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Started by upstream project "BIOFORMATS-test-repo" build number 31 originally caused by: Started by upstream project "Trigger" build number 35 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/jenkins9007205812491629395.sh + '[' microct = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_4086_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] 07:11:11,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 07:11:11,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 07:11:12,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 07:11:12,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 07:11:12,024 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 07:11:12,024 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 07:11:12,024 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 07:11:12,025 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 07:11:12,025 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5c30a9b0 - End of configuration. [testng] 07:11:12,027 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@7a69b07 - Registering current configuration as safe fallback point [testng] 07:11:12,027 |-INFO in ch.qos.logback.classic.util.ContextInitializer@5e82df6a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 425 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-12 07:11:12,043] [main] java.version = 1.8.0_342 [testng] 07:11:12,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:11:12,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:12,110 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-12_07-11-12.log] [testng] 07:11:12,112 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-12 07:11:12,122] [main] testng.directory = /data [testng] [2024-04-12 07:11:12,123] [main] testng.configDirectory = /config [testng] [2024-04-12 07:11:12,149] [main] testng.multiplier = 1.0 [testng] [2024-04-12 07:11:12,149] [main] testng.in-memory = false [testng] [2024-04-12 07:11:12,149] [main] testng.allow-missing = false [testng] [2024-04-12 07:11:12,149] [main] user.language = en [testng] [2024-04-12 07:11:12,149] [main] user.country = ${user.country} [testng] [2024-04-12 07:11:12,150] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-12 07:11:13,552] [main] ---------------------------------------- [testng] [2024-04-12 07:11:13,552] [main] Total files: 53 [testng] [2024-04-12 07:11:13,552] [main] Scan time: 1.402 s (26 ms/file) [testng] [2024-04-12 07:11:13,552] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 53 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-12 07:11:42,103] [pool-1-thread-1] Initializing /data/samples/hox-wt-2005050901-humerus/hox-wt-20050509-01-humerus.vff: [testng] 07:11:42,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 07:11:42,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:42,106 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-12_07-11-42.log] [testng] 07:11:42,107 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25bbb810 - End of configuration. [testng] [2024-04-12 07:11:42,377] [pool-1-thread-12] Initializing /data/samples/how-wt-2005043001-humerus/how-wt-2005043001-humerus.vff: [testng] 07:11:42,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 07:11:42,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:42,378 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-12_07-11-42.log] [testng] 07:11:42,379 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c4eec84 - End of configuration. [testng] [2024-04-12 07:11:42,913] [pool-1-thread-11] Initializing /data/samples/orig.Mouse_Hand_2004010900/Mouse_Hand_2004010900.vff: [testng] 07:11:42,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 07:11:42,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:42,914 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-12_07-11-42.log] [testng] 07:11:42,915 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35616516 - End of configuration. [testng] [2024-04-12 07:11:43,653] [pool-1-thread-10] Initializing /data/samples/hox-wt-2005050501-hand/hox-wt-20050505-01-hand.vff: [testng] 07:11:43,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 07:11:43,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:43,655 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-12_07-11-43.log] [testng] 07:11:43,655 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67b916de - End of configuration. [testng] [2024-04-12 07:11:44,133] [pool-1-thread-9] Initializing /data/samples/Pepper_2003112000/Pepper_2003112000.vff: [testng] 07:11:44,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 07:11:44,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:44,135 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-12_07-11-44.log] [testng] 07:11:44,136 |-INFO in ch.qos.logback.core.sift.SiftProcessor@457e1f4e - End of configuration. [testng] [2024-04-12 07:11:45,455] [pool-1-thread-8] Initializing /data/samples/hox_wt_2005041401/hox-wt-04142005.vff: [testng] 07:11:45,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 07:11:45,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:45,456 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-12_07-11-45.log] [testng] 07:11:45,456 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64ab61d0 - End of configuration. [testng] [2024-04-12 07:11:46,795] [pool-1-thread-7] Initializing /data/samples/hox_wt_2005040401/hox-wt-04042005-a.vff: [testng] 07:11:46,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 07:11:46,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:46,795 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-12_07-11-46.log] [testng] 07:11:46,796 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34b75209 - End of configuration. [testng] [2024-04-12 07:11:47,236] [pool-1-thread-6] Initializing /data/samples/hox-wt-2005042701-humerus/hox-wt-2005042701-humerus.vff: [testng] 07:11:47,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 07:11:47,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:47,237 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-12_07-11-47.log] [testng] 07:11:47,237 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e7163a4 - End of configuration. [testng] [2024-04-12 07:11:47,979] [pool-1-thread-5] Initializing /data/samples/hox-wt-2005050904-hand/hox-wt-20050509-04-hand.vff: [testng] 07:11:47,980 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 07:11:47,980 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:47,980 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-12_07-11-47.log] [testng] 07:11:47,981 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44f20de - End of configuration. [testng] [2024-04-12 07:11:48,605] [pool-1-thread-4] Initializing /data/samples/Chick_Embryo_2003121201/Chick_Embryo_2003121201.vff: [testng] 07:11:48,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 07:11:48,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:48,605 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-12_07-11-48.log] [testng] 07:11:48,606 |-INFO in ch.qos.logback.core.sift.SiftProcessor@272d78d - End of configuration. [testng] [2024-04-12 07:11:49,341] [pool-1-thread-3] Initializing /data/samples/hox-wt-2005050901-hand/hox-wt-20050509-01-hand.vff: [testng] 07:11:49,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 07:11:49,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:49,341 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-12_07-11-49.log] [testng] 07:11:49,342 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68f0ea5c - End of configuration. [testng] [2024-04-12 07:11:49,953] [pool-1-thread-2] Initializing /data/samples/hox-wt-2005042601-hand/hox-wt-2005042601-hand.vff: [testng] 07:11:49,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 07:11:49,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:49,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-12_07-11-49.log] [testng] 07:11:49,955 |-INFO in ch.qos.logback.core.sift.SiftProcessor@502fc4d1 - End of configuration. [testng] [2024-04-12 07:12:29,344] [pool-1-thread-5] Initializing /data/samples/hox-wt-2005050904-humerus/hox-wt-20050509-04-humerus.vff: [testng] [2024-04-12 07:12:32,752] [pool-1-thread-6] Initializing /data/samples/hox-wt-2005050903-humerus/hox-wt-20050509-03-humerus.vff: [testng] [2024-04-12 07:12:35,153] [pool-1-thread-10] Initializing /data/samples/hox_wt_2005040701/hox-wt-04072005-a.vff: [testng] [2024-04-12 07:12:37,661] [pool-1-thread-12] Initializing /data/samples/hox-wt-2005042201-hand/hox-wt-2005042201-hand.vff: [testng] [2024-04-12 07:12:40,362] [pool-1-thread-1] Initializing /data/samples/hox_wt_2005041101/hox-wt-04112005-a.vff: [testng] [2024-04-12 07:12:41,671] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005050801-humerus/hox-wt-20050508-01-humerus.vff: [testng] [2024-04-12 07:12:43,411] [pool-1-thread-2] Initializing /data/samples/hox-wt-2005050902-hand/hox-wt-20050509-02-hand.vff: [testng] [2024-04-12 07:12:44,870] [pool-1-thread-3] Initializing /data/samples/hox_wt_2005040501/hox-wt-04052005-a.vff: [testng] [2024-04-12 07:12:45,252] [pool-1-thread-7] Initializing /data/samples/hox-wt-2005042601-humerus/hox-wt-2005042601-humerus.vff: [testng] [2024-04-12 07:12:55,489] [pool-1-thread-11] Initializing /data/samples/hox-wt-2005050201-humerus/hox-wt-20050502-01-humerus.vff: [testng] [2024-04-12 07:12:57,727] [pool-1-thread-4] Initializing /data/samples/Chick_Embryo_2003121700/Chick_Embryo_2003121700.vff: [testng] [2024-04-12 07:13:00,766] [pool-1-thread-9] Initializing /data/samples/hox-wt-2005050201-hand/hox-wt-20050502-01-hand.vff: [testng] [2024-04-12 07:13:21,564] [pool-1-thread-3] Initializing /data/samples/hox_wt_2005041201/hox-wt-04122005.vff: [testng] [2024-04-12 07:13:27,121] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005050801-hand/hox-wt-20050508-01-hand.vff: [testng] [2024-04-12 07:13:29,290] [pool-1-thread-7] Initializing /data/samples/hox-wt-2005042301-hand/hox-wt-2005042301-hand.vff: [testng] [2024-04-12 07:13:31,365] [pool-1-thread-6] Initializing /data/samples/hox-wt-2005042101-humerus/hox-wt-2005042101-humerus.vff: [testng] [2024-04-12 07:13:32,191] [pool-1-thread-5] Initializing /data/samples/hox-wt-2005050903-hand/hox-wt-20050509-03-hand.vff: [testng] [2024-04-12 07:13:32,609] [pool-1-thread-2] Initializing /data/samples/Ping_1_2003112001/Ping_1_2003112001.vff: [testng] [2024-04-12 07:13:33,214] [pool-1-thread-12] Initializing /data/samples/hox_wt_2005041301/hox-wt-04132005.vff: [testng] [2024-04-12 07:13:33,677] [pool-1-thread-10] Initializing /data/samples/Hersheys_Kiss_2003120100/Hersheys_Kiss_2003120100.vff: [testng] [2024-04-12 07:13:35,419] [pool-1-thread-1] Initializing /data/samples/hox-wt-2005042301-humerus/hox-wt-2005042301-humerus.vff: [testng] [2024-04-12 07:13:36,663] [pool-1-thread-11] Initializing /data/samples/hox_wt_2005042701/hox-wt-2005042701-hand.vff: [testng] [2024-04-12 07:13:38,804] [pool-1-thread-9] Initializing /data/samples/Mouse_ankle_2003091500/AnkleJoint21umvoxels.vff: [testng] [2024-04-12 07:14:08,503] [pool-1-thread-5] Initializing /data/samples/Chick_Embryo_2003121200/Chick_Embryo_2003121200.vff: [testng] [2024-04-12 07:14:13,466] [pool-1-thread-9] Initializing /data/samples/Mouse_Hand_2004010900/Mouse_Hand_2004010900.vff: [testng] [2024-04-12 07:14:17,286] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005050902-humerus/hox-wt-20050509-02-humerus.vff: [testng] [2024-04-12 07:14:19,681] [pool-1-thread-7] Initializing /data/samples/Mouse_Hand_2004011200/Mouse_Hand_2004011200.vff: [testng] [2024-04-12 07:14:22,340] [pool-1-thread-6] Initializing /data/samples/hox-wt-2005050501-humerus/hox-wt-20050505-01-humerus.vff: [testng] [2024-04-12 07:14:23,167] [pool-1-thread-1] Initializing /data/samples/how-wt-2005043001/how-wt-2005043001-hand.vff: [testng] [2024-04-12 07:14:23,902] [pool-1-thread-4] Initializing /data/samples/Mouse_Hand_2004010700/Mouse_Hand_2004010700.vff: [testng] [2024-04-12 07:14:25,442] [pool-1-thread-3] Initializing /data/samples/Ping_1_2003112002/Ping_1_2003112002.vff: [testng] [2024-04-12 07:14:27,506] [pool-1-thread-11] Initializing /data/samples/Bat_Small_2003092500/Bat_Small_2003092500.vff: [testng] [2024-04-12 07:14:28,638] [pool-1-thread-12] Initializing /data/samples/hox-wt-2005042201-humerus/hox-wt-2005042201-humerus.vff: [testng] [2024-04-12 07:14:29,215] [pool-1-thread-10] Initializing /data/samples/hox_wt_2005041501/hox-wt-04152005.vff: [testng] [2024-04-12 07:14:39,133] [pool-1-thread-2] Initializing /data/samples/mouse_skull_93um/mouse_skull_93um.vff: [testng] [2024-04-12 07:15:05,982] [pool-1-thread-12] Initializing /data/samples/Ping_1_2003112000/Ping_1_2003112000.vff: [testng] [2024-04-12 07:15:10,097] [pool-1-thread-2] Initializing /data/samples/Bat_Large_2003092500/Bat_Large_2003092500.vff: [testng] [2024-04-12 07:15:14,853] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005042101-hand/hox-wt-2005042101-hand.vff: [testng] [2024-04-12 07:15:18,377] [pool-1-thread-6] Initializing /data/samples/Mouse_Hand_2004010701/Mouse_Hand_2004010701.vff: [testng] [2024-04-12 07:15:20,128] [pool-1-thread-10] Initializing /data/samples/Almond_Kiss_2003112600/Almond_Kiss_2003112600.vff: [testng] [2024-04-12 07:15:24,867] [pool-1-thread-1] Initializing /data/samples/Statuette_2003112100/Statuette_2003112100.vff: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2809, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 4 minutes 56 seconds Finished: SUCCESS