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Started by upstream project "BIOFORMATS-test-repo" build number 5 originally caused by: Started by upstream project "Trigger" build number 6 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/jenkins11514633306571008599.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_686_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] 00:46:53,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:46:53,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:46:53,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:46:53,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:46:53,858 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:46:53,858 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:46:53,858 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:46:53,859 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:46:53,859 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5c30a9b0 - End of configuration. [testng] 00:46:53,860 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@7a69b07 - Registering current configuration as safe fallback point [testng] 00:46:53,860 |-INFO in ch.qos.logback.classic.util.ContextInitializer@5e82df6a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 394 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-18 00:46:53,870] [main] java.version = 1.8.0_342 [testng] 00:46:53,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:46:53,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:53,923 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-18_00-46-53.log] [testng] 00:46:53,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-03-18 00:46:53,927] [main] testng.directory = /data [testng] [2024-03-18 00:46:53,927] [main] testng.configDirectory = /config [testng] [2024-03-18 00:46:54,445] [main] testng.multiplier = 1.0 [testng] [2024-03-18 00:46:54,445] [main] testng.in-memory = false [testng] [2024-03-18 00:46:54,445] [main] testng.allow-missing = false [testng] [2024-03-18 00:46:54,445] [main] user.language = fr [testng] [2024-03-18 00:46:54,445] [main] user.country = FR [testng] [2024-03-18 00:46:54,445] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-03-18 00:46:58,488] [main] ---------------------------------------- [testng] [2024-03-18 00:46:58,489] [main] Total files: 20 [testng] [2024-03-18 00:46:58,489] [main] Scan time: 4.042 s (202 ms/file) [testng] [2024-03-18 00:46:58,489] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-18 00:47:02,313] [pool-1-thread-1] Initializing /data/ascb/c191.st: [testng] 00:47:02,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:47:02,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:02,314 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-18_00-47-02.log] [testng] 00:47:02,315 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ca68aa6 - End of configuration. [testng] [2024-03-18 00:47:02,483] [pool-1-thread-12] Initializing /data/dan/one.mrc: [testng] 00:47:02,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:47:02,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:02,484 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-18_00-47-02.log] [testng] 00:47:02,485 |-INFO in ch.qos.logback.core.sift.SiftProcessor@553c8196 - End of configuration. [testng] [2024-03-18 00:47:02,669] [pool-1-thread-11] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 00:47:02,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:47:02,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:02,681 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-18_00-47-02.log] [testng] 00:47:02,682 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d218b63 - End of configuration. [testng] [2024-03-18 00:47:02,807] [pool-1-thread-10] Initializing /data/ascb/c191ali.mrc: [testng] 00:47:02,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:47:02,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:02,808 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-18_00-47-02.log] [testng] 00:47:02,809 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18f73a37 - End of configuration. [testng] [2024-03-18 00:47:02,981] [pool-1-thread-9] Initializing /data/strand/Series1_A.mrc: [testng] 00:47:02,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:47:02,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:02,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-18_00-47-02.log] [testng] 00:47:02,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5efb7803 - End of configuration. [testng] [2024-03-18 00:47:03,146] [pool-1-thread-8] Initializing /data/dan/two.mrc: [testng] 00:47:03,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:47:03,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:03,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-18_00-47-03.log] [testng] 00:47:03,147 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56f78f24 - End of configuration. [testng] [2024-03-18 00:47:03,280] [pool-1-thread-7] Initializing /data/samples/golgi.mrc: [testng] 00:47:03,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:47:03,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:03,281 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-18_00-47-03.log] [testng] 00:47:03,282 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4322e9ef - End of configuration. [testng] [2024-03-18 00:47:03,408] [pool-1-thread-6] Initializing /data/ticket-10073/wtjoin4.rec: [testng] 00:47:03,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:47:03,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:03,409 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-18_00-47-03.log] [testng] 00:47:03,410 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64c15fbe - End of configuration. [testng] [2024-03-18 00:47:03,548] [pool-1-thread-5] Initializing /data/jcb/thyl-apr23-4.rec: [testng] 00:47:03,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:47:03,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:03,550 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-18_00-47-03.log] [testng] 00:47:03,550 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c64a71a - End of configuration. [testng] [2024-03-18 00:47:03,667] [pool-1-thread-4] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] 00:47:03,667 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:47:03,667 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:03,668 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-18_00-47-03.log] [testng] 00:47:03,669 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47a6a28f - End of configuration. [testng] [2024-03-18 00:47:03,801] [pool-1-thread-3] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 00:47:03,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:47:03,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:03,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-18_00-47-03.log] [testng] 00:47:03,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c9625fc - End of configuration. [testng] [2024-03-18 00:47:03,975] [pool-1-thread-2] Initializing /data/ascb/514_9903.mrc: [testng] 00:47:03,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:47:03,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:03,976 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-18_00-47-03.log] [testng] 00:47:03,976 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5718b32 - End of configuration. [testng] [2024-03-18 00:47:07,049] [pool-1-thread-3] Initializing /data/dan/three.mrc: [testng] [2024-03-18 00:47:07,199] [pool-1-thread-11] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] [2024-03-18 00:47:07,444] [pool-1-thread-7] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] [2024-03-18 00:47:07,561] [pool-1-thread-5] Initializing /data/jcb/thylakoid5.rec: [testng] [2024-03-18 00:47:07,665] [pool-1-thread-10] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] [2024-03-18 00:47:07,814] [pool-1-thread-1] Initializing /data/ascb/cfa1071.mrc: [testng] [2024-03-18 00:47:08,636] [pool-1-thread-12] Initializing /data/samples/1160.mrc: [testng] [2024-03-18 00:47:08,815] [pool-1-thread-6] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 24 seconds Finished: SUCCESS