:53:07,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:53:07,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:07,033 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-21_00-53-07.log] [testng] 00:53:07,033 |-INFO in ch.qos.logback.core.sift.SiftProcessor@780f351c - End of configuration. [testng] [2024-03-21 00:53:07,053] [pool-1-thread-7] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info2.png: [testng] 00:53:07,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:53:07,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:07,054 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-21_00-53-07.log] [testng] 00:53:07,054 |-INFO in ch.qos.logback.core.sift.SiftProcessor@431ec3e0 - End of configuration. [testng] [2024-03-21 00:53:07,058] [pool-1-thread-6] Initializing /data/imagic/not read correctly/Zucchini_preview.png: [testng] 00:53:07,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:53:07,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:07,060 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-21_00-53-07.log] [testng] 00:53:07,060 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2594738e - End of configuration. [testng] [2024-03-21 00:53:07,065] [pool-1-thread-5] Initializing /data/imagic/1-1.dm2: [testng] 00:53:07,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:53:07,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:07,066 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-21_00-53-07.log] [testng] 00:53:07,067 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21b6b058 - End of configuration. [testng] [2024-03-21 00:53:07,083] [pool-1-thread-4] Initializing /data/imagic/13008.dm2: [testng] 00:53:07,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:53:07,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:07,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-21_00-53-07.log] [testng] 00:53:07,084 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32bade10 - End of configuration. [testng] [2024-03-21 00:53:07,105] [pool-1-thread-3] Initializing /data/pang/grating025k.dm2: [testng] 00:53:07,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:53:07,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:07,108 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-21_00-53-07.log] [testng] 00:53:07,109 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50b02226 - End of configuration. [testng] [2024-03-21 00:53:07,122] [pool-1-thread-2] Initializing /data/pang/screen capture of metadata/tem_dm_general_info.png: [testng] 00:53:07,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:53:07,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:07,123 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-21_00-53-07.log] [testng] 00:53:07,123 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66451f6b - End of configuration. [testng] [2024-03-21 00:53:09,202] [pool-1-thread-12] Initializing /data/imagic/not read correctly/Abeta Moon.dm2: [testng] [2024-03-21 00:53:09,241] [pool-1-thread-3] Initializing /data/pang/signed: [testng] [2024-03-21 00:53:09,271] [pool-1-thread-10] Initializing /data/imagic/Histiocyte in Skin Dermis.dm2: [testng] [2024-03-21 00:53:09,305] [pool-1-thread-9] Initializing /data/pang/screen capture of metadata/tem_dm_microscope_info.png: [testng] [2024-03-21 00:53:09,311] [pool-1-thread-8] Initializing /data/pang/10500x-o4: [testng] [2024-03-21 00:53:09,346] [pool-1-thread-5] Initializing /data/imagic/not read correctly/Zucchini.dm2: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 954, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 9 seconds Finished: SUCCESS