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Started by upstream project "BIOFORMATS-test-repo" build number 114 originally caused by: Started by upstream project "Trigger" build number 127 originally caused by: Started by timer 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/jenkins17743590452893586977.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_17745_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] 01:33:29,581 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:33:29,583 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:33:29,583 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:33:29,584 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:33:29,584 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:33:29,585 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:33:29,585 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:33:29,585 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:33:29,586 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:33:29,586 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:33:29,587 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:33:29,587 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:33:29,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:33:29,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:33:29,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:33:29,833 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:33:29,840 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:33:29,840 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:33:29,840 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:33:29,840 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:33:29,840 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:33:29,841 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:33:29,841 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 255 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-07 01:33:29,852] [main] java.version = 17.0.2 [testng] 01:33:29,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:33:29,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:29,917 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-07_01-33-29.log] [testng] 01:33:29,919 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-07-07 01:33:29,923] [main] testng.directory = /data [testng] [2024-07-07 01:33:29,924] [main] testng.configDirectory = /config [testng] [2024-07-07 01:33:29,937] [main] testng.multiplier = 1.0 [testng] [2024-07-07 01:33:29,939] [main] testng.in-memory = false [testng] [2024-07-07 01:33:29,939] [main] testng.allow-missing = false [testng] [2024-07-07 01:33:29,939] [main] user.language = en [testng] [2024-07-07 01:33:29,939] [main] user.country = ${user.country} [testng] [2024-07-07 01:33:29,939] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-07 01:33:31,255] [main] ---------------------------------------- [testng] [2024-07-07 01:33:31,255] [main] Total files: 20 [testng] [2024-07-07 01:33:31,255] [main] Scan time: 1.316 s (65 ms/file) [testng] [2024-07-07 01:33:31,255] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-07 01:33:31,810] [pool-1-thread-1] Initializing /data/ticket-10073/wtjoin4.rec: [testng] 01:33:31,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:33:31,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:31,812 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-07_01-33-31.log] [testng] 01:33:31,812 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32383a8f - End of configuration. [testng] [2024-07-07 01:33:31,841] [pool-1-thread-12] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 01:33:31,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:33:31,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:31,852 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-07_01-33-31.log] [testng] 01:33:31,853 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f0a1d62 - End of configuration. [testng] [2024-07-07 01:33:31,879] [pool-1-thread-11] Initializing /data/dan/three.mrc: [testng] 01:33:31,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:33:31,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:31,881 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-07_01-33-31.log] [testng] 01:33:31,881 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d571851 - End of configuration. [testng] [2024-07-07 01:33:31,899] [pool-1-thread-10] Initializing /data/ascb/cfa1071.mrc: [testng] 01:33:31,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:33:31,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:31,901 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-07_01-33-31.log] [testng] 01:33:31,902 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57034d4 - End of configuration. [testng] [2024-07-07 01:33:31,926] [pool-1-thread-9] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 01:33:31,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:33:31,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:31,928 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-07_01-33-31.log] [testng] 01:33:31,928 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d5c5f96 - End of configuration. [testng] [2024-07-07 01:33:31,952] [pool-1-thread-8] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] 01:33:31,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:33:31,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:31,953 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-07_01-33-31.log] [testng] 01:33:31,954 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e83da82 - End of configuration. [testng] [2024-07-07 01:33:31,972] [pool-1-thread-7] Initializing /data/strand/Series1_A.mrc: [testng] 01:33:31,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:33:31,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:31,974 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-07_01-33-31.log] [testng] 01:33:31,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27b7fd8d - End of configuration. [testng] [2024-07-07 01:33:32,051] [pool-1-thread-6] Initializing /data/jcb/thylakoid5.rec: [testng] 01:33:32,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:33:32,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:32,054 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-07_01-33-32.log] [testng] 01:33:32,055 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a334a43 - End of configuration. [testng] [2024-07-07 01:33:32,127] [pool-1-thread-5] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 01:33:32,127 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:33:32,127 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:32,128 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-07_01-33-32.log] [testng] 01:33:32,128 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1891e8b7 - End of configuration. [testng] [2024-07-07 01:33:32,164] [pool-1-thread-4] Initializing /data/ascb/c191.st: [testng] 01:33:32,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:33:32,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:32,165 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-07_01-33-32.log] [testng] 01:33:32,166 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f1bfb64 - End of configuration. [testng] [2024-07-07 01:33:32,178] [pool-1-thread-3] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] 01:33:32,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:33:32,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:32,179 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-07_01-33-32.log] [testng] 01:33:32,180 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43043779 - End of configuration. [testng] [2024-07-07 01:33:32,194] [pool-1-thread-2] Initializing /data/samples/golgi.mrc: [testng] 01:33:32,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:33:32,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:32,195 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-07_01-33-32.log] [testng] 01:33:32,196 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fdc01c3 - End of configuration. [testng] [2024-07-07 01:33:33,639] [pool-1-thread-9] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] [2024-07-07 01:33:33,659] [pool-1-thread-2] Initializing /data/ascb/514_9903.mrc: [testng] [2024-07-07 01:33:33,684] [pool-1-thread-12] Initializing /data/ascb/c191ali.mrc: [testng] [2024-07-07 01:33:33,699] [pool-1-thread-3] Initializing /data/samples/1160.mrc: [testng] [2024-07-07 01:33:33,722] [pool-1-thread-5] Initializing /data/dan/one.mrc: [testng] [2024-07-07 01:33:33,822] [pool-1-thread-8] Initializing /data/dan/two.mrc: [testng] [2024-07-07 01:33:33,948] [pool-1-thread-4] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] [2024-07-07 01:33:34,148] [pool-1-thread-6] Initializing /data/jcb/thyl-apr23-4.rec: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 15 seconds Finished: SUCCESS