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Started by upstream project "BIOFORMATS-test-repo" build number 231 originally caused by: Started by upstream project "Trigger" build number 256 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins16050179209503406182.sh + '[' gatan-dm2 = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_36266_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] 02:27:00,793 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:27:00,794 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 02:27:00,794 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:27:00,795 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:27:00,796 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:27:00,796 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:27:00,797 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:27:00,797 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:27:00,797 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:27:00,798 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:27:00,798 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:27:00,798 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:27:00,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:27:00,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:27:00,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:27:00,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:27:01,003 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:27:01,004 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:27:01,004 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:27:01,004 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:27:01,004 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 02:27:01,005 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 02:27:01,005 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 208 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-22 02:27:01,014] [main] java.version = 11.0.16 [testng] 02:27:01,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:27:01,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:01,063 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-22_02-27-01.log] [testng] 02:27:01,064 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-22 02:27:01,067] [main] testng.directory = /data [testng] [2024-10-22 02:27:01,067] [main] testng.configDirectory = /config [testng] [2024-10-22 02:27:01,077] [main] testng.multiplier = 1.0 [testng] [2024-10-22 02:27:01,079] [main] testng.in-memory = false [testng] [2024-10-22 02:27:01,079] [main] testng.allow-missing = false [testng] [2024-10-22 02:27:01,079] [main] user.language = en [testng] [2024-10-22 02:27:01,079] [main] user.country = ${user.country} [testng] [2024-10-22 02:27:01,079] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-22 02:27:23,195] [main] ---------------------------------------- [testng] [2024-10-22 02:27:23,195] [main] Total files: 25 [testng] [2024-10-22 02:27:23,195] [main] Scan time: 22.116 s (884 ms/file) [testng] [2024-10-22 02:27:23,195] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 18 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-22 02:27:45,093] [pool-1-thread-1] Initializing /data/pang/DLMeD2E1_010500x03.dm2: [testng] 02:27:45,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:27:45,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:45,096 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-22_02-27-45.log] [testng] 02:27:45,097 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40a2e47a - End of configuration. [testng] [2024-10-22 02:27:45,386] [pool-1-thread-12] Initializing /data/imagic/not read correctly/Abeta Moon.dm2: [testng] 02:27:45,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:27:45,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:45,388 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-22_02-27-45.log] [testng] 02:27:45,388 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fad7e21 - End of configuration. [testng] [2024-10-22 02:27:45,674] [pool-1-thread-11] Initializing /data/pang/screen capture of metadata/tem_dm_microscope_info.png: [testng] 02:27:45,674 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:27:45,674 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:45,675 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-22_02-27-45.log] [testng] 02:27:45,675 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f2e700b - End of configuration. [testng] [2024-10-22 02:27:45,747] [pool-1-thread-10] Initializing /data/pang/10500x-o4: [testng] 02:27:45,747 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:27:45,747 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:45,748 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-22_02-27-45.log] [testng] 02:27:45,748 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5557bc09 - End of configuration. [testng] [2024-10-22 02:27:46,015] [pool-1-thread-9] Initializing /data/imagic/13008.dm2: [testng] 02:27:46,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:27:46,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:46,016 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-22_02-27-46.log] [testng] 02:27:46,016 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49262a98 - End of configuration. [testng] [2024-10-22 02:27:46,230] [pool-1-thread-8] Initializing /data/pang/grating025k.dm2: [testng] 02:27:46,231 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:27:46,231 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:46,231 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-22_02-27-46.log] [testng] 02:27:46,232 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e92145c - End of configuration. [testng] [2024-10-22 02:27:46,444] [pool-1-thread-7] Initializing /data/imagic/not read correctly/Abeta Moon_preview.png: [testng] 02:27:46,444 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:27:46,444 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:46,445 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-22_02-27-46.log] [testng] 02:27:46,446 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58a9cd8e - End of configuration. [testng] [2024-10-22 02:27:46,481] [pool-1-thread-6] Initializing /data/pang/signed: [testng] 02:27:46,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:27:46,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:46,482 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-22_02-27-46.log] [testng] 02:27:46,482 |-INFO in ch.qos.logback.core.sift.SiftProcessor@572e274c - End of configuration. [testng] [2024-10-22 02:27:46,705] [pool-1-thread-5] Initializing /data/imagic/Histiocyte in Skin Dermis.dm2: [testng] 02:27:46,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:27:46,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:46,706 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-22_02-27-46.log] [testng] 02:27:46,706 |-INFO in ch.qos.logback.core.sift.SiftProcessor@528347c3 - End of configuration. [testng] [2024-10-22 02:27:46,919] [pool-1-thread-4] Initializing /data/pang/screen capture of metadata/tem_dm_keywords_info.png: [testng] 02:27:46,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:27:46,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:46,920 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-22_02-27-46.log] [testng] 02:27:46,921 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7983f5e6 - End of configuration. [testng] [2024-10-22 02:27:46,963] [pool-1-thread-3] Initializing /data/imagic/not read correctly/Zucchini.dm2: [testng] 02:27:46,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:27:46,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:46,963 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-22_02-27-46.log] [testng] 02:27:46,964 |-INFO in ch.qos.logback.core.sift.SiftProcessor@678253fa - End of configuration. [testng] [2024-10-22 02:27:47,230] [pool-1-thread-2] Initializing /data/imagic/TEM 10118.dm2: [testng] 02:27:47,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:27:47,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:47,231 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-22_02-27-47.log] [testng] 02:27:47,231 |-INFO in ch.qos.logback.core.sift.SiftProcessor@230ddb93 - End of configuration. [testng] [2024-10-22 02:27:50,606] [pool-1-thread-4] Initializing /data/pang/unproc-auto: [testng] [2024-10-22 02:27:51,216] [pool-1-thread-11] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info2.png: [testng] [2024-10-22 02:27:51,314] [pool-1-thread-7] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info1.png: [testng] [2024-10-22 02:27:51,753] [pool-1-thread-12] Initializing /data/imagic/not read correctly/Zucchini_preview.png: [testng] [2024-10-22 02:27:52,869] [pool-1-thread-5] Initializing /data/imagic/1-1.dm2: [testng] [2024-10-22 02:27:55,314] [pool-1-thread-3] 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 0 seconds Finished: SUCCESS