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Started by upstream project "BIOFORMATS-test-repo" build number 235 originally caused by: Started by upstream project "Trigger" build number 260 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins638941918808278054.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_36916_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] 02:08:48,785 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:08:48,787 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 02:08:48,787 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:08:48,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:08:48,788 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:08:48,788 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:08:48,789 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:08:48,789 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:08:48,789 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:08:48,790 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:08:48,790 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:08:48,791 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:08:48,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:08:48,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:08:49,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:08:49,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:08:49,030 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:08:49,030 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:08:49,030 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:08:49,031 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:08:49,031 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 02:08:49,032 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 02:08:49,032 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 243 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-26 02:08:49,046] [main] java.version = 11.0.16 [testng] 02:08:49,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:08:49,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:08:49,095 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-26_02-08-49.log] [testng] 02:08:49,096 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-26 02:08:49,099] [main] testng.directory = /data [testng] [2024-10-26 02:08:49,099] [main] testng.configDirectory = /config [testng] [2024-10-26 02:08:49,110] [main] testng.multiplier = 1.0 [testng] [2024-10-26 02:08:49,111] [main] testng.in-memory = false [testng] [2024-10-26 02:08:49,111] [main] testng.allow-missing = false [testng] [2024-10-26 02:08:49,111] [main] user.language = en [testng] [2024-10-26 02:08:49,111] [main] user.country = ${user.country} [testng] [2024-10-26 02:08:49,111] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-26 02:08:54,907] [main] ---------------------------------------- [testng] [2024-10-26 02:08:54,907] [main] Total files: 20 [testng] [2024-10-26 02:08:54,907] [main] Scan time: 5.795 s (289 ms/file) [testng] [2024-10-26 02:08:54,907] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-26 02:09:00,817] [pool-1-thread-1] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] 02:09:00,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:09:00,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:00,820 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-26_02-09-00.log] [testng] 02:09:00,821 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b76050f - End of configuration. [testng] [2024-10-26 02:09:01,031] [pool-1-thread-12] Initializing /data/strand/Series1_A.mrc: [testng] 02:09:01,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:09:01,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:01,155 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-26_02-09-01.log] [testng] 02:09:01,156 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2715c772 - End of configuration. [testng] [2024-10-26 02:09:02,254] [pool-1-thread-11] Initializing /data/ascb/c191.st: [testng] 02:09:02,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:09:02,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:02,255 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-26_02-09-02.log] [testng] 02:09:02,256 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3182ffa0 - End of configuration. [testng] [2024-10-26 02:09:02,543] [pool-1-thread-10] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] 02:09:02,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:09:02,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:02,544 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-26_02-09-02.log] [testng] 02:09:02,544 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14d9a16d - End of configuration. [testng] [2024-10-26 02:09:02,843] [pool-1-thread-9] Initializing /data/dan/two.mrc: [testng] 02:09:02,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:09:02,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:02,844 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-26_02-09-02.log] [testng] 02:09:02,845 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29311de - End of configuration. [testng] [2024-10-26 02:09:03,345] [pool-1-thread-8] Initializing /data/ascb/cfa1071.mrc: [testng] 02:09:03,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:09:03,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:03,485 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-26_02-09-03.log] [testng] 02:09:03,486 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3224cb70 - End of configuration. [testng] [2024-10-26 02:09:03,777] [pool-1-thread-7] Initializing /data/ascb/c191ali.mrc: [testng] 02:09:03,777 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:09:03,777 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:03,778 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-26_02-09-03.log] [testng] 02:09:03,779 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d3968fb - End of configuration. [testng] [2024-10-26 02:09:04,035] [pool-1-thread-6] Initializing /data/jcb/thyl-apr23-4.rec: [testng] 02:09:04,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:09:04,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:04,036 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-26_02-09-04.log] [testng] 02:09:04,036 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67d52c4b - End of configuration. [testng] [2024-10-26 02:09:04,208] [pool-1-thread-5] Initializing /data/samples/1160.mrc: [testng] 02:09:04,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:09:04,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:04,208 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-26_02-09-04.log] [testng] 02:09:04,209 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45d4b692 - End of configuration. [testng] [2024-10-26 02:09:04,370] [pool-1-thread-4] Initializing /data/samples/golgi.mrc: [testng] 02:09:04,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:09:04,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:04,371 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-26_02-09-04.log] [testng] 02:09:04,372 |-INFO in ch.qos.logback.core.sift.SiftProcessor@339e99d1 - End of configuration. [testng] [2024-10-26 02:09:04,887] [pool-1-thread-3] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 02:09:04,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:09:04,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:04,888 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-26_02-09-04.log] [testng] 02:09:04,888 |-INFO in ch.qos.logback.core.sift.SiftProcessor@115d85fe - End of configuration. [testng] [2024-10-26 02:09:07,405] [pool-1-thread-2] Initializing /data/jcb/thylakoid5.rec: [testng] 02:09:07,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:09:07,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:07,406 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-26_02-09-07.log] [testng] 02:09:07,406 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a83fbe7 - End of configuration. [testng] [2024-10-26 02:09:11,654] [pool-1-thread-3] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] [2024-10-26 02:09:11,843] [pool-1-thread-10] Initializing /data/ticket-10073/wtjoin4.rec: [testng] [2024-10-26 02:09:12,017] [pool-1-thread-4] Initializing /data/ascb/514_9903.mrc: [testng] [2024-10-26 02:09:12,242] [pool-1-thread-6] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] [2024-10-26 02:09:12,460] [pool-1-thread-7] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] [2024-10-26 02:09:12,680] [pool-1-thread-11] Initializing /data/dan/three.mrc: [testng] [2024-10-26 02:09:12,886] [pool-1-thread-2] Initializing /data/dan/one.mrc: [testng] [2024-10-26 02:09:13,855] [pool-1-thread-9] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 33 seconds Finished: SUCCESS