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Started by upstream project "BIOFORMATS-test-repo" build number 40 originally caused by: Started by upstream project "Trigger" build number 46 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins16109410263926005479.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_5608_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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 01:36:59,083 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:36:59,084 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:36:59,084 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:36:59,085 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:36:59,085 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:36:59,086 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:36:59,086 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:36:59,086 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:36:59,086 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:36:59,087 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:36:59,087 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:36:59,087 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:36:59,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:36:59,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:36:59,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:36:59,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:36:59,267 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:36:59,268 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:36:59,268 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:36:59,268 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:36:59,268 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:36:59,269 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:36:59,269 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 183 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-21 01:36:59,277] [main] java.version = 17.0.2 [testng] 01:36:59,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:36:59,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:59,319 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-21_01-36-59.log] [testng] 01:36:59,321 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-04-21 01:36:59,322] [main] testng.directory = /data [testng] [2024-04-21 01:36:59,323] [main] testng.configDirectory = /config [testng] [2024-04-21 01:36:59,331] [main] testng.multiplier = 1.0 [testng] [2024-04-21 01:36:59,332] [main] testng.in-memory = false [testng] [2024-04-21 01:36:59,332] [main] testng.allow-missing = false [testng] [2024-04-21 01:36:59,332] [main] user.language = en [testng] [2024-04-21 01:36:59,332] [main] user.country = ${user.country} [testng] [2024-04-21 01:36:59,332] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-21 01:37:00,415] [main] ---------------------------------------- [testng] [2024-04-21 01:37:00,415] [main] Total files: 20 [testng] [2024-04-21 01:37:00,415] [main] Scan time: 1.083 s (54 ms/file) [testng] [2024-04-21 01:37:00,415] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-21 01:37:00,873] [pool-1-thread-1] Initializing /data/ticket-10073/wtjoin4.rec: [testng] 01:37:00,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:37:00,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:00,874 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-21_01-37-00.log] [testng] 01:37:00,874 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32383a8f - End of configuration. [testng] [2024-04-21 01:37:00,892] [pool-1-thread-12] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 01:37:00,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:37:00,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:00,894 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-21_01-37-00.log] [testng] 01:37:00,895 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6742228a - End of configuration. [testng] [2024-04-21 01:37:00,917] [pool-1-thread-11] Initializing /data/dan/three.mrc: [testng] 01:37:00,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:37:00,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:00,918 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-21_01-37-00.log] [testng] 01:37:00,919 |-INFO in ch.qos.logback.core.sift.SiftProcessor@501ff8a5 - End of configuration. [testng] [2024-04-21 01:37:00,936] [pool-1-thread-10] Initializing /data/ascb/cfa1071.mrc: [testng] 01:37:00,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:37:00,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:00,937 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-21_01-37-00.log] [testng] 01:37:00,938 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46233177 - End of configuration. [testng] [2024-04-21 01:37:00,958] [pool-1-thread-9] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 01:37:00,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:37:00,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:00,960 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-21_01-37-00.log] [testng] 01:37:00,961 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7eec7a4b - End of configuration. [testng] [2024-04-21 01:37:00,972] [pool-1-thread-8] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] 01:37:00,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:37:00,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:00,973 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-21_01-37-00.log] [testng] 01:37:00,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@631a25e6 - End of configuration. [testng] [2024-04-21 01:37:00,995] [pool-1-thread-7] Initializing /data/strand/Series1_A.mrc: [testng] 01:37:00,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:37:00,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:00,999 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-21_01-37-00.log] [testng] 01:37:01,005 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e83da82 - End of configuration. [testng] [2024-04-21 01:37:01,028] [pool-1-thread-6] Initializing /data/jcb/thylakoid5.rec: [testng] 01:37:01,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:37:01,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:01,029 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-21_01-37-01.log] [testng] 01:37:01,029 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a334a43 - End of configuration. [testng] [2024-04-21 01:37:01,094] [pool-1-thread-5] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 01:37:01,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:37:01,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:01,097 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-21_01-37-01.log] [testng] 01:37:01,097 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1891e8b7 - End of configuration. [testng] [2024-04-21 01:37:01,119] [pool-1-thread-4] Initializing /data/ascb/c191.st: [testng] 01:37:01,119 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:37:01,119 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:01,120 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-21_01-37-01.log] [testng] 01:37:01,120 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f1bfb64 - End of configuration. [testng] [2024-04-21 01:37:01,132] [pool-1-thread-3] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] 01:37:01,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:37:01,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:01,133 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-21_01-37-01.log] [testng] 01:37:01,134 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43043779 - End of configuration. [testng] [2024-04-21 01:37:01,144] [pool-1-thread-2] Initializing /data/samples/golgi.mrc: [testng] 01:37:01,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:37:01,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:01,145 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-21_01-37-01.log] [testng] 01:37:01,145 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fdc01c3 - End of configuration. [testng] [2024-04-21 01:37:02,393] [pool-1-thread-9] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] [2024-04-21 01:37:02,407] [pool-1-thread-2] Initializing /data/dan/two.mrc: [testng] [2024-04-21 01:37:02,425] [pool-1-thread-12] Initializing /data/ascb/514_9903.mrc: [testng] [2024-04-21 01:37:02,436] [pool-1-thread-3] Initializing /data/ascb/c191ali.mrc: [testng] [2024-04-21 01:37:02,447] [pool-1-thread-5] Initializing /data/samples/1160.mrc: [testng] [2024-04-21 01:37:02,461] [pool-1-thread-8] Initializing /data/dan/one.mrc: [testng] [2024-04-21 01:37:02,717] [pool-1-thread-4] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] [2024-04-21 01:37:02,873] [pool-1-thread-6] Initializing /data/jcb/thyl-apr23-4.rec: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 13 seconds Finished: SUCCESS