Started by upstream project "BIOFORMATS-test-repo" build number 245 originally caused by: Started by upstream project "Trigger" build number 269 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins13930874025387430386.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_38556_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 -Duser.language=fr -Duser.country=FR 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] 03:30:07,672 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:30:07,674 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 03:30:07,674 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:30:07,675 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:30:07,675 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:30:07,675 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:30:07,676 |-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] 03:30:07,676 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:30:07,676 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:30:07,676 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:30:07,676 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:30:07,676 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:30:07,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:30:07,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:30:07,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:30:07,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:30:07,926 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:30:07,926 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:30:07,926 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:30:07,927 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:30:07,927 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 03:30:07,927 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 03:30:07,927 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 251 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-04 03:30:07,938] [main] java.version = 1.8.0_342 [testng] 03:30:07,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:30:07,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:30:07,991 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-04_03-30-07.log] [testng] 03:30:07,993 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-04 03:30:07,995] [main] testng.directory = /data [testng] [2024-11-04 03:30:07,995] [main] testng.configDirectory = /config [testng] [2024-11-04 03:30:08,006] [main] testng.multiplier = 1.0 [testng] [2024-11-04 03:30:08,007] [main] testng.in-memory = false [testng] [2024-11-04 03:30:08,007] [main] testng.allow-missing = false [testng] [2024-11-04 03:30:08,007] [main] user.language = fr [testng] [2024-11-04 03:30:08,007] [main] user.country = FR [testng] [2024-11-04 03:30:08,007] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-04 03:30:34,844] [main] ---------------------------------------- [testng] [2024-11-04 03:30:34,844] [main] Total files: 20 [testng] [2024-11-04 03:30:34,845] [main] Scan time: 26.837 s (1341 ms/file) [testng] [2024-11-04 03:30:34,845] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-04 03:31:04,469] [pool-1-thread-1] Initializing /data/ascb/514_9903.mrc: [testng] 03:31:04,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:31:04,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:31:04,470 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-04_03-31-04.log] [testng] 03:31:04,470 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e7b9e09 - End of configuration. [testng] [2024-11-04 03:31:06,069] [pool-1-thread-12] Initializing /data/samples/golgi.mrc: [testng] 03:31:06,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:31:06,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:31:06,070 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-04_03-31-06.log] [testng] 03:31:06,070 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22903f9f - End of configuration. [testng] [2024-11-04 03:31:06,899] [pool-1-thread-11] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] 03:31:06,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:31:06,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:31:06,900 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-04_03-31-06.log] [testng] 03:31:06,900 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d363b1a - End of configuration. [testng] [2024-11-04 03:31:07,446] [pool-1-thread-10] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] 03:31:07,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:31:07,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:31:07,447 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-04_03-31-07.log] [testng] 03:31:07,447 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f560006 - End of configuration. [testng] [2024-11-04 03:31:08,412] [pool-1-thread-9] Initializing /data/samples/1160.mrc: [testng] 03:31:08,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:31:08,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:31:08,413 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-04_03-31-08.log] [testng] 03:31:08,413 |-INFO in ch.qos.logback.core.sift.SiftProcessor@141df20c - End of configuration. [testng] [2024-11-04 03:31:09,917] [pool-1-thread-8] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 03:31:09,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:31:09,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:31:09,918 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-04_03-31-09.log] [testng] 03:31:09,919 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56bc7b84 - End of configuration. [testng] [2024-11-04 03:31:11,922] [pool-1-thread-7] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 03:31:11,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:31:11,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:31:11,923 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-04_03-31-11.log] [testng] 03:31:11,923 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b13e13f - End of configuration. [testng] [2024-11-04 03:31:13,528] [pool-1-thread-6] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 03:31:13,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:31:13,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:31:13,529 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-04_03-31-13.log] [testng] 03:31:13,529 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9673fea - End of configuration. [testng] [2024-11-04 03:31:14,706] [pool-1-thread-5] Initializing /data/jcb/thyl-apr23-4.rec: [testng] 03:31:14,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:31:14,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:31:14,707 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-04_03-31-14.log] [testng] 03:31:14,707 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bb0f086 - End of configuration. [testng] [2024-11-04 03:31:15,534] [pool-1-thread-4] Initializing /data/ascb/cfa1071.mrc: [testng] 03:31:15,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:31:15,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:31:15,552 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-04_03-31-15.log] [testng] 03:31:15,552 |-INFO in ch.qos.logback.core.sift.SiftProcessor@460d039f - End of configuration. [testng] [2024-11-04 03:31:16,449] [pool-1-thread-3] Initializing /data/dan/one.mrc: [testng] 03:31:16,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:31:16,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:31:16,450 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-04_03-31-16.log] [testng] 03:31:16,465 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d09d37b - End of configuration. [testng] [2024-11-04 03:31:17,796] [pool-1-thread-2] Initializing /data/dan/two.mrc: [testng] 03:31:17,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:31:17,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:31:17,797 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-04_03-31-17.log] [testng] 03:31:17,797 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50557eb8 - End of configuration. [testng] [2024-11-04 03:31:36,651] [pool-1-thread-7] Initializing /data/dan/three.mrc: [testng] [2024-11-04 03:31:37,029] [pool-1-thread-11] Initializing /data/strand/Series1_A.mrc: [testng] [2024-11-04 03:31:38,086] [pool-1-thread-10] Initializing /data/ticket-10073/wtjoin4.rec: [testng] [2024-11-04 03:31:39,655] [pool-1-thread-6] Initializing /data/jcb/thylakoid5.rec: [testng] [2024-11-04 03:31:40,864] [pool-1-thread-12] Initializing /data/ascb/c191ali.mrc: [testng] [2024-11-04 03:31:41,800] [pool-1-thread-8] Initializing /data/ascb/c191.st: [testng] [2024-11-04 03:31:43,382] [pool-1-thread-5] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] [2024-11-04 03:31:44,253] [pool-1-thread-2] 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: 1 minute 57 seconds Finished: SUCCESS