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Started by upstream project "BIOFORMATS-test-repo" build number 296 originally caused by: Started by upstream project "Trigger" build number 315 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins12418229473699678212.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_46798_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 test-automated: [testng] File leak detector installed [testng] 01:36:54,233 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:36:54,235 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 01:36:54,235 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:36:54,236 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:36:54,236 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:36:54,236 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:36:54,237 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:36:54,237 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:36:54,237 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:36:54,237 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:36:54,238 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:36:54,238 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:36:54,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:36:54,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:36:54,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:36:54,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:36:54,498 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:36:54,498 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:36:54,498 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:36:54,499 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:36:54,499 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 01:36:54,500 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 01:36:54,500 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 263 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-20 01:36:54,509] [main] java.version = 1.8.0_342 [testng] 01:36:54,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:36:54,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:54,558 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-20_01-36-54.log] [testng] 01:36:54,559 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-20 01:36:54,561] [main] testng.directory = /data [testng] [2024-12-20 01:36:54,561] [main] testng.configDirectory = /config [testng] [2024-12-20 01:36:54,574] [main] testng.multiplier = 1.0 [testng] [2024-12-20 01:36:54,574] [main] testng.in-memory = false [testng] [2024-12-20 01:36:54,574] [main] testng.allow-missing = false [testng] [2024-12-20 01:36:54,574] [main] user.language = en [testng] [2024-12-20 01:36:54,574] [main] user.country = ${user.country} [testng] [2024-12-20 01:36:54,574] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-20 01:37:04,481] [main] ---------------------------------------- [testng] [2024-12-20 01:37:04,481] [main] Total files: 20 [testng] [2024-12-20 01:37:04,481] [main] Scan time: 9.906 s (495 ms/file) [testng] [2024-12-20 01:37:04,482] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-20 01:37:15,072] [pool-1-thread-1] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 01:37:15,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:37:15,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:15,073 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-20_01-37-15.log] [testng] 01:37:15,073 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23d92c20 - End of configuration. [testng] [2024-12-20 01:37:15,587] [pool-1-thread-12] Initializing /data/samples/golgi.mrc: [testng] 01:37:15,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:37:15,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:15,588 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-20_01-37-15.log] [testng] 01:37:15,589 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ceb6841 - End of configuration. [testng] [2024-12-20 01:37:16,090] [pool-1-thread-11] Initializing /data/jcb/thylakoid5.rec: [testng] 01:37:16,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:37:16,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:16,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-20_01-37-16.log] [testng] 01:37:16,091 |-INFO in ch.qos.logback.core.sift.SiftProcessor@160efbbf - End of configuration. [testng] [2024-12-20 01:37:16,634] [pool-1-thread-10] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] 01:37:16,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:37:16,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:16,635 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-20_01-37-16.log] [testng] 01:37:16,635 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44523ffc - End of configuration. [testng] [2024-12-20 01:37:17,065] [pool-1-thread-9] Initializing /data/jcb/thyl-apr23-4.rec: [testng] 01:37:17,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:37:17,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:17,066 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-20_01-37-17.log] [testng] 01:37:17,067 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e7163a4 - End of configuration. [testng] [2024-12-20 01:37:17,647] [pool-1-thread-8] Initializing /data/ticket-10073/wtjoin4.rec: [testng] 01:37:17,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:37:17,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:17,649 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-20_01-37-17.log] [testng] 01:37:17,649 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79558c21 - End of configuration. [testng] [2024-12-20 01:37:18,123] [pool-1-thread-7] Initializing /data/ascb/c191.st: [testng] 01:37:18,123 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:37:18,123 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:18,124 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-20_01-37-18.log] [testng] 01:37:18,124 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6dd2355b - End of configuration. [testng] [2024-12-20 01:37:18,636] [pool-1-thread-6] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] 01:37:18,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:37:18,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:18,637 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-20_01-37-18.log] [testng] 01:37:18,637 |-INFO in ch.qos.logback.core.sift.SiftProcessor@139f3026 - End of configuration. [testng] [2024-12-20 01:37:19,204] [pool-1-thread-5] Initializing /data/dan/three.mrc: [testng] 01:37:19,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:37:19,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:19,207 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-20_01-37-19.log] [testng] 01:37:19,207 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e2e2465 - End of configuration. [testng] [2024-12-20 01:37:19,683] [pool-1-thread-4] Initializing /data/ascb/514_9903.mrc: [testng] 01:37:19,683 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:37:19,683 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:19,684 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-20_01-37-19.log] [testng] 01:37:19,684 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6661c090 - End of configuration. [testng] [2024-12-20 01:37:20,139] [pool-1-thread-3] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] 01:37:20,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:37:20,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:20,140 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-20_01-37-20.log] [testng] 01:37:20,158 |-INFO in ch.qos.logback.core.sift.SiftProcessor@390fffa0 - End of configuration. [testng] [2024-12-20 01:37:20,573] [pool-1-thread-2] Initializing /data/ascb/c191ali.mrc: [testng] 01:37:20,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:37:20,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:20,574 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-20_01-37-20.log] [testng] 01:37:20,575 |-INFO in ch.qos.logback.core.sift.SiftProcessor@391aa6a6 - End of configuration. [testng] [2024-12-20 01:37:27,981] [pool-1-thread-1] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] [2024-12-20 01:37:28,420] [pool-1-thread-9] Initializing /data/dan/two.mrc: [testng] [2024-12-20 01:37:28,936] [pool-1-thread-2] Initializing /data/dan/one.mrc: [testng] [2024-12-20 01:37:29,306] [pool-1-thread-3] Initializing /data/ascb/cfa1071.mrc: [testng] [2024-12-20 01:37:29,759] [pool-1-thread-12] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] [2024-12-20 01:37:30,180] [pool-1-thread-11] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] [2024-12-20 01:37:30,550] [pool-1-thread-10] Initializing /data/strand/Series1_A.mrc: [testng] [2024-12-20 01:37:30,911] [pool-1-thread-7] Initializing /data/samples/1160.mrc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 50 seconds Finished: SUCCESS