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Started by upstream project "BIOFORMATS-test-repo" build number 77 originally caused by: Started by upstream project "Trigger" build number 85 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins16959203531812246454.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_11677_merge_ci -v /uod/idr/repos/curated/mrc:/data -v /uod/idr-scratch/merge-ci/curated/mrc:/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] 01:35:52,671 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:35:52,673 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:35:52,673 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:35:52,674 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:35:52,674 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:35:52,674 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:35:52,675 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:35:52,675 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:35:52,675 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:35:52,676 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:35:52,676 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:35:52,676 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:35:52,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:35:52,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:35:52,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:35:52,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:35:52,876 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:35:52,876 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:35:52,876 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:35:52,877 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:35:52,877 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:35:52,878 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:35:52,878 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 203 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-28 01:35:52,887] [main] java.version = 11.0.16 [testng] 01:35:52,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:35:52,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:35:52,935 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-28_01-35-52.log] [testng] 01:35:52,936 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-05-28 01:35:52,938] [main] testng.directory = /data [testng] [2024-05-28 01:35:52,939] [main] testng.configDirectory = /config [testng] [2024-05-28 01:35:52,949] [main] testng.multiplier = 1.0 [testng] [2024-05-28 01:35:52,951] [main] testng.in-memory = false [testng] [2024-05-28 01:35:52,951] [main] testng.allow-missing = false [testng] [2024-05-28 01:35:52,951] [main] user.language = en [testng] [2024-05-28 01:35:52,951] [main] user.country = ${user.country} [testng] [2024-05-28 01:35:52,951] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-28 01:35:54,057] [main] ---------------------------------------- [testng] [2024-05-28 01:35:54,057] [main] Total files: 20 [testng] [2024-05-28 01:35:54,058] [main] Scan time: 1.106 s (55 ms/file) [testng] [2024-05-28 01:35:54,058] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-28 01:35:54,507] [pool-1-thread-1] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 01:35:54,507 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:35:54,507 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:35:54,509 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-28_01-35-54.log] [testng] 01:35:54,509 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ea475b8 - End of configuration. [testng] [2024-05-28 01:35:54,530] [pool-1-thread-12] Initializing /data/ascb/c191.st: [testng] 01:35:54,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:35:54,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:35:54,532 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-28_01-35-54.log] [testng] 01:35:54,532 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6535a1df - End of configuration. [testng] [2024-05-28 01:35:54,546] [pool-1-thread-11] Initializing /data/dan/two.mrc: [testng] 01:35:54,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:35:54,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:35:54,548 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-28_01-35-54.log] [testng] 01:35:54,548 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66f2c1ec - End of configuration. [testng] [2024-05-28 01:35:54,565] [pool-1-thread-10] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] 01:35:54,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:35:54,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:35:54,566 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-28_01-35-54.log] [testng] 01:35:54,567 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3df9a0a6 - End of configuration. [testng] [2024-05-28 01:35:54,588] [pool-1-thread-9] Initializing /data/samples/golgi.mrc: [testng] 01:35:54,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:35:54,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:35:54,627 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-28_01-35-54.log] [testng] 01:35:54,628 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7426a972 - End of configuration. [testng] [2024-05-28 01:35:54,710] [pool-1-thread-8] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] 01:35:54,710 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:35:54,710 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:35:54,711 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-28_01-35-54.log] [testng] 01:35:54,712 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c6ce2c6 - End of configuration. [testng] [2024-05-28 01:35:54,724] [pool-1-thread-7] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 01:35:54,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:35:54,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:35:54,725 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-28_01-35-54.log] [testng] 01:35:54,725 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ad4fb32 - End of configuration. [testng] [2024-05-28 01:35:54,733] [pool-1-thread-6] Initializing /data/ascb/514_9903.mrc: [testng] 01:35:54,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:35:54,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:35:54,734 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-28_01-35-54.log] [testng] 01:35:54,734 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ca0e0b5 - End of configuration. [testng] [2024-05-28 01:35:54,763] [pool-1-thread-5] Initializing /data/jcb/thyl-apr23-4.rec: [testng] 01:35:54,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:35:54,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:35:54,765 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-28_01-35-54.log] [testng] 01:35:54,766 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42bcb890 - End of configuration. [testng] [2024-05-28 01:35:54,789] [pool-1-thread-4] Initializing /data/jcb/thylakoid5.rec: [testng] 01:35:54,789 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:35:54,789 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:35:54,790 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-28_01-35-54.log] [testng] 01:35:54,790 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b77fe1a - End of configuration. [testng] [2024-05-28 01:35:54,807] [pool-1-thread-3] Initializing /data/dan/one.mrc: [testng] 01:35:54,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:35:54,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:35:54,808 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-28_01-35-54.log] [testng] 01:35:54,809 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d3a6287 - End of configuration. [testng] [2024-05-28 01:35:54,830] [pool-1-thread-2] Initializing /data/ascb/cfa1071.mrc: [testng] 01:35:54,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:35:54,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:35:54,831 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-28_01-35-54.log] [testng] 01:35:54,832 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6be4386f - End of configuration. [testng] [2024-05-28 01:35:56,153] [pool-1-thread-7] Initializing /data/ascb/c191ali.mrc: [testng] [2024-05-28 01:35:56,259] [pool-1-thread-1] Initializing /data/samples/1160.mrc: [testng] [2024-05-28 01:35:56,279] [pool-1-thread-9] Initializing /data/ticket-10073/wtjoin4.rec: [testng] [2024-05-28 01:35:56,293] [pool-1-thread-8] Initializing /data/strand/Series1_A.mrc: [testng] [2024-05-28 01:35:56,433] [pool-1-thread-5] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] [2024-05-28 01:35:56,447] [pool-1-thread-12] Initializing /data/dan/three.mrc: [testng] [2024-05-28 01:35:56,580] [pool-1-thread-4] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] [2024-05-28 01:35:56,755] [pool-1-thread-3] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 14 seconds Finished: SUCCESS