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Started by upstream project "BIOFORMATS-test-repo" build number 66 originally caused by: Started by upstream project "Trigger" build number 74 originally caused by: Started by user devspace 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/jenkins4337760002451717198.sh + '[' microct = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_9827_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 test-automated: [testng] File leak detector installed [testng] 07:53:56,755 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 07:53:56,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 07:53:56,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 07:53:56,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 07:53:56,874 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 07:53:56,875 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 07:53:56,875 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 07:53:56,875 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 07:53:56,875 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5c30a9b0 - End of configuration. [testng] 07:53:56,876 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@7a69b07 - Registering current configuration as safe fallback point [testng] 07:53:56,877 |-INFO in ch.qos.logback.classic.util.ContextInitializer@5e82df6a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 447 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-17 07:53:56,889] [main] java.version = 1.8.0_342 [testng] 07:53:56,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:53:56,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:56,957 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-17_07-53-56.log] [testng] 07:53:56,960 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-05-17 07:53:56,963] [main] testng.directory = /data [testng] [2024-05-17 07:53:56,963] [main] testng.configDirectory = /config [testng] [2024-05-17 07:53:56,983] [main] testng.multiplier = 1.0 [testng] [2024-05-17 07:53:56,984] [main] testng.in-memory = false [testng] [2024-05-17 07:53:56,984] [main] testng.allow-missing = false [testng] [2024-05-17 07:53:56,984] [main] user.language = en [testng] [2024-05-17 07:53:56,984] [main] user.country = ${user.country} [testng] [2024-05-17 07:53:56,984] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-05-17 07:53:58,611] [main] ---------------------------------------- [testng] [2024-05-17 07:53:58,612] [main] Total files: 53 [testng] [2024-05-17 07:53:58,612] [main] Scan time: 1.627 s (30 ms/file) [testng] [2024-05-17 07:53:58,612] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 53 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-17 07:54:28,497] [pool-1-thread-1] Initializing /data/samples/hox-wt-2005050501-humerus/hox-wt-20050505-01-humerus.vff: [testng] 07:54:28,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 07:54:28,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:54:28,498 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-17_07-54-28.log] [testng] 07:54:28,499 |-INFO in ch.qos.logback.core.sift.SiftProcessor@901ee2f - End of configuration. [testng] [2024-05-17 07:54:28,710] [pool-1-thread-12] Initializing /data/samples/hox_wt_2005042701/hox-wt-2005042701-hand.vff: [testng] 07:54:28,710 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 07:54:28,710 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:54:28,711 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-17_07-54-28.log] [testng] 07:54:28,712 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50cb4505 - End of configuration. [testng] [2024-05-17 07:54:29,303] [pool-1-thread-11] Initializing /data/samples/hox-wt-2005042601-humerus/hox-wt-2005042601-humerus.vff: [testng] 07:54:29,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 07:54:29,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:54:29,304 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-17_07-54-29.log] [testng] 07:54:29,304 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e8f02f2 - End of configuration. [testng] [2024-05-17 07:54:29,895] [pool-1-thread-10] Initializing /data/samples/Mouse_Hand_2004010701/Mouse_Hand_2004010701.vff: [testng] 07:54:29,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 07:54:29,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:54:29,896 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-17_07-54-29.log] [testng] 07:54:29,896 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d91763d - End of configuration. [testng] [2024-05-17 07:54:30,451] [pool-1-thread-9] Initializing /data/samples/hox_wt_2005040701/hox-wt-04072005-a.vff: [testng] 07:54:30,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 07:54:30,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:54:30,452 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-17_07-54-30.log] [testng] 07:54:30,452 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29be074b - End of configuration. [testng] [2024-05-17 07:54:31,360] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005050903-hand/hox-wt-20050509-03-hand.vff: [testng] 07:54:31,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 07:54:31,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:54:31,361 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-17_07-54-31.log] [testng] 07:54:31,361 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39c875 - End of configuration. [testng] [2024-05-17 07:54:31,844] [pool-1-thread-7] Initializing /data/samples/hox-wt-2005042301-hand/hox-wt-2005042301-hand.vff: [testng] 07:54:31,845 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 07:54:31,845 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:54:31,846 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-17_07-54-31.log] [testng] 07:54:31,846 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e847d21 - End of configuration. [testng] [2024-05-17 07:54:32,334] [pool-1-thread-6] Initializing /data/samples/hox-wt-2005050902-hand/hox-wt-20050509-02-hand.vff: [testng] 07:54:32,334 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 07:54:32,334 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:54:32,334 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-17_07-54-32.log] [testng] 07:54:32,335 |-INFO in ch.qos.logback.core.sift.SiftProcessor@648c111e - End of configuration. [testng] [2024-05-17 07:54:32,893] [pool-1-thread-5] Initializing /data/samples/Almond_Kiss_2003112600/Almond_Kiss_2003112600.vff: [testng] 07:54:32,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 07:54:32,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:54:32,894 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-17_07-54-32.log] [testng] 07:54:32,894 |-INFO in ch.qos.logback.core.sift.SiftProcessor@82cf177 - End of configuration. [testng] [2024-05-17 07:54:33,548] [pool-1-thread-4] Initializing /data/samples/hox-wt-2005050501-hand/hox-wt-20050505-01-hand.vff: [testng] 07:54:33,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 07:54:33,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:54:33,549 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-17_07-54-33.log] [testng] 07:54:33,549 |-INFO in ch.qos.logback.core.sift.SiftProcessor@315d0ae6 - End of configuration. [testng] [2024-05-17 07:54:34,104] [pool-1-thread-3] Initializing /data/samples/hox-wt-2005042201-hand/hox-wt-2005042201-hand.vff: [testng] 07:54:34,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 07:54:34,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:54:34,105 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-17_07-54-34.log] [testng] 07:54:34,105 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d3e93a8 - End of configuration. [testng] [2024-05-17 07:54:34,803] [pool-1-thread-2] Initializing /data/samples/hox_wt_2005041501/hox-wt-04152005.vff: [testng] 07:54:34,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 07:54:34,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:54:34,804 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-17_07-54-34.log] [testng] 07:54:34,804 |-INFO in ch.qos.logback.core.sift.SiftProcessor@500653ad - End of configuration. [testng] [2024-05-17 07:55:14,617] [pool-1-thread-4] Initializing /data/samples/hox_wt_2005041401/hox-wt-04142005.vff: [testng] [2024-05-17 07:55:17,998] [pool-1-thread-8] Initializing /data/samples/Ping_1_2003112001/Ping_1_2003112001.vff: [testng] [2024-05-17 07:55:20,800] [pool-1-thread-2] Initializing /data/samples/hox-wt-2005050904-hand/hox-wt-20050509-04-hand.vff: [testng] [2024-05-17 07:55:22,010] [pool-1-thread-6] Initializing /data/samples/how-wt-2005043001/how-wt-2005043001-hand.vff: [testng] [2024-05-17 07:55:23,683] [pool-1-thread-3] Initializing /data/samples/hox-wt-2005050904-humerus/hox-wt-20050509-04-humerus.vff: [testng] [2024-05-17 07:55:24,401] [pool-1-thread-11] Initializing /data/samples/hox-wt-2005050901-humerus/hox-wt-20050509-01-humerus.vff: [testng] [2024-05-17 07:55:24,872] [pool-1-thread-1] Initializing /data/samples/hox-wt-2005050902-humerus/hox-wt-20050509-02-humerus.vff: [testng] [2024-05-17 07:55:25,401] [pool-1-thread-12] Initializing /data/samples/orig.Mouse_Hand_2004010900/Mouse_Hand_2004010900.vff: [testng] [2024-05-17 07:55:27,796] [pool-1-thread-7] Initializing /data/samples/hox-wt-2005050903-humerus/hox-wt-20050509-03-humerus.vff: [testng] [2024-05-17 07:55:28,434] [pool-1-thread-9] Initializing /data/samples/hox-wt-2005050801-hand/hox-wt-20050508-01-hand.vff: [testng] [2024-05-17 07:55:39,991] [pool-1-thread-10] Initializing /data/samples/hox-wt-2005050201-humerus/hox-wt-20050502-01-humerus.vff: [testng] [2024-05-17 07:55:42,329] [pool-1-thread-5] Initializing /data/samples/hox-wt-2005042201-humerus/hox-wt-2005042201-humerus.vff: [testng] [2024-05-17 07:56:04,047] [pool-1-thread-2] Initializing /data/samples/hox-wt-2005042601-hand/hox-wt-2005042601-hand.vff: [testng] [2024-05-17 07:56:07,825] [pool-1-thread-11] Initializing /data/samples/Bat_Large_2003092500/Bat_Large_2003092500.vff: [testng] [2024-05-17 07:56:11,566] [pool-1-thread-1] Initializing /data/samples/hox-wt-2005042301-humerus/hox-wt-2005042301-humerus.vff: [testng] [2024-05-17 07:56:13,929] [pool-1-thread-4] Initializing /data/samples/hox_wt_2005040501/hox-wt-04052005-a.vff: [testng] [2024-05-17 07:56:16,238] [pool-1-thread-3] Initializing /data/samples/hox-wt-2005050201-hand/hox-wt-20050502-01-hand.vff: [testng] [2024-05-17 07:56:17,721] [pool-1-thread-7] Initializing /data/samples/hox_wt_2005040401/hox-wt-04042005-a.vff: [testng] [2024-05-17 07:56:18,865] [pool-1-thread-9] Initializing /data/samples/Mouse_Hand_2004011200/Mouse_Hand_2004011200.vff: [testng] [2024-05-17 07:56:22,052] [pool-1-thread-6] Initializing /data/samples/hox-wt-2005050901-hand/hox-wt-20050509-01-hand.vff: [testng] [2024-05-17 07:56:23,541] [pool-1-thread-10] Initializing /data/samples/Statuette_2003112100/Statuette_2003112100.vff: [testng] [2024-05-17 07:56:26,042] [pool-1-thread-5] Initializing /data/samples/hox-wt-2005042101-hand/hox-wt-2005042101-hand.vff: [testng] [2024-05-17 07:56:28,764] [pool-1-thread-8] Initializing /data/samples/Bat_Small_2003092500/Bat_Small_2003092500.vff: [testng] [2024-05-17 07:56:35,220] [pool-1-thread-12] Initializing /data/samples/hox-wt-2005042101-humerus/hox-wt-2005042101-humerus.vff: [testng] [2024-05-17 07:57:03,422] [pool-1-thread-3] Initializing /data/samples/hox_wt_2005041201/hox-wt-04122005.vff: [testng] [2024-05-17 07:57:05,929] [pool-1-thread-1] Initializing /data/samples/Mouse_Hand_2004010700/Mouse_Hand_2004010700.vff: [testng] [2024-05-17 07:57:08,484] [pool-1-thread-2] Initializing /data/samples/Chick_Embryo_2003121700/Chick_Embryo_2003121700.vff: [testng] [2024-05-17 07:57:13,099] [pool-1-thread-4] Initializing /data/samples/hox-wt-2005042701-humerus/hox-wt-2005042701-humerus.vff: [testng] [2024-05-17 07:57:14,772] [pool-1-thread-6] Initializing /data/samples/Ping_1_2003112000/Ping_1_2003112000.vff: [testng] [2024-05-17 07:57:17,342] [pool-1-thread-5] Initializing /data/samples/hox-wt-2005050801-humerus/hox-wt-20050508-01-humerus.vff: [testng] [2024-05-17 07:57:18,232] [pool-1-thread-12] Initializing /data/samples/Hersheys_Kiss_2003120100/Hersheys_Kiss_2003120100.vff: [testng] [2024-05-17 07:57:19,921] [pool-1-thread-10] Initializing /data/samples/mouse_skull_93um/mouse_skull_93um.vff: [testng] [2024-05-17 07:57:20,682] [pool-1-thread-7] Initializing /data/samples/Chick_Embryo_2003121200/Chick_Embryo_2003121200.vff: [testng] [2024-05-17 07:57:22,018] [pool-1-thread-11] Initializing /data/samples/how-wt-2005043001-humerus/how-wt-2005043001-humerus.vff: [testng] [2024-05-17 07:57:22,561] [pool-1-thread-9] Initializing /data/samples/Mouse_ankle_2003091500/AnkleJoint21umvoxels.vff: [testng] [2024-05-17 07:57:46,247] [pool-1-thread-10] Initializing /data/samples/hox_wt_2005041101/hox-wt-04112005-a.vff: [testng] [2024-05-17 07:57:59,657] [pool-1-thread-9] Initializing /data/samples/hox_wt_2005041301/hox-wt-04132005.vff: [testng] [2024-05-17 07:58:03,189] [pool-1-thread-11] Initializing /data/samples/Mouse_Hand_2004010900/Mouse_Hand_2004010900.vff: [testng] [2024-05-17 07:58:06,727] [pool-1-thread-5] Initializing /data/samples/Pepper_2003112000/Pepper_2003112000.vff: [testng] [2024-05-17 07:58:11,897] [pool-1-thread-4] Initializing /data/samples/Ping_1_2003112002/Ping_1_2003112002.vff: [testng] [2024-05-17 07:58:14,883] [pool-1-thread-8] Initializing /data/samples/Chick_Embryo_2003121201/Chick_Embryo_2003121201.vff: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2809, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 5 minutes 4 seconds Finished: SUCCESS