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Started by upstream project "BIOFORMATS-test-repo" build number 26 originally caused by: Started by upstream project "Trigger" build number 29 originally caused by: Started by timer 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/jenkins18265806361114389341.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_3312_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] 01:37:53,015 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:37:53,016 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:37:53,016 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:37:53,017 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:37:53,017 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:37:53,018 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:37:53,018 |-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] 01:37:53,018 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:37:53,018 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:37:53,019 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:37:53,019 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:37:53,019 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:37:53,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:37:53,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:37:53,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:37:53,201 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:37:53,207 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:37:53,207 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:37:53,207 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:37:53,207 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:37:53,208 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:37:53,208 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:37:53,208 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 190 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-07 01:37:53,217] [main] java.version = 17.0.2 [testng] 01:37:53,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:37:53,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:53,261 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-07_01-37-53.log] [testng] 01:37:53,262 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-04-07 01:37:53,264] [main] testng.directory = /data [testng] [2024-04-07 01:37:53,265] [main] testng.configDirectory = /config [testng] [2024-04-07 01:37:53,273] [main] testng.multiplier = 1.0 [testng] [2024-04-07 01:37:53,274] [main] testng.in-memory = false [testng] [2024-04-07 01:37:53,274] [main] testng.allow-missing = false [testng] [2024-04-07 01:37:53,274] [main] user.language = en [testng] [2024-04-07 01:37:53,274] [main] user.country = ${user.country} [testng] [2024-04-07 01:37:53,274] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-07 01:37:54,432] [main] ---------------------------------------- [testng] [2024-04-07 01:37:54,432] [main] Total files: 20 [testng] [2024-04-07 01:37:54,432] [main] Scan time: 1.157 s (57 ms/file) [testng] [2024-04-07 01:37:54,432] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-07 01:37:54,868] [pool-1-thread-1] Initializing /data/ticket-10073/wtjoin4.rec: [testng] 01:37:54,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:37:54,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:54,870 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-07_01-37-54.log] [testng] 01:37:54,870 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5efe52e5 - End of configuration. [testng] [2024-04-07 01:37:54,889] [pool-1-thread-12] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 01:37:54,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:37:54,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:54,891 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-07_01-37-54.log] [testng] 01:37:54,892 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1aede51d - End of configuration. [testng] [2024-04-07 01:37:54,918] [pool-1-thread-11] Initializing /data/dan/three.mrc: [testng] 01:37:54,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:37:54,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:54,919 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-07_01-37-54.log] [testng] 01:37:54,920 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19c27a86 - End of configuration. [testng] [2024-04-07 01:37:54,936] [pool-1-thread-10] Initializing /data/ascb/cfa1071.mrc: [testng] 01:37:54,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:37:54,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:54,937 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-07_01-37-54.log] [testng] 01:37:54,938 |-INFO in ch.qos.logback.core.sift.SiftProcessor@306304b9 - End of configuration. [testng] [2024-04-07 01:37:54,951] [pool-1-thread-9] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 01:37:54,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:37:54,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:54,953 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-07_01-37-54.log] [testng] 01:37:54,953 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d39b66d - End of configuration. [testng] [2024-04-07 01:37:54,962] [pool-1-thread-8] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] 01:37:54,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:37:54,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:54,963 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-07_01-37-54.log] [testng] 01:37:54,963 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a334a43 - End of configuration. [testng] [2024-04-07 01:37:54,989] [pool-1-thread-7] Initializing /data/strand/Series1_A.mrc: [testng] 01:37:54,990 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:37:54,990 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:54,991 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-07_01-37-54.log] [testng] 01:37:54,991 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1891e8b7 - End of configuration. [testng] [2024-04-07 01:37:55,012] [pool-1-thread-6] Initializing /data/jcb/thylakoid5.rec: [testng] 01:37:55,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:37:55,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:55,025 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-07_01-37-55.log] [testng] 01:37:55,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cd45fd8 - End of configuration. [testng] [2024-04-07 01:37:55,067] [pool-1-thread-5] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 01:37:55,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:37:55,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:55,069 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-07_01-37-55.log] [testng] 01:37:55,069 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67100144 - End of configuration. [testng] [2024-04-07 01:37:55,100] [pool-1-thread-4] Initializing /data/ascb/c191.st: [testng] 01:37:55,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:37:55,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:55,101 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-07_01-37-55.log] [testng] 01:37:55,102 |-INFO in ch.qos.logback.core.sift.SiftProcessor@417ee16a - End of configuration. [testng] [2024-04-07 01:37:55,123] [pool-1-thread-3] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] 01:37:55,123 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:37:55,123 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:55,124 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-07_01-37-55.log] [testng] 01:37:55,124 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60dfd808 - End of configuration. [testng] [2024-04-07 01:37:55,137] [pool-1-thread-2] Initializing /data/samples/golgi.mrc: [testng] 01:37:55,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:37:55,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:55,138 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-07_01-37-55.log] [testng] 01:37:55,139 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25cfda94 - End of configuration. [testng] [2024-04-07 01:37:56,726] [pool-1-thread-9] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] [2024-04-07 01:37:56,746] [pool-1-thread-12] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] [2024-04-07 01:37:56,778] [pool-1-thread-3] Initializing /data/dan/two.mrc: [testng] [2024-04-07 01:37:56,806] [pool-1-thread-5] Initializing /data/ascb/514_9903.mrc: [testng] [2024-04-07 01:37:56,820] [pool-1-thread-2] Initializing /data/ascb/c191ali.mrc: [testng] [2024-04-07 01:37:56,841] [pool-1-thread-8] Initializing /data/samples/1160.mrc: [testng] [2024-04-07 01:37:56,872] [pool-1-thread-4] Initializing /data/dan/one.mrc: [testng] [2024-04-07 01:37:57,021] [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: 13 seconds Finished: SUCCESS