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Started by upstream project "BIOFORMATS-test-repo" build number 93 originally caused by: Started by upstream project "Trigger" build number 104 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins8624640656438368217.sh + '[' microct = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_14255_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 01:21:32,457 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:21:32,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:21:32,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:21:32,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:21:32,567 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:21:32,567 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:21:32,568 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:21:32,568 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:21:32,568 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@41a0aa7d - End of configuration. [testng] 01:21:32,570 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6574a52c - Registering current configuration as safe fallback point [testng] 01:21:32,570 |-INFO in ch.qos.logback.classic.util.ContextInitializer@6c1a5b54 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 503 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-15 01:21:32,589] [main] java.version = 11.0.16 [testng] 01:21:32,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:21:32,595 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:32,670 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-15_01-21-32.log] [testng] 01:21:32,675 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-06-15 01:21:32,683] [main] testng.directory = /data [testng] [2024-06-15 01:21:32,685] [main] testng.configDirectory = /config [testng] [2024-06-15 01:21:32,715] [main] testng.multiplier = 1.0 [testng] [2024-06-15 01:21:32,719] [main] testng.in-memory = false [testng] [2024-06-15 01:21:32,719] [main] testng.allow-missing = false [testng] [2024-06-15 01:21:32,719] [main] user.language = en [testng] [2024-06-15 01:21:32,719] [main] user.country = ${user.country} [testng] [2024-06-15 01:21:32,720] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-15 01:21:34,349] [main] ---------------------------------------- [testng] [2024-06-15 01:21:34,349] [main] Total files: 53 [testng] [2024-06-15 01:21:34,349] [main] Scan time: 1.629 s (30 ms/file) [testng] [2024-06-15 01:21:34,349] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 53 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-15 01:22:01,300] [pool-1-thread-1] Initializing /data/samples/Mouse_Hand_2004010701/Mouse_Hand_2004010701.vff: [testng] 01:22:01,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:22:01,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:01,304 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-15_01-22-01.log] [testng] 01:22:01,304 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ae40cf1 - End of configuration. [testng] [2024-06-15 01:22:01,572] [pool-1-thread-12] Initializing /data/samples/hox_wt_2005041501/hox-wt-04152005.vff: [testng] 01:22:01,573 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:22:01,573 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:01,574 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-15_01-22-01.log] [testng] 01:22:01,575 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b0ab901 - End of configuration. [testng] [2024-06-15 01:22:01,764] [pool-1-thread-11] Initializing /data/samples/Bat_Large_2003092500/Bat_Large_2003092500.vff: [testng] 01:22:01,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:22:01,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:01,766 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-15_01-22-01.log] [testng] 01:22:01,766 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73fe3107 - End of configuration. [testng] [2024-06-15 01:22:02,092] [pool-1-thread-10] Initializing /data/samples/Mouse_Hand_2004010700/Mouse_Hand_2004010700.vff: [testng] 01:22:02,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:22:02,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:02,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-15_01-22-02.log] [testng] 01:22:02,094 |-INFO in ch.qos.logback.core.sift.SiftProcessor@eaea136 - End of configuration. [testng] [2024-06-15 01:22:02,389] [pool-1-thread-9] Initializing /data/samples/Chick_Embryo_2003121201/Chick_Embryo_2003121201.vff: [testng] 01:22:02,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:22:02,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:02,390 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-15_01-22-02.log] [testng] 01:22:02,391 |-INFO in ch.qos.logback.core.sift.SiftProcessor@247f9c78 - End of configuration. [testng] [2024-06-15 01:22:02,673] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005050903-humerus/hox-wt-20050509-03-humerus.vff: [testng] 01:22:02,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:22:02,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:02,674 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-15_01-22-02.log] [testng] 01:22:02,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4963b1e6 - End of configuration. [testng] [2024-06-15 01:22:02,856] [pool-1-thread-7] Initializing /data/samples/Almond_Kiss_2003112600/Almond_Kiss_2003112600.vff: [testng] 01:22:02,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:22:02,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:02,857 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-15_01-22-02.log] [testng] 01:22:02,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31ce5c5a - End of configuration. [testng] [2024-06-15 01:22:03,089] [pool-1-thread-6] Initializing /data/samples/Ping_1_2003112002/Ping_1_2003112002.vff: [testng] 01:22:03,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:22:03,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:03,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-15_01-22-03.log] [testng] 01:22:03,091 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ff4dbb3 - End of configuration. [testng] [2024-06-15 01:22:03,352] [pool-1-thread-5] Initializing /data/samples/how-wt-2005043001-humerus/how-wt-2005043001-humerus.vff: [testng] 01:22:03,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:22:03,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:03,353 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-15_01-22-03.log] [testng] 01:22:03,354 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c590946 - End of configuration. [testng] [2024-06-15 01:22:03,526] [pool-1-thread-4] Initializing /data/samples/hox-wt-2005050904-hand/hox-wt-20050509-04-hand.vff: [testng] 01:22:03,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:22:03,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:03,527 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-15_01-22-03.log] [testng] 01:22:03,527 |-INFO in ch.qos.logback.core.sift.SiftProcessor@682c38c2 - End of configuration. [testng] [2024-06-15 01:22:03,708] [pool-1-thread-3] Initializing /data/samples/hox_wt_2005040401/hox-wt-04042005-a.vff: [testng] 01:22:03,708 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:22:03,708 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:03,709 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-15_01-22-03.log] [testng] 01:22:03,709 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18e014ce - End of configuration. [testng] [2024-06-15 01:22:03,911] [pool-1-thread-2] Initializing /data/samples/Pepper_2003112000/Pepper_2003112000.vff: [testng] 01:22:03,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:22:03,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:03,912 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-15_01-22-03.log] [testng] 01:22:03,913 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f6cff2c - End of configuration. [testng] [2024-06-15 01:22:07,111] [pool-1-thread-4] Initializing /data/samples/hox-wt-2005042701-humerus/hox-wt-2005042701-humerus.vff: [testng] [2024-06-15 01:22:07,285] [pool-1-thread-5] Initializing /data/samples/hox_wt_2005040501/hox-wt-04052005-a.vff: [testng] [2024-06-15 01:22:07,519] [pool-1-thread-12] Initializing /data/samples/hox-wt-2005050201-humerus/hox-wt-20050502-01-humerus.vff: [testng] [2024-06-15 01:22:07,845] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005042101-hand/hox-wt-2005042101-hand.vff: [testng] [2024-06-15 01:22:08,146] [pool-1-thread-3] Initializing /data/samples/hox-wt-2005042601-humerus/hox-wt-2005042601-humerus.vff: [testng] [2024-06-15 01:22:08,557] [pool-1-thread-2] Initializing /data/samples/hox-wt-2005050901-humerus/hox-wt-20050509-01-humerus.vff: [testng] [2024-06-15 01:22:08,721] [pool-1-thread-10] Initializing /data/samples/hox-wt-2005042101-humerus/hox-wt-2005042101-humerus.vff: [testng] [2024-06-15 01:22:08,875] [pool-1-thread-11] Initializing /data/samples/how-wt-2005043001/how-wt-2005043001-hand.vff: [testng] [2024-06-15 01:22:09,046] [pool-1-thread-1] Initializing /data/samples/orig.Mouse_Hand_2004010900/Mouse_Hand_2004010900.vff: [testng] [2024-06-15 01:22:09,326] [pool-1-thread-6] Initializing /data/samples/hox-wt-2005050903-hand/hox-wt-20050509-03-hand.vff: [testng] [2024-06-15 01:22:09,483] [pool-1-thread-9] Initializing /data/samples/hox-wt-2005050201-hand/hox-wt-20050502-01-hand.vff: [testng] [2024-06-15 01:22:09,652] [pool-1-thread-7] Initializing /data/samples/hox_wt_2005041401/hox-wt-04142005.vff: [testng] [2024-06-15 01:22:10,838] [pool-1-thread-4] Initializing /data/samples/Chick_Embryo_2003121200/Chick_Embryo_2003121200.vff: [testng] [2024-06-15 01:22:11,142] [pool-1-thread-5] Initializing /data/samples/hox-wt-2005050904-humerus/hox-wt-20050509-04-humerus.vff: [testng] [2024-06-15 01:22:11,642] [pool-1-thread-12] Initializing /data/samples/hox-wt-2005042201-hand/hox-wt-2005042201-hand.vff: [testng] [2024-06-15 01:22:11,873] [pool-1-thread-2] Initializing /data/samples/hox-wt-2005050801-hand/hox-wt-20050508-01-hand.vff: [testng] [2024-06-15 01:22:12,038] [pool-1-thread-6] Initializing /data/samples/hox-wt-2005050501-humerus/hox-wt-20050505-01-humerus.vff: [testng] [2024-06-15 01:22:12,187] [pool-1-thread-8] Initializing /data/samples/Chick_Embryo_2003121700/Chick_Embryo_2003121700.vff: [testng] [2024-06-15 01:22:12,433] [pool-1-thread-3] Initializing /data/samples/hox-wt-2005050902-humerus/hox-wt-20050509-02-humerus.vff: [testng] [2024-06-15 01:22:12,575] [pool-1-thread-9] Initializing /data/samples/hox-wt-2005042601-hand/hox-wt-2005042601-hand.vff: [testng] [2024-06-15 01:22:12,720] [pool-1-thread-10] Initializing /data/samples/hox_wt_2005040701/hox-wt-04072005-a.vff: [testng] [2024-06-15 01:22:12,895] [pool-1-thread-11] Initializing /data/samples/hox-wt-2005042301-hand/hox-wt-2005042301-hand.vff: [testng] [2024-06-15 01:22:13,063] [pool-1-thread-7] Initializing /data/samples/hox-wt-2005050901-hand/hox-wt-20050509-01-hand.vff: [testng] [2024-06-15 01:22:13,302] [pool-1-thread-1] Initializing /data/samples/Ping_1_2003112000/Ping_1_2003112000.vff: [testng] [2024-06-15 01:22:14,619] [pool-1-thread-5] Initializing /data/samples/hox_wt_2005041301/hox-wt-04132005.vff: [testng] [2024-06-15 01:22:15,168] [pool-1-thread-12] Initializing /data/samples/mouse_skull_93um/mouse_skull_93um.vff: [testng] [2024-06-15 01:22:15,321] [pool-1-thread-11] Initializing /data/samples/hox-wt-2005042201-humerus/hox-wt-2005042201-humerus.vff: [testng] [2024-06-15 01:22:15,509] [pool-1-thread-3] Initializing /data/samples/Ping_1_2003112001/Ping_1_2003112001.vff: [testng] [2024-06-15 01:22:15,756] [pool-1-thread-9] Initializing /data/samples/Mouse_Hand_2004010900/Mouse_Hand_2004010900.vff: [testng] [2024-06-15 01:22:16,041] [pool-1-thread-2] Initializing /data/samples/hox-wt-2005050501-hand/hox-wt-20050505-01-hand.vff: [testng] [2024-06-15 01:22:16,199] [pool-1-thread-7] Initializing /data/samples/hox-wt-2005050902-hand/hox-wt-20050509-02-hand.vff: [testng] [2024-06-15 01:22:16,384] [pool-1-thread-10] Initializing /data/samples/Statuette_2003112100/Statuette_2003112100.vff: [testng] [2024-06-15 01:22:16,582] [pool-1-thread-4] Initializing /data/samples/Mouse_Hand_2004011200/Mouse_Hand_2004011200.vff: [testng] [2024-06-15 01:22:16,890] [pool-1-thread-6] Initializing /data/samples/hox_wt_2005041201/hox-wt-04122005.vff: [testng] [2024-06-15 01:22:18,074] [pool-1-thread-1] Initializing /data/samples/Mouse_ankle_2003091500/AnkleJoint21umvoxels.vff: [testng] [2024-06-15 01:22:18,719] [pool-1-thread-8] Initializing /data/samples/hox_wt_2005042701/hox-wt-2005042701-hand.vff: [testng] [2024-06-15 01:22:18,992] [pool-1-thread-12] Initializing /data/samples/hox_wt_2005041101/hox-wt-04112005-a.vff: [testng] [2024-06-15 01:22:19,291] [pool-1-thread-5] Initializing /data/samples/Hersheys_Kiss_2003120100/Hersheys_Kiss_2003120100.vff: [testng] [2024-06-15 01:22:19,815] [pool-1-thread-11] Initializing /data/samples/hox-wt-2005050801-humerus/hox-wt-20050508-01-humerus.vff: [testng] [2024-06-15 01:22:20,375] [pool-1-thread-2] Initializing /data/samples/Bat_Small_2003092500/Bat_Small_2003092500.vff: [testng] [2024-06-15 01:22:20,676] [pool-1-thread-6] Initializing /data/samples/hox-wt-2005042301-humerus/hox-wt-2005042301-humerus.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