Started by upstream project "BIOFORMATS-test-repo" build number 202 originally caused by: Started by upstream project "Trigger" build number 228 originally caused by: Started by user devspace 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/jenkins10250390559062240156.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_32020_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] 05:50:55,659 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 05:50:55,661 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 05:50:55,661 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:50:55,662 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:50:55,662 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 05:50:55,662 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 05:50:55,662 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 05:50:55,662 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:50:55,663 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:50:55,663 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 05:50:55,663 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 05:50:55,663 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 05:50:55,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 05:50:55,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 05:50:55,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 05:50:55,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 05:50:55,948 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 05:50:55,948 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 05:50:55,948 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 05:50:55,949 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 05:50:55,949 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 05:50:55,949 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 05:50:55,950 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 286 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-27 05:50:55,960] [main] java.version = 1.8.0_342 [testng] 05:50:55,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:50:55,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:50:56,011 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-27_05-50-55.log] [testng] 05:50:56,013 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-09-27 05:50:56,015] [main] testng.directory = /data [testng] [2024-09-27 05:50:56,015] [main] testng.configDirectory = /config [testng] [2024-09-27 05:50:56,028] [main] testng.multiplier = 1.0 [testng] [2024-09-27 05:50:56,028] [main] testng.in-memory = false [testng] [2024-09-27 05:50:56,028] [main] testng.allow-missing = false [testng] [2024-09-27 05:50:56,028] [main] user.language = en [testng] [2024-09-27 05:50:56,028] [main] user.country = ${user.country} [testng] [2024-09-27 05:50:56,028] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-09-27 05:50:59,008] [main] ---------------------------------------- [testng] [2024-09-27 05:50:59,008] [main] Total files: 20 [testng] [2024-09-27 05:50:59,008] [main] Scan time: 2.98 s (149 ms/file) [testng] [2024-09-27 05:50:59,008] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-27 05:51:02,901] [pool-1-thread-1] Initializing /data/ascb/c191ali.mrc: [testng] 05:51:02,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:51:02,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:51:02,902 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-27_05-51-02.log] [testng] 05:51:02,903 |-INFO in ch.qos.logback.core.sift.SiftProcessor@153187a8 - End of configuration. [testng] [2024-09-27 05:51:02,993] [pool-1-thread-12] Initializing /data/ticket-10073/wtjoin4.rec: [testng] 05:51:02,993 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:51:02,993 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:51:02,994 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-27_05-51-02.log] [testng] 05:51:02,995 |-INFO in ch.qos.logback.core.sift.SiftProcessor@391aa6a6 - End of configuration. [testng] [2024-09-27 05:51:03,093] [pool-1-thread-11] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 05:51:03,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:51:03,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:51:03,094 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-27_05-51-03.log] [testng] 05:51:03,095 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33fd23b - End of configuration. [testng] [2024-09-27 05:51:03,189] [pool-1-thread-10] Initializing /data/strand/Series1_A.mrc: [testng] 05:51:03,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:51:03,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:51:03,191 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-27_05-51-03.log] [testng] 05:51:03,191 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6beabf7d - End of configuration. [testng] [2024-09-27 05:51:03,299] [pool-1-thread-9] Initializing /data/samples/golgi.mrc: [testng] 05:51:03,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:51:03,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:51:03,300 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-27_05-51-03.log] [testng] 05:51:03,301 |-INFO in ch.qos.logback.core.sift.SiftProcessor@415fc1ed - End of configuration. [testng] [2024-09-27 05:51:03,454] [pool-1-thread-8] Initializing /data/dan/three.mrc: [testng] 05:51:03,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:51:03,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:51:03,456 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-27_05-51-03.log] [testng] 05:51:03,456 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a2195e9 - End of configuration. [testng] [2024-09-27 05:51:03,623] [pool-1-thread-7] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] 05:51:03,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:51:03,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:51:03,624 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-27_05-51-03.log] [testng] 05:51:03,625 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5fce4ecc - End of configuration. [testng] [2024-09-27 05:51:03,740] [pool-1-thread-6] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 05:51:03,741 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:51:03,741 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:51:03,741 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-27_05-51-03.log] [testng] 05:51:03,742 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cee035f - End of configuration. [testng] [2024-09-27 05:51:03,903] [pool-1-thread-5] Initializing /data/dan/one.mrc: [testng] 05:51:03,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:51:03,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:51:03,904 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-27_05-51-03.log] [testng] 05:51:03,905 |-INFO in ch.qos.logback.core.sift.SiftProcessor@645d605a - End of configuration. [testng] [2024-09-27 05:51:03,983] [pool-1-thread-4] Initializing /data/dan/two.mrc: [testng] 05:51:03,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:51:03,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:51:03,984 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-27_05-51-03.log] [testng] 05:51:03,984 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a85b25d - End of configuration. [testng] [2024-09-27 05:51:04,100] [pool-1-thread-3] Initializing /data/ascb/514_9903.mrc: [testng] 05:51:04,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:51:04,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:51:04,101 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-27_05-51-04.log] [testng] 05:51:04,102 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62a5b0a - End of configuration. [testng] [2024-09-27 05:51:04,296] [pool-1-thread-2] Initializing /data/jcb/thyl-apr23-4.rec: [testng] 05:51:04,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:51:04,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:51:04,297 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-27_05-51-04.log] [testng] 05:51:04,297 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2826bee5 - End of configuration. [testng] [2024-09-27 05:51:07,000] [pool-1-thread-6] Initializing /data/ascb/c191.st: [testng] [2024-09-27 05:51:07,084] [pool-1-thread-11] Initializing /data/samples/1160.mrc: [testng] [2024-09-27 05:51:07,205] [pool-1-thread-7] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] [2024-09-27 05:51:07,290] [pool-1-thread-9] Initializing /data/ascb/cfa1071.mrc: [testng] [2024-09-27 05:51:07,364] [pool-1-thread-2] Initializing /data/jcb/thylakoid5.rec: [testng] [2024-09-27 05:51:07,466] [pool-1-thread-1] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] [2024-09-27 05:51:07,998] [pool-1-thread-5] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] [2024-09-27 05:51:08,072] [pool-1-thread-12] 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: 20 seconds Finished: SUCCESS