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Started by upstream project "BIOFORMATS-test-repo" build number 282 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins3947221557686016628.sh + '[' gatan-dm2 = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_44504_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] 11:11:37,712 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:11:37,714 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 11:11:37,714 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:11:37,716 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:11:37,716 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:11:37,716 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:11:37,716 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:11:37,716 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:11:37,717 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:11:37,717 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:11:37,717 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:11:37,717 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:11:37,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:11:37,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:11:38,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:11:38,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:11:38,015 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:11:38,015 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:11:38,015 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:11:38,016 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:11:38,016 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 11:11:38,017 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 11:11:38,017 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 300 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-06 11:11:38,029] [main] java.version = 1.8.0_342 [testng] 11:11:38,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:11:38,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:11:38,088 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-06_11-11-38.log] [testng] 11:11:38,090 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-06 11:11:38,092] [main] testng.directory = /data [testng] [2024-12-06 11:11:38,092] [main] testng.configDirectory = /config [testng] [2024-12-06 11:11:38,106] [main] testng.multiplier = 1.0 [testng] [2024-12-06 11:11:38,106] [main] testng.in-memory = false [testng] [2024-12-06 11:11:38,107] [main] testng.allow-missing = false [testng] [2024-12-06 11:11:38,107] [main] user.language = en [testng] [2024-12-06 11:11:38,107] [main] user.country = ${user.country} [testng] [2024-12-06 11:11:38,107] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-06 11:11:51,239] [main] ---------------------------------------- [testng] [2024-12-06 11:11:51,240] [main] Total files: 25 [testng] [2024-12-06 11:11:51,240] [main] Scan time: 13.132 s (525 ms/file) [testng] [2024-12-06 11:11:51,240] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 18 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-06 11:12:07,816] [pool-1-thread-1] Initializing /data/imagic/1-1.dm2: [testng] 11:12:07,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:12:07,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:07,818 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-06_11-12-07.log] [testng] 11:12:07,818 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64435363 - End of configuration. [testng] [2024-12-06 11:12:08,045] [pool-1-thread-12] Initializing /data/pang/screen capture of metadata/tem_dm_microscope_info.png: [testng] 11:12:08,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:12:08,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:08,047 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-06_11-12-08.log] [testng] 11:12:08,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@656a21b5 - End of configuration. [testng] [2024-12-06 11:12:08,083] [pool-1-thread-11] Initializing /data/imagic/not read correctly/Abeta Moon.dm2: [testng] 11:12:08,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:12:08,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:08,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-06_11-12-08.log] [testng] 11:12:08,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2da5eb40 - End of configuration. [testng] [2024-12-06 11:12:08,308] [pool-1-thread-10] Initializing /data/imagic/TEM 10118.dm2: [testng] 11:12:08,308 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:12:08,308 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:08,309 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-06_11-12-08.log] [testng] 11:12:08,309 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e7ba82e - End of configuration. [testng] [2024-12-06 11:12:08,547] [pool-1-thread-9] Initializing /data/pang/unproc-auto: [testng] 11:12:08,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:12:08,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:08,548 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-06_11-12-08.log] [testng] 11:12:08,549 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7423c75 - End of configuration. [testng] [2024-12-06 11:12:08,828] [pool-1-thread-8] Initializing /data/pang/grating025k.dm2: [testng] 11:12:08,829 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:12:08,829 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:08,830 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-06_11-12-08.log] [testng] 11:12:08,830 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bdca26c - End of configuration. [testng] [2024-12-06 11:12:09,120] [pool-1-thread-7] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info2.png: [testng] 11:12:09,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:12:09,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:09,121 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-06_11-12-09.log] [testng] 11:12:09,122 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c1fe3e7 - End of configuration. [testng] [2024-12-06 11:12:09,178] [pool-1-thread-6] Initializing /data/pang/DLMeD2E1_010500x03.dm2: [testng] 11:12:09,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:12:09,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:09,179 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-06_11-12-09.log] [testng] 11:12:09,179 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1914ad7c - End of configuration. [testng] [2024-12-06 11:12:09,421] [pool-1-thread-5] Initializing /data/pang/10500x-o4: [testng] 11:12:09,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:12:09,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:09,422 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-06_11-12-09.log] [testng] 11:12:09,422 |-INFO in ch.qos.logback.core.sift.SiftProcessor@346cc407 - End of configuration. [testng] [2024-12-06 11:12:09,694] [pool-1-thread-4] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info1.png: [testng] 11:12:09,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:12:09,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:09,695 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-06_11-12-09.log] [testng] 11:12:09,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@734f37e8 - End of configuration. [testng] [2024-12-06 11:12:09,751] [pool-1-thread-3] Initializing /data/pang/screen capture of metadata/tem_dm_keywords_info.png: [testng] 11:12:09,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:12:09,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:09,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-06_11-12-09.log] [testng] 11:12:09,752 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ba9a2d7 - End of configuration. [testng] [2024-12-06 11:12:09,800] [pool-1-thread-2] Initializing /data/imagic/not read correctly/Zucchini_preview.png: [testng] 11:12:09,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:12:09,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:09,801 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-06_11-12-09.log] [testng] 11:12:09,802 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c0631d - End of configuration. [testng] [2024-12-06 11:12:13,152] [pool-1-thread-3] Initializing /data/imagic/not read correctly/Zucchini.dm2: [testng] [2024-12-06 11:12:13,351] [pool-1-thread-11] Initializing /data/pang/signed: [testng] [2024-12-06 11:12:13,570] [pool-1-thread-8] Initializing /data/pang/screen capture of metadata/tem_dm_general_info.png: [testng] [2024-12-06 11:12:13,609] [pool-1-thread-9] Initializing /data/imagic/Histiocyte in Skin Dermis.dm2: [testng] [2024-12-06 11:12:13,812] [pool-1-thread-6] Initializing /data/imagic/13008.dm2: [testng] [2024-12-06 11:12:14,011] [pool-1-thread-1] Initializing /data/imagic/not read correctly/Abeta Moon_preview.png: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 954, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 43 seconds Finished: SUCCESS