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Started by upstream project "BIOFORMATS-test-repo" build number 384 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins7525040653395833374.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_60742_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] 12:54:28,152 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 12:54:28,153 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 12:54:28,153 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:54:28,154 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:54:28,154 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:54:28,155 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:54:28,155 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 12:54:28,155 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:54:28,155 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:54:28,156 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:54:28,156 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:54:28,156 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:54:28,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:54:28,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:54:28,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:54:28,342 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:54:28,347 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:54:28,347 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:54:28,347 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:54:28,347 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:54:28,348 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 12:54:28,348 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 12:54:28,348 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 193 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-19 12:54:28,358] [main] java.version = 17.0.2 [testng] 12:54:28,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:54:28,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:54:28,402 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-19_12-54-28.log] [testng] 12:54:28,403 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-19 12:54:28,405] [main] testng.directory = /data [testng] [2025-03-19 12:54:28,405] [main] testng.configDirectory = /config [testng] [2025-03-19 12:54:28,414] [main] testng.multiplier = 1.0 [testng] [2025-03-19 12:54:28,414] [main] testng.in-memory = false [testng] [2025-03-19 12:54:28,414] [main] testng.allow-missing = false [testng] [2025-03-19 12:54:28,414] [main] user.language = en [testng] [2025-03-19 12:54:28,415] [main] user.country = ${user.country} [testng] [2025-03-19 12:54:28,415] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-19 12:54:40,840] [main] ---------------------------------------- [testng] [2025-03-19 12:54:40,840] [main] Total files: 20 [testng] [2025-03-19 12:54:40,840] [main] Scan time: 12.425 s (621 ms/file) [testng] [2025-03-19 12:54:40,840] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-19 12:54:49,610] [pool-1-thread-1] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] 12:54:49,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:54:49,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:54:49,612 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-19_12-54-49.log] [testng] 12:54:49,612 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34e163ce - End of configuration. [testng] [2025-03-19 12:54:50,010] [pool-1-thread-12] Initializing /data/ascb/cfa1071.mrc: [testng] 12:54:50,010 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:54:50,010 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:54:50,011 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-19_12-54-50.log] [testng] 12:54:50,012 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fb92bee - End of configuration. [testng] [2025-03-19 12:54:50,363] [pool-1-thread-11] Initializing /data/ascb/514_9903.mrc: [testng] 12:54:50,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:54:50,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:54:50,364 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-19_12-54-50.log] [testng] 12:54:50,365 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b75f68c - End of configuration. [testng] [2025-03-19 12:54:50,771] [pool-1-thread-10] Initializing /data/ascb/c191.st: [testng] 12:54:50,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:54:50,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:54:50,773 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-19_12-54-50.log] [testng] 12:54:50,773 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37ce8782 - End of configuration. [testng] [2025-03-19 12:54:51,157] [pool-1-thread-9] Initializing /data/jcb/thylakoid5.rec: [testng] 12:54:51,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:54:51,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:54:51,158 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-19_12-54-51.log] [testng] 12:54:51,158 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74a44f6c - End of configuration. [testng] [2025-03-19 12:54:51,553] [pool-1-thread-8] Initializing /data/samples/1160.mrc: [testng] 12:54:51,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:54:51,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:54:51,554 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-19_12-54-51.log] [testng] 12:54:51,555 |-INFO in ch.qos.logback.core.sift.SiftProcessor@719a1e83 - End of configuration. [testng] [2025-03-19 12:54:51,957] [pool-1-thread-7] Initializing /data/dan/two.mrc: [testng] 12:54:51,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:54:51,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:54:51,958 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-19_12-54-51.log] [testng] 12:54:51,958 |-INFO in ch.qos.logback.core.sift.SiftProcessor@99aa2e8 - End of configuration. [testng] [2025-03-19 12:54:52,376] [pool-1-thread-6] Initializing /data/ticket-10073/wtjoin4.rec: [testng] 12:54:52,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:54:52,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:54:52,377 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-19_12-54-52.log] [testng] 12:54:52,378 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76110ba6 - End of configuration. [testng] [2025-03-19 12:54:52,923] [pool-1-thread-5] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] 12:54:52,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:54:52,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:54:52,924 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-19_12-54-52.log] [testng] 12:54:52,924 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a2cce9f - End of configuration. [testng] [2025-03-19 12:54:53,330] [pool-1-thread-4] Initializing /data/samples/golgi.mrc: [testng] 12:54:53,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:54:53,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:54:53,331 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-19_12-54-53.log] [testng] 12:54:53,332 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38577afe - End of configuration. [testng] [2025-03-19 12:54:53,770] [pool-1-thread-3] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 12:54:53,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:54:53,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:54:53,771 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-19_12-54-53.log] [testng] 12:54:53,772 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f564c66 - End of configuration. [testng] [2025-03-19 12:54:54,144] [pool-1-thread-2] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 12:54:54,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:54:54,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:54:54,145 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-19_12-54-54.log] [testng] 12:54:54,145 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1adfcd6f - End of configuration. [testng] [2025-03-19 12:54:59,633] [pool-1-thread-3] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] [2025-03-19 12:54:59,998] [pool-1-thread-2] Initializing /data/jcb/thyl-apr23-4.rec: [testng] [2025-03-19 12:55:00,528] [pool-1-thread-1] Initializing /data/ascb/c191ali.mrc: [testng] [2025-03-19 12:55:01,120] [pool-1-thread-4] Initializing /data/strand/Series1_A.mrc: [testng] [2025-03-19 12:55:01,821] [pool-1-thread-6] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] [2025-03-19 12:55:02,505] [pool-1-thread-10] Initializing /data/dan/three.mrc: [testng] [2025-03-19 12:55:03,154] [pool-1-thread-9] Initializing /data/dan/one.mrc: [testng] [2025-03-19 12:55:03,880] [pool-1-thread-5] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 47 seconds Finished: SUCCESS