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Started by upstream project "BIOFORMATS-test-repo" build number 97 originally caused by: Started by upstream project "Trigger" build number 108 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins10860335668619631765.sh + '[' microct = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_14911_merge_ci -v /uod/idr/repos/curated/microct:/data -v /uod/idr-scratch/merge-ci/curated/microct:/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] 01:21:21,919 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:21:21,920 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:21:21,921 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:21:22,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:21:22,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:21:22,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:21:22,373 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:21:22,385 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:21:22,386 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:21:22,386 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:21:22,387 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:21:22,387 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5e600dd5 - End of configuration. [testng] 01:21:22,389 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@a38c7fe - Registering current configuration as safe fallback point [testng] 01:21:22,389 |-INFO in ch.qos.logback.classic.util.ContextInitializer@6fdbe764 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 472 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-19 01:21:22,405] [main] java.version = 17.0.2 [testng] 01:21:22,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:21:22,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:22,496 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-19_01-21-22.log] [testng] 01:21:22,499 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-19 01:21:22,503] [main] testng.directory = /data [testng] [2024-06-19 01:21:22,504] [main] testng.configDirectory = /config [testng] [2024-06-19 01:21:22,524] [main] testng.multiplier = 1.0 [testng] [2024-06-19 01:21:22,526] [main] testng.in-memory = false [testng] [2024-06-19 01:21:22,526] [main] testng.allow-missing = false [testng] [2024-06-19 01:21:22,526] [main] user.language = en [testng] [2024-06-19 01:21:22,526] [main] user.country = ${user.country} [testng] [2024-06-19 01:21:22,526] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-19 01:21:24,328] [main] ---------------------------------------- [testng] [2024-06-19 01:21:24,328] [main] Total files: 53 [testng] [2024-06-19 01:21:24,329] [main] Scan time: 1.801 s (33 ms/file) [testng] [2024-06-19 01:21:24,329] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 53 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-19 01:21:50,920] [pool-1-thread-1] Initializing /data/samples/hox-wt-2005050801-humerus/hox-wt-20050508-01-humerus.vff: [testng] 01:21:50,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:21:50,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:50,922 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-19_01-21-50.log] [testng] 01:21:50,922 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bc7f612 - End of configuration. [testng] [2024-06-19 01:21:51,165] [pool-1-thread-12] Initializing /data/samples/hox-wt-2005050201-humerus/hox-wt-20050502-01-humerus.vff: [testng] 01:21:51,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:21:51,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:51,167 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-19_01-21-51.log] [testng] 01:21:51,167 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e82b3ec - End of configuration. [testng] [2024-06-19 01:21:51,377] [pool-1-thread-11] Initializing /data/samples/Mouse_Hand_2004010701/Mouse_Hand_2004010701.vff: [testng] 01:21:51,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:21:51,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:51,378 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-19_01-21-51.log] [testng] 01:21:51,379 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cc56c92 - End of configuration. [testng] [2024-06-19 01:21:51,662] [pool-1-thread-10] Initializing /data/samples/hox-wt-2005042301-humerus/hox-wt-2005042301-humerus.vff: [testng] 01:21:51,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:21:51,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:51,662 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-19_01-21-51.log] [testng] 01:21:51,663 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c3fdfa4 - End of configuration. [testng] [2024-06-19 01:21:51,807] [pool-1-thread-9] Initializing /data/samples/hox-wt-2005042601-hand/hox-wt-2005042601-hand.vff: [testng] 01:21:51,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:21:51,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:51,808 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-19_01-21-51.log] [testng] 01:21:51,808 |-INFO in ch.qos.logback.core.sift.SiftProcessor@780f351c - End of configuration. [testng] [2024-06-19 01:21:51,952] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005050904-hand/hox-wt-20050509-04-hand.vff: [testng] 01:21:51,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:21:51,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:51,953 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-19_01-21-51.log] [testng] 01:21:51,954 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d3347d - End of configuration. [testng] [2024-06-19 01:21:52,087] [pool-1-thread-7] Initializing /data/samples/hox_wt_2005040501/hox-wt-04052005-a.vff: [testng] 01:21:52,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:21:52,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:52,088 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-19_01-21-52.log] [testng] 01:21:52,088 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2dbaf66d - End of configuration. [testng] [2024-06-19 01:21:52,243] [pool-1-thread-6] Initializing /data/samples/Ping_1_2003112000/Ping_1_2003112000.vff: [testng] 01:21:52,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:21:52,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:52,244 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-19_01-21-52.log] [testng] 01:21:52,245 |-INFO in ch.qos.logback.core.sift.SiftProcessor@577fe8b7 - End of configuration. [testng] [2024-06-19 01:21:52,488] [pool-1-thread-5] Initializing /data/samples/Chick_Embryo_2003121200/Chick_Embryo_2003121200.vff: [testng] 01:21:52,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:21:52,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:52,489 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-19_01-21-52.log] [testng] 01:21:52,489 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32f05904 - End of configuration. [testng] [2024-06-19 01:21:52,785] [pool-1-thread-4] Initializing /data/samples/Mouse_Hand_2004011200/Mouse_Hand_2004011200.vff: [testng] 01:21:52,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:21:52,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:52,786 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-19_01-21-52.log] [testng] 01:21:52,786 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62672652 - End of configuration. [testng] [2024-06-19 01:21:53,078] [pool-1-thread-3] Initializing /data/samples/Chick_Embryo_2003121201/Chick_Embryo_2003121201.vff: [testng] 01:21:53,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:21:53,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:53,080 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-19_01-21-53.log] [testng] 01:21:53,081 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14b72186 - End of configuration. [testng] [2024-06-19 01:21:53,508] [pool-1-thread-2] Initializing /data/samples/hox-wt-2005050902-humerus/hox-wt-20050509-02-humerus.vff: [testng] 01:21:53,508 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:21:53,508 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:53,509 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-19_01-21-53.log] [testng] 01:21:53,510 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21d1e195 - End of configuration. [testng] [2024-06-19 01:21:58,532] [pool-1-thread-10] Initializing /data/samples/hox-wt-2005050801-hand/hox-wt-20050508-01-hand.vff: [testng] [2024-06-19 01:21:58,755] [pool-1-thread-2] Initializing /data/samples/how-wt-2005043001/how-wt-2005043001-hand.vff: [testng] [2024-06-19 01:21:58,943] [pool-1-thread-12] Initializing /data/samples/Hersheys_Kiss_2003120100/Hersheys_Kiss_2003120100.vff: [testng] [2024-06-19 01:21:59,218] [pool-1-thread-1] Initializing /data/samples/hox-wt-2005042601-humerus/hox-wt-2005042601-humerus.vff: [testng] [2024-06-19 01:21:59,428] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005042101-hand/hox-wt-2005042101-hand.vff: [testng] [2024-06-19 01:21:59,667] [pool-1-thread-7] Initializing /data/samples/Almond_Kiss_2003112600/Almond_Kiss_2003112600.vff: [testng] [2024-06-19 01:21:59,912] [pool-1-thread-9] Initializing /data/samples/Chick_Embryo_2003121700/Chick_Embryo_2003121700.vff: [testng] [2024-06-19 01:22:00,226] [pool-1-thread-11] Initializing /data/samples/hox-wt-2005042301-hand/hox-wt-2005042301-hand.vff: [testng] [2024-06-19 01:22:00,498] [pool-1-thread-3] Initializing /data/samples/orig.Mouse_Hand_2004010900/Mouse_Hand_2004010900.vff: [testng] [2024-06-19 01:22:00,764] [pool-1-thread-6] Initializing /data/samples/hox_wt_2005040701/hox-wt-04072005-a.vff: [testng] [2024-06-19 01:22:00,991] [pool-1-thread-5] Initializing /data/samples/hox-wt-2005042101-humerus/hox-wt-2005042101-humerus.vff: [testng] [2024-06-19 01:22:01,161] [pool-1-thread-4] Initializing /data/samples/mouse_skull_93um/mouse_skull_93um.vff: [testng] [2024-06-19 01:22:02,960] [pool-1-thread-4] Initializing /data/samples/hox_wt_2005040401/hox-wt-04042005-a.vff: [testng] [2024-06-19 01:22:03,174] [pool-1-thread-10] Initializing /data/samples/hox_wt_2005041101/hox-wt-04112005-a.vff: [testng] [2024-06-19 01:22:03,367] [pool-1-thread-1] Initializing /data/samples/Ping_1_2003112001/Ping_1_2003112001.vff: [testng] [2024-06-19 01:22:03,660] [pool-1-thread-5] Initializing /data/samples/hox-wt-2005050201-hand/hox-wt-20050502-01-hand.vff: [testng] [2024-06-19 01:22:03,820] [pool-1-thread-8] Initializing /data/samples/hox_wt_2005041201/hox-wt-04122005.vff: [testng] [2024-06-19 01:22:04,061] [pool-1-thread-11] Initializing /data/samples/hox-wt-2005042201-hand/hox-wt-2005042201-hand.vff: [testng] [2024-06-19 01:22:04,250] [pool-1-thread-6] Initializing /data/samples/Mouse_Hand_2004010700/Mouse_Hand_2004010700.vff: [testng] [2024-06-19 01:22:04,479] [pool-1-thread-12] Initializing /data/samples/hox-wt-2005050501-hand/hox-wt-20050505-01-hand.vff: [testng] [2024-06-19 01:22:04,621] [pool-1-thread-2] Initializing /data/samples/Pepper_2003112000/Pepper_2003112000.vff: [testng] [2024-06-19 01:22:04,905] [pool-1-thread-7] Initializing /data/samples/hox_wt_2005042701/hox-wt-2005042701-hand.vff: [testng] [2024-06-19 01:22:05,076] [pool-1-thread-9] Initializing /data/samples/how-wt-2005043001-humerus/how-wt-2005043001-humerus.vff: [testng] [2024-06-19 01:22:05,403] [pool-1-thread-3] Initializing /data/samples/hox_wt_2005041401/hox-wt-04142005.vff: [testng] [2024-06-19 01:22:06,631] [pool-1-thread-12] Initializing /data/samples/hox-wt-2005050903-hand/hox-wt-20050509-03-hand.vff: [testng] [2024-06-19 01:22:06,794] [pool-1-thread-4] Initializing /data/samples/hox_wt_2005041301/hox-wt-04132005.vff: [testng] [2024-06-19 01:22:06,983] [pool-1-thread-5] Initializing /data/samples/hox-wt-2005050903-humerus/hox-wt-20050509-03-humerus.vff: [testng] [2024-06-19 01:22:07,201] [pool-1-thread-10] Initializing /data/samples/Mouse_ankle_2003091500/AnkleJoint21umvoxels.vff: [testng] [2024-06-19 01:22:07,322] [pool-1-thread-11] Initializing /data/samples/Bat_Small_2003092500/Bat_Small_2003092500.vff: [testng] [2024-06-19 01:22:07,595] [pool-1-thread-7] Initializing /data/samples/hox-wt-2005050901-hand/hox-wt-20050509-01-hand.vff: [testng] [2024-06-19 01:22:07,760] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005050901-humerus/hox-wt-20050509-01-humerus.vff: [testng] [2024-06-19 01:22:07,918] [pool-1-thread-9] Initializing /data/samples/hox-wt-2005042201-humerus/hox-wt-2005042201-humerus.vff: [testng] [2024-06-19 01:22:08,086] [pool-1-thread-1] Initializing /data/samples/hox-wt-2005050904-humerus/hox-wt-20050509-04-humerus.vff: [testng] [2024-06-19 01:22:08,255] [pool-1-thread-2] Initializing /data/samples/hox-wt-2005050902-hand/hox-wt-20050509-02-hand.vff: [testng] [2024-06-19 01:22:08,428] [pool-1-thread-3] Initializing /data/samples/Ping_1_2003112002/Ping_1_2003112002.vff: [testng] [2024-06-19 01:22:08,681] [pool-1-thread-6] Initializing /data/samples/Bat_Large_2003092500/Bat_Large_2003092500.vff: [testng] [2024-06-19 01:22:10,570] [pool-1-thread-10] Initializing /data/samples/hox-wt-2005050501-humerus/hox-wt-20050505-01-humerus.vff: [testng] [2024-06-19 01:22:10,756] [pool-1-thread-9] Initializing /data/samples/Statuette_2003112100/Statuette_2003112100.vff: [testng] [2024-06-19 01:22:10,953] [pool-1-thread-8] Initializing /data/samples/Mouse_Hand_2004010900/Mouse_Hand_2004010900.vff: [testng] [2024-06-19 01:22:11,195] [pool-1-thread-7] Initializing /data/samples/hox-wt-2005042701-humerus/hox-wt-2005042701-humerus.vff: [testng] [2024-06-19 01:22:11,340] [pool-1-thread-5] Initializing /data/samples/hox_wt_2005041501/hox-wt-04152005.vff: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2809, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 58 seconds Finished: SUCCESS