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Started by upstream project "BIOFORMATS-test-repo" build number 122 originally caused by: Started by upstream project "Trigger" build number 139 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/jenkins12998774647220305609.sh + '[' microct = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_19011_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] 01:20:47,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:20:47,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:20:47,935 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:20:47,935 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:20:47,946 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:20:47,947 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:20:47,947 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:20:47,948 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:20:47,948 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@41a0aa7d - End of configuration. [testng] 01:20:47,949 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6574a52c - Registering current configuration as safe fallback point [testng] 01:20:47,950 |-INFO in ch.qos.logback.classic.util.ContextInitializer@6c1a5b54 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 413 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-16 01:20:47,971] [main] java.version = 11.0.16 [testng] 01:20:47,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:20:47,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:48,092 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-16_01-20-48.log] [testng] 01:20:48,094 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-16 01:20:48,096] [main] testng.directory = /data [testng] [2024-07-16 01:20:48,097] [main] testng.configDirectory = /config [testng] [2024-07-16 01:20:48,152] [main] testng.multiplier = 1.0 [testng] [2024-07-16 01:20:48,154] [main] testng.in-memory = false [testng] [2024-07-16 01:20:48,155] [main] testng.allow-missing = false [testng] [2024-07-16 01:20:48,155] [main] user.language = en [testng] [2024-07-16 01:20:48,155] [main] user.country = ${user.country} [testng] [2024-07-16 01:20:48,155] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-16 01:20:49,999] [main] ---------------------------------------- [testng] [2024-07-16 01:20:50,000] [main] Total files: 53 [testng] [2024-07-16 01:20:50,000] [main] Scan time: 1.844 s (34 ms/file) [testng] [2024-07-16 01:20:50,000] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 53 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-16 01:21:17,067] [pool-1-thread-1] Initializing /data/samples/Mouse_Hand_2004010701/Mouse_Hand_2004010701.vff: [testng] 01:21:17,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:21:17,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:17,071 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-16_01-21-17.log] [testng] 01:21:17,071 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5124a11f - End of configuration. [testng] [2024-07-16 01:21:17,390] [pool-1-thread-12] Initializing /data/samples/hox_wt_2005041501/hox-wt-04152005.vff: [testng] 01:21:17,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:21:17,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:17,392 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-16_01-21-17.log] [testng] 01:21:17,392 |-INFO in ch.qos.logback.core.sift.SiftProcessor@705c8ed6 - End of configuration. [testng] [2024-07-16 01:21:17,622] [pool-1-thread-11] Initializing /data/samples/Bat_Large_2003092500/Bat_Large_2003092500.vff: [testng] 01:21:17,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:21:17,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:17,623 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-16_01-21-17.log] [testng] 01:21:17,623 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ff09f61 - End of configuration. [testng] [2024-07-16 01:21:17,889] [pool-1-thread-10] Initializing /data/samples/Mouse_Hand_2004010700/Mouse_Hand_2004010700.vff: [testng] 01:21:17,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:21:17,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:17,890 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-16_01-21-17.log] [testng] 01:21:17,891 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3aa4df47 - End of configuration. [testng] [2024-07-16 01:21:18,141] [pool-1-thread-9] Initializing /data/samples/Chick_Embryo_2003121201/Chick_Embryo_2003121201.vff: [testng] 01:21:18,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:21:18,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:18,142 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-16_01-21-18.log] [testng] 01:21:18,143 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6846bddf - End of configuration. [testng] [2024-07-16 01:21:18,511] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005050903-humerus/hox-wt-20050509-03-humerus.vff: [testng] 01:21:18,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:21:18,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:18,512 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-16_01-21-18.log] [testng] 01:21:18,512 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6732c003 - End of configuration. [testng] [2024-07-16 01:21:18,706] [pool-1-thread-7] Initializing /data/samples/Almond_Kiss_2003112600/Almond_Kiss_2003112600.vff: [testng] 01:21:18,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:21:18,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:18,707 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-16_01-21-18.log] [testng] 01:21:18,707 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f2e83c5 - End of configuration. [testng] [2024-07-16 01:21:18,985] [pool-1-thread-6] Initializing /data/samples/Ping_1_2003112002/Ping_1_2003112002.vff: [testng] 01:21:18,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:21:18,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:18,986 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-16_01-21-18.log] [testng] 01:21:18,986 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b344e98 - End of configuration. [testng] [2024-07-16 01:21:19,256] [pool-1-thread-5] Initializing /data/samples/how-wt-2005043001-humerus/how-wt-2005043001-humerus.vff: [testng] 01:21:19,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:21:19,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:19,257 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-16_01-21-19.log] [testng] 01:21:19,258 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c5e4fd5 - End of configuration. [testng] [2024-07-16 01:21:19,425] [pool-1-thread-4] Initializing /data/samples/hox-wt-2005050904-hand/hox-wt-20050509-04-hand.vff: [testng] 01:21:19,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:21:19,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:19,426 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-16_01-21-19.log] [testng] 01:21:19,427 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6020a301 - End of configuration. [testng] [2024-07-16 01:21:19,575] [pool-1-thread-3] Initializing /data/samples/hox_wt_2005040401/hox-wt-04042005-a.vff: [testng] 01:21:19,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:21:19,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:19,576 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-16_01-21-19.log] [testng] 01:21:19,576 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ce37081 - End of configuration. [testng] [2024-07-16 01:21:19,784] [pool-1-thread-2] Initializing /data/samples/Pepper_2003112000/Pepper_2003112000.vff: [testng] 01:21:19,784 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:21:19,784 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:19,785 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-16_01-21-19.log] [testng] 01:21:19,786 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e867699 - End of configuration. [testng] [2024-07-16 01:21:22,861] [pool-1-thread-4] Initializing /data/samples/hox-wt-2005042701-humerus/hox-wt-2005042701-humerus.vff: [testng] [2024-07-16 01:21:23,227] [pool-1-thread-5] Initializing /data/samples/hox_wt_2005040501/hox-wt-04052005-a.vff: [testng] [2024-07-16 01:21:23,384] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005050201-humerus/hox-wt-20050502-01-humerus.vff: [testng] [2024-07-16 01:21:23,617] [pool-1-thread-12] Initializing /data/samples/hox-wt-2005042101-hand/hox-wt-2005042101-hand.vff: [testng] [2024-07-16 01:21:23,943] [pool-1-thread-3] Initializing /data/samples/hox-wt-2005042601-humerus/hox-wt-2005042601-humerus.vff: [testng] [2024-07-16 01:21:24,156] [pool-1-thread-10] Initializing /data/samples/orig.Mouse_Hand_2004010900/Mouse_Hand_2004010900.vff: [testng] [2024-07-16 01:21:24,399] [pool-1-thread-11] Initializing /data/samples/hox-wt-2005050901-humerus/hox-wt-20050509-01-humerus.vff: [testng] [2024-07-16 01:21:24,572] [pool-1-thread-1] Initializing /data/samples/hox-wt-2005042101-humerus/hox-wt-2005042101-humerus.vff: [testng] [2024-07-16 01:21:24,751] [pool-1-thread-7] Initializing /data/samples/how-wt-2005043001/how-wt-2005043001-hand.vff: [testng] [2024-07-16 01:21:24,952] [pool-1-thread-2] Initializing /data/samples/hox-wt-2005050201-hand/hox-wt-20050502-01-hand.vff: [testng] [2024-07-16 01:21:25,100] [pool-1-thread-6] Initializing /data/samples/hox_wt_2005041401/hox-wt-04142005.vff: [testng] [2024-07-16 01:21:25,986] [pool-1-thread-9] Initializing /data/samples/hox-wt-2005050903-hand/hox-wt-20050509-03-hand.vff: [testng] [2024-07-16 01:21:26,743] [pool-1-thread-4] Initializing /data/samples/Chick_Embryo_2003121200/Chick_Embryo_2003121200.vff: [testng] [2024-07-16 01:21:27,070] [pool-1-thread-5] Initializing /data/samples/hox-wt-2005050904-humerus/hox-wt-20050509-04-humerus.vff: [testng] [2024-07-16 01:21:27,372] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005042201-hand/hox-wt-2005042201-hand.vff: [testng] [2024-07-16 01:21:27,618] [pool-1-thread-7] Initializing /data/samples/hox-wt-2005050801-hand/hox-wt-20050508-01-hand.vff: [testng] [2024-07-16 01:21:27,816] [pool-1-thread-2] Initializing /data/samples/Chick_Embryo_2003121700/Chick_Embryo_2003121700.vff: [testng] [2024-07-16 01:21:28,102] [pool-1-thread-11] Initializing /data/samples/hox-wt-2005050501-humerus/hox-wt-20050505-01-humerus.vff: [testng] [2024-07-16 01:21:28,279] [pool-1-thread-1] Initializing /data/samples/hox-wt-2005050902-humerus/hox-wt-20050509-02-humerus.vff: [testng] [2024-07-16 01:21:28,442] [pool-1-thread-12] Initializing /data/samples/hox-wt-2005042601-hand/hox-wt-2005042601-hand.vff: [testng] [2024-07-16 01:21:28,655] [pool-1-thread-6] Initializing /data/samples/hox_wt_2005040701/hox-wt-04072005-a.vff: [testng] [2024-07-16 01:21:28,892] [pool-1-thread-3] Initializing /data/samples/hox-wt-2005042301-hand/hox-wt-2005042301-hand.vff: [testng] [2024-07-16 01:21:29,547] [pool-1-thread-9] Initializing /data/samples/hox-wt-2005050901-hand/hox-wt-20050509-01-hand.vff: [testng] [2024-07-16 01:21:29,869] [pool-1-thread-10] Initializing /data/samples/Ping_1_2003112000/Ping_1_2003112000.vff: [testng] [2024-07-16 01:21:31,539] [pool-1-thread-1] Initializing /data/samples/hox_wt_2005041301/hox-wt-04132005.vff: [testng] [2024-07-16 01:21:31,781] [pool-1-thread-11] Initializing /data/samples/mouse_skull_93um/mouse_skull_93um.vff: [testng] [2024-07-16 01:21:31,895] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005050501-hand/hox-wt-20050505-01-hand.vff: [testng] [2024-07-16 01:21:32,056] [pool-1-thread-5] Initializing /data/samples/Mouse_Hand_2004010900/Mouse_Hand_2004010900.vff: [testng] [2024-07-16 01:21:32,298] [pool-1-thread-7] Initializing /data/samples/Ping_1_2003112001/Ping_1_2003112001.vff: [testng] [2024-07-16 01:21:32,532] [pool-1-thread-12] Initializing /data/samples/hox-wt-2005042201-humerus/hox-wt-2005042201-humerus.vff: [testng] [2024-07-16 01:21:32,680] [pool-1-thread-3] Initializing /data/samples/hox-wt-2005050902-hand/hox-wt-20050509-02-hand.vff: [testng] [2024-07-16 01:21:32,823] [pool-1-thread-4] Initializing /data/samples/Statuette_2003112100/Statuette_2003112100.vff: [testng] [2024-07-16 01:21:33,034] [pool-1-thread-6] Initializing /data/samples/Mouse_Hand_2004011200/Mouse_Hand_2004011200.vff: [testng] [2024-07-16 01:21:33,331] [pool-1-thread-9] Initializing /data/samples/hox_wt_2005041201/hox-wt-04122005.vff: [testng] [2024-07-16 01:21:33,897] [pool-1-thread-2] Initializing /data/samples/Mouse_ankle_2003091500/AnkleJoint21umvoxels.vff: [testng] [2024-07-16 01:21:34,663] [pool-1-thread-11] Initializing /data/samples/hox_wt_2005042701/hox-wt-2005042701-hand.vff: [testng] [2024-07-16 01:21:34,934] [pool-1-thread-10] Initializing /data/samples/hox_wt_2005041101/hox-wt-04112005-a.vff: [testng] [2024-07-16 01:21:35,122] [pool-1-thread-8] Initializing /data/samples/Hersheys_Kiss_2003120100/Hersheys_Kiss_2003120100.vff: [testng] [2024-07-16 01:21:35,327] [pool-1-thread-3] Initializing /data/samples/hox-wt-2005050801-humerus/hox-wt-20050508-01-humerus.vff: [testng] [2024-07-16 01:21:35,489] [pool-1-thread-12] Initializing /data/samples/Bat_Small_2003092500/Bat_Small_2003092500.vff: [testng] [2024-07-16 01:21:35,747] [pool-1-thread-1] 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: 56 seconds Finished: SUCCESS