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Started by upstream project "BIOFORMATS-test-repo" build number 20 originally caused by: Started by upstream project "Trigger" build number 23 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins10122940364215354353.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_2492_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] 01:36:57,681 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:36:57,683 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:36:57,683 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:36:57,684 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:36:57,684 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:36:57,685 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:36:57,685 |-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] 01:36:57,685 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:36:57,685 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:36:57,686 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:36:57,686 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:36:57,686 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:36:57,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:36:57,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:36:57,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:36:57,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:36:57,877 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:36:57,878 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:36:57,878 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:36:57,879 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:36:57,879 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:36:57,879 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:36:57,879 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 194 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-02 01:36:57,888] [main] java.version = 11.0.16 [testng] 01:36:57,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:36:57,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:57,932 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-02_01-36-57.log] [testng] 01:36:57,934 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-04-02 01:36:57,936] [main] testng.directory = /data [testng] [2024-04-02 01:36:57,936] [main] testng.configDirectory = /config [testng] [2024-04-02 01:36:57,946] [main] testng.multiplier = 1.0 [testng] [2024-04-02 01:36:57,947] [main] testng.in-memory = false [testng] [2024-04-02 01:36:57,947] [main] testng.allow-missing = false [testng] [2024-04-02 01:36:57,947] [main] user.language = en [testng] [2024-04-02 01:36:57,947] [main] user.country = ${user.country} [testng] [2024-04-02 01:36:57,947] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-02 01:36:59,146] [main] ---------------------------------------- [testng] [2024-04-02 01:36:59,146] [main] Total files: 20 [testng] [2024-04-02 01:36:59,146] [main] Scan time: 1.199 s (59 ms/file) [testng] [2024-04-02 01:36:59,147] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-02 01:36:59,638] [pool-1-thread-1] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 01:36:59,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:36:59,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:59,641 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-02_01-36-59.log] [testng] 01:36:59,641 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40f98032 - End of configuration. [testng] [2024-04-02 01:36:59,663] [pool-1-thread-12] Initializing /data/ascb/c191.st: [testng] 01:36:59,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:36:59,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:59,666 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-02_01-36-59.log] [testng] 01:36:59,667 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ff4dbb3 - End of configuration. [testng] [2024-04-02 01:36:59,683] [pool-1-thread-11] Initializing /data/dan/two.mrc: [testng] 01:36:59,683 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:36:59,683 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:59,684 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-02_01-36-59.log] [testng] 01:36:59,685 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1516e912 - End of configuration. [testng] [2024-04-02 01:36:59,703] [pool-1-thread-10] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] 01:36:59,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:36:59,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:59,705 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-02_01-36-59.log] [testng] 01:36:59,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a18c3dd - End of configuration. [testng] [2024-04-02 01:36:59,720] [pool-1-thread-9] Initializing /data/samples/golgi.mrc: [testng] 01:36:59,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:36:59,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:59,721 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-02_01-36-59.log] [testng] 01:36:59,721 |-INFO in ch.qos.logback.core.sift.SiftProcessor@141e7d0c - End of configuration. [testng] [2024-04-02 01:36:59,785] [pool-1-thread-8] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] 01:36:59,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:36:59,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:59,786 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-02_01-36-59.log] [testng] 01:36:59,786 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2367fac4 - End of configuration. [testng] [2024-04-02 01:36:59,833] [pool-1-thread-7] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 01:36:59,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:36:59,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:59,834 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-02_01-36-59.log] [testng] 01:36:59,835 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7dc0ef37 - End of configuration. [testng] [2024-04-02 01:36:59,841] [pool-1-thread-6] Initializing /data/ascb/514_9903.mrc: [testng] 01:36:59,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:36:59,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:59,843 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-02_01-36-59.log] [testng] 01:36:59,844 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ab58e56 - End of configuration. [testng] [2024-04-02 01:36:59,857] [pool-1-thread-5] Initializing /data/jcb/thyl-apr23-4.rec: [testng] 01:36:59,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:36:59,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:59,859 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-02_01-36-59.log] [testng] 01:36:59,859 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3467d1f5 - End of configuration. [testng] [2024-04-02 01:36:59,892] [pool-1-thread-4] Initializing /data/jcb/thylakoid5.rec: [testng] 01:36:59,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:36:59,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:59,893 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-02_01-36-59.log] [testng] 01:36:59,894 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6647ca85 - End of configuration. [testng] [2024-04-02 01:36:59,911] [pool-1-thread-3] Initializing /data/dan/one.mrc: [testng] 01:36:59,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:36:59,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:59,912 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-02_01-36-59.log] [testng] 01:36:59,912 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61c5e6fa - End of configuration. [testng] [2024-04-02 01:36:59,940] [pool-1-thread-2] Initializing /data/ascb/cfa1071.mrc: [testng] 01:36:59,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:36:59,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:59,941 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-02_01-36-59.log] [testng] 01:36:59,942 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5300cb8d - End of configuration. [testng] [2024-04-02 01:37:01,131] [pool-1-thread-7] Initializing /data/ascb/c191ali.mrc: [testng] [2024-04-02 01:37:01,346] [pool-1-thread-8] Initializing /data/samples/1160.mrc: [testng] [2024-04-02 01:37:01,356] [pool-1-thread-9] Initializing /data/ticket-10073/wtjoin4.rec: [testng] [2024-04-02 01:37:01,372] [pool-1-thread-5] Initializing /data/strand/Series1_A.mrc: [testng] [2024-04-02 01:37:01,600] [pool-1-thread-12] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] [2024-04-02 01:37:01,610] [pool-1-thread-1] Initializing /data/dan/three.mrc: [testng] [2024-04-02 01:37:01,672] [pool-1-thread-4] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] [2024-04-02 01:37:01,928] [pool-1-thread-7] 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: 12 seconds Finished: SUCCESS