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Started by upstream project "BIOFORMATS-test-repo" build number 222 originally caused by: Started by upstream project "Trigger" build number 249 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/jenkins4475311741508017370.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35301_merge_ci -v /uod/idr/repos/curated/analyze:/data -v /uod/idr-scratch/merge-ci/curated/analyze:/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] 13:18:48,329 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 13:18:48,331 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 13:18:48,331 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:18:48,331 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:18:48,332 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 13:18:48,332 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 13:18:48,332 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 13:18:48,332 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:18:48,333 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:18:48,333 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 13:18:48,334 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 13:18:48,334 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 13:18:48,487 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 13:18:48,487 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 13:18:48,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 13:18:48,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 13:18:48,514 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 13:18:48,515 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 13:18:48,515 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 13:18:48,515 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 13:18:48,515 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 13:18:48,516 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 13:18:48,516 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 183 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-16 13:18:48,524] [main] java.version = 17.0.2 [testng] 13:18:48,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 13:18:48,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:18:48,566 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-16_13-18-48.log] [testng] 13:18:48,567 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-16 13:18:48,569] [main] testng.directory = /data [testng] [2024-10-16 13:18:48,569] [main] testng.configDirectory = /config [testng] [2024-10-16 13:18:48,577] [main] testng.multiplier = 1.0 [testng] [2024-10-16 13:18:48,578] [main] testng.in-memory = false [testng] [2024-10-16 13:18:48,578] [main] testng.allow-missing = false [testng] [2024-10-16 13:18:48,578] [main] user.language = en [testng] [2024-10-16 13:18:48,578] [main] user.country = ${user.country} [testng] [2024-10-16 13:18:48,578] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-16 13:20:12,578] [main] ---------------------------------------- [testng] [2024-10-16 13:20:12,578] [main] Total files: 21 [testng] [2024-10-16 13:20:12,578] [main] Scan time: 84.0 s (4000 ms/file) [testng] [2024-10-16 13:20:12,578] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-16 13:21:41,758] [pool-1-thread-1] Initializing /data/frans/CT_CRANI.hdr: [testng] 13:21:41,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 13:21:41,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:21:41,760 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-16_13-21-41.log] [testng] 13:21:41,761 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14b12d7 - End of configuration. [testng] [2024-10-16 13:21:45,056] [pool-1-thread-12] Initializing /data/frans/aal.hdr: [testng] 13:21:45,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 13:21:45,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:21:45,058 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-16_13-21-45.log] [testng] 13:21:45,058 |-INFO in ch.qos.logback.core.sift.SiftProcessor@655d0bd0 - End of configuration. [testng] [2024-10-16 13:21:48,499] [pool-1-thread-11] Initializing /data/frans/CT_APERT.hdr: [testng] 13:21:48,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 13:21:48,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:21:48,500 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-16_13-21-48.log] [testng] 13:21:48,500 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73594e19 - End of configuration. [testng] [2024-10-16 13:21:52,574] [pool-1-thread-10] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] 13:21:52,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 13:21:52,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:21:52,575 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-16_13-21-52.log] [testng] 13:21:52,575 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b002e0d - End of configuration. [testng] [2024-10-16 13:21:56,597] [pool-1-thread-9] Initializing /data/frans/CT_CHEST.hdr: [testng] 13:21:56,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 13:21:56,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:21:56,598 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-16_13-21-56.log] [testng] 13:21:56,598 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22f74e8f - End of configuration. [testng] [2024-10-16 13:22:02,571] [pool-1-thread-8] Initializing /data/frans/ch2bet.hdr: [testng] 13:22:02,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 13:22:02,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:02,572 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-16_13-22-02.log] [testng] 13:22:02,572 |-INFO in ch.qos.logback.core.sift.SiftProcessor@644a2176 - End of configuration. [testng] [2024-10-16 13:22:06,471] [pool-1-thread-7] Initializing /data/frans/betmask.hdr: [testng] 13:22:06,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 13:22:06,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:06,472 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-16_13-22-06.log] [testng] 13:22:06,472 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ac61b6d - End of configuration. [testng] [2024-10-16 13:22:11,865] [pool-1-thread-6] Initializing /data/frans/MR_CHEST.hdr: [testng] 13:22:11,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 13:22:11,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:11,866 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-16_13-22-11.log] [testng] 13:22:11,866 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4635a024 - End of configuration. [testng] [2024-10-16 13:22:15,039] [pool-1-thread-5] Initializing /data/frans/CT_KNEE.hdr: [testng] 13:22:15,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 13:22:15,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:15,040 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-16_13-22-15.log] [testng] 13:22:15,041 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b48e57c - End of configuration. [testng] [2024-10-16 13:22:19,773] [pool-1-thread-4] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] 13:22:19,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 13:22:19,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:19,774 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-16_13-22-19.log] [testng] 13:22:19,774 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e8e6e1d - End of configuration. [testng] [2024-10-16 13:22:23,671] [pool-1-thread-3] Initializing /data/frans/CT_HAND.hdr: [testng] 13:22:23,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 13:22:23,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:23,672 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-16_13-22-23.log] [testng] 13:22:23,672 |-INFO in ch.qos.logback.core.sift.SiftProcessor@685fc38c - End of configuration. [testng] [2024-10-16 13:22:29,080] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] 13:22:29,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 13:22:29,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:29,081 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-16_13-22-29.log] [testng] 13:22:29,081 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75d551e9 - End of configuration. [testng] [2024-10-16 13:23:18,554] [pool-1-thread-7] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] [2024-10-16 13:23:21,395] [pool-1-thread-11] Initializing /data/frans/m000-MR_CHEST.gif: [testng] [2024-10-16 13:23:21,673] [pool-1-thread-6] Initializing /data/frans/CT_WHOLE.hdr: [testng] [2024-10-16 13:23:24,601] [pool-1-thread-1] Initializing /data/frans/brodmann.hdr: [testng] [2024-10-16 13:23:28,553] [pool-1-thread-5] Initializing /data/frans/CT_FOOT.hdr: [testng] [2024-10-16 13:23:32,157] [pool-1-thread-12] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] [2024-10-16 13:23:35,534] [pool-1-thread-3] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] [2024-10-16 13:23:39,427] [pool-1-thread-4] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] [2024-10-16 13:23:43,009] [pool-1-thread-9] Initializing /data/frans/ch2.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1113, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 5 minutes 35 seconds Finished: SUCCESS