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Started by upstream project "BIOFORMATS-test-repo" build number 99 originally caused by: Started by upstream project "Trigger" build number 110 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins14617959881766103047.sh + '[' microct = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_15239_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] 01:23:16,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:23:16,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:23:16,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:23:16,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:23:16,638 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:23:16,639 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:23:16,639 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:23:16,640 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:23:16,640 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5c30a9b0 - End of configuration. [testng] 01:23:16,641 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@7a69b07 - Registering current configuration as safe fallback point [testng] 01:23:16,641 |-INFO in ch.qos.logback.classic.util.ContextInitializer@5e82df6a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 499 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-21 01:23:16,658] [main] java.version = 1.8.0_342 [testng] 01:23:16,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:23:16,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:16,736 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-21_01-23-16.log] [testng] 01:23:16,739 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-06-21 01:23:16,741] [main] testng.directory = /data [testng] [2024-06-21 01:23:16,742] [main] testng.configDirectory = /config [testng] [2024-06-21 01:23:16,762] [main] testng.multiplier = 1.0 [testng] [2024-06-21 01:23:16,762] [main] testng.in-memory = false [testng] [2024-06-21 01:23:16,762] [main] testng.allow-missing = false [testng] [2024-06-21 01:23:16,762] [main] user.language = en [testng] [2024-06-21 01:23:16,762] [main] user.country = ${user.country} [testng] [2024-06-21 01:23:16,763] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-06-21 01:23:18,322] [main] ---------------------------------------- [testng] [2024-06-21 01:23:18,323] [main] Total files: 53 [testng] [2024-06-21 01:23:18,324] [main] Scan time: 1.559 s (29 ms/file) [testng] [2024-06-21 01:23:18,324] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 53 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-21 01:23:47,411] [pool-1-thread-1] Initializing /data/samples/hox-wt-2005050501-humerus/hox-wt-20050505-01-humerus.vff: [testng] 01:23:47,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:23:47,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:47,413 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-21_01-23-47.log] [testng] 01:23:47,414 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ebc7ae - End of configuration. [testng] [2024-06-21 01:23:47,634] [pool-1-thread-12] Initializing /data/samples/hox_wt_2005042701/hox-wt-2005042701-hand.vff: [testng] 01:23:47,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:23:47,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:47,635 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-21_01-23-47.log] [testng] 01:23:47,635 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5699662a - End of configuration. [testng] [2024-06-21 01:23:48,099] [pool-1-thread-11] Initializing /data/samples/hox-wt-2005042601-humerus/hox-wt-2005042601-humerus.vff: [testng] 01:23:48,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:23:48,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:48,100 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-21_01-23-48.log] [testng] 01:23:48,100 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cc6640 - End of configuration. [testng] [2024-06-21 01:23:48,538] [pool-1-thread-10] Initializing /data/samples/Mouse_Hand_2004010701/Mouse_Hand_2004010701.vff: [testng] 01:23:48,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:23:48,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:48,539 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-21_01-23-48.log] [testng] 01:23:48,540 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f578de3 - End of configuration. [testng] [2024-06-21 01:23:49,163] [pool-1-thread-9] Initializing /data/samples/hox_wt_2005040701/hox-wt-04072005-a.vff: [testng] 01:23:49,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:23:49,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:49,163 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-21_01-23-49.log] [testng] 01:23:49,164 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cdc25be - End of configuration. [testng] [2024-06-21 01:23:50,239] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005050903-hand/hox-wt-20050509-03-hand.vff: [testng] 01:23:50,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:23:50,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:50,241 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-21_01-23-50.log] [testng] 01:23:50,241 |-INFO in ch.qos.logback.core.sift.SiftProcessor@615d35b0 - End of configuration. [testng] [2024-06-21 01:23:50,699] [pool-1-thread-7] Initializing /data/samples/hox-wt-2005042301-hand/hox-wt-2005042301-hand.vff: [testng] 01:23:50,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:23:50,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:50,700 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-21_01-23-50.log] [testng] 01:23:50,700 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1431b118 - End of configuration. [testng] [2024-06-21 01:23:51,235] [pool-1-thread-6] Initializing /data/samples/hox-wt-2005050902-hand/hox-wt-20050509-02-hand.vff: [testng] 01:23:51,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:23:51,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:51,236 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-21_01-23-51.log] [testng] 01:23:51,237 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2369cc17 - End of configuration. [testng] [2024-06-21 01:23:51,654] [pool-1-thread-5] Initializing /data/samples/Almond_Kiss_2003112600/Almond_Kiss_2003112600.vff: [testng] 01:23:51,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:23:51,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:51,655 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-21_01-23-51.log] [testng] 01:23:51,655 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47735069 - End of configuration. [testng] [2024-06-21 01:23:52,337] [pool-1-thread-4] Initializing /data/samples/hox-wt-2005050501-hand/hox-wt-20050505-01-hand.vff: [testng] 01:23:52,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:23:52,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:52,338 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-21_01-23-52.log] [testng] 01:23:52,338 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cd19254 - End of configuration. [testng] [2024-06-21 01:23:52,868] [pool-1-thread-3] Initializing /data/samples/hox-wt-2005042201-hand/hox-wt-2005042201-hand.vff: [testng] 01:23:52,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:23:52,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:52,869 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-21_01-23-52.log] [testng] 01:23:52,869 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4782c138 - End of configuration. [testng] [2024-06-21 01:23:53,547] [pool-1-thread-2] Initializing /data/samples/hox_wt_2005041501/hox-wt-04152005.vff: [testng] 01:23:53,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:23:53,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:53,548 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-21_01-23-53.log] [testng] 01:23:53,548 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31fab0f8 - End of configuration. [testng] [2024-06-21 01:24:33,425] [pool-1-thread-11] Initializing /data/samples/hox_wt_2005041401/hox-wt-04142005.vff: [testng] [2024-06-21 01:24:36,144] [pool-1-thread-3] Initializing /data/samples/Ping_1_2003112001/Ping_1_2003112001.vff: [testng] [2024-06-21 01:24:38,844] [pool-1-thread-2] Initializing /data/samples/hox-wt-2005050903-humerus/hox-wt-20050509-03-humerus.vff: [testng] [2024-06-21 01:24:40,489] [pool-1-thread-6] Initializing /data/samples/hox-wt-2005050904-hand/hox-wt-20050509-04-hand.vff: [testng] [2024-06-21 01:24:42,431] [pool-1-thread-1] Initializing /data/samples/how-wt-2005043001/how-wt-2005043001-hand.vff: [testng] [2024-06-21 01:24:43,527] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005050904-humerus/hox-wt-20050509-04-humerus.vff: [testng] [2024-06-21 01:24:44,086] [pool-1-thread-4] Initializing /data/samples/hox-wt-2005050901-humerus/hox-wt-20050509-01-humerus.vff: [testng] [2024-06-21 01:24:44,532] [pool-1-thread-7] Initializing /data/samples/hox-wt-2005050902-humerus/hox-wt-20050509-02-humerus.vff: [testng] [2024-06-21 01:24:45,061] [pool-1-thread-12] Initializing /data/samples/orig.Mouse_Hand_2004010900/Mouse_Hand_2004010900.vff: [testng] [2024-06-21 01:24:47,329] [pool-1-thread-9] Initializing /data/samples/hox-wt-2005050801-hand/hox-wt-20050508-01-hand.vff: [testng] [2024-06-21 01:24:52,921] [pool-1-thread-10] Initializing /data/samples/hox-wt-2005050201-humerus/hox-wt-20050502-01-humerus.vff: [testng] [2024-06-21 01:25:01,337] [pool-1-thread-5] Initializing /data/samples/hox-wt-2005042201-humerus/hox-wt-2005042201-humerus.vff: [testng] [2024-06-21 01:25:22,333] [pool-1-thread-6] Initializing /data/samples/hox-wt-2005042601-hand/hox-wt-2005042601-hand.vff: [testng] [2024-06-21 01:25:24,347] [pool-1-thread-7] Initializing /data/samples/Bat_Large_2003092500/Bat_Large_2003092500.vff: [testng] [2024-06-21 01:25:29,712] [pool-1-thread-4] Initializing /data/samples/hox-wt-2005042301-humerus/hox-wt-2005042301-humerus.vff: [testng] [2024-06-21 01:25:32,434] [pool-1-thread-11] Initializing /data/samples/hox_wt_2005040401/hox-wt-04042005-a.vff: [testng] [2024-06-21 01:25:34,369] [pool-1-thread-9] Initializing /data/samples/hox-wt-2005050901-hand/hox-wt-20050509-01-hand.vff: [testng] [2024-06-21 01:25:35,869] [pool-1-thread-1] Initializing /data/samples/Mouse_Hand_2004011200/Mouse_Hand_2004011200.vff: [testng] [2024-06-21 01:25:37,813] [pool-1-thread-8] Initializing /data/samples/hox_wt_2005040501/hox-wt-04052005-a.vff: [testng] [2024-06-21 01:25:38,850] [pool-1-thread-2] Initializing /data/samples/hox-wt-2005050201-hand/hox-wt-20050502-01-hand.vff: [testng] [2024-06-21 01:25:39,540] [pool-1-thread-5] Initializing /data/samples/Statuette_2003112100/Statuette_2003112100.vff: [testng] [2024-06-21 01:25:42,605] [pool-1-thread-10] Initializing /data/samples/hox-wt-2005042101-hand/hox-wt-2005042101-hand.vff: [testng] [2024-06-21 01:25:44,740] [pool-1-thread-3] Initializing /data/samples/Bat_Small_2003092500/Bat_Small_2003092500.vff: [testng] [2024-06-21 01:25:50,775] [pool-1-thread-12] Initializing /data/samples/hox-wt-2005042101-humerus/hox-wt-2005042101-humerus.vff: [testng] [2024-06-21 01:26:16,400] [pool-1-thread-6] Initializing /data/samples/hox_wt_2005041201/hox-wt-04122005.vff: [testng] [2024-06-21 01:26:19,404] [pool-1-thread-4] Initializing /data/samples/Mouse_Hand_2004010700/Mouse_Hand_2004010700.vff: [testng] [2024-06-21 01:26:23,326] [pool-1-thread-10] Initializing /data/samples/Chick_Embryo_2003121700/Chick_Embryo_2003121700.vff: [testng] [2024-06-21 01:26:28,251] [pool-1-thread-9] Initializing /data/samples/Ping_1_2003112000/Ping_1_2003112000.vff: [testng] [2024-06-21 01:26:32,584] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005042701-humerus/hox-wt-2005042701-humerus.vff: [testng] [2024-06-21 01:26:34,149] [pool-1-thread-12] Initializing /data/samples/hox-wt-2005050801-humerus/hox-wt-20050508-01-humerus.vff: [testng] [2024-06-21 01:26:35,991] [pool-1-thread-2] Initializing /data/samples/Hersheys_Kiss_2003120100/Hersheys_Kiss_2003120100.vff: [testng] [2024-06-21 01:26:37,969] [pool-1-thread-7] Initializing /data/samples/Chick_Embryo_2003121200/Chick_Embryo_2003121200.vff: [testng] [2024-06-21 01:26:41,557] [pool-1-thread-11] Initializing /data/samples/how-wt-2005043001-humerus/how-wt-2005043001-humerus.vff: [testng] [2024-06-21 01:26:43,213] [pool-1-thread-5] Initializing /data/samples/mouse_skull_93um/mouse_skull_93um.vff: [testng] [2024-06-21 01:26:44,168] [pool-1-thread-1] Initializing /data/samples/Mouse_ankle_2003091500/AnkleJoint21umvoxels.vff: [testng] [2024-06-21 01:27:09,092] [pool-1-thread-3] Initializing /data/samples/hox_wt_2005041101/hox-wt-04112005-a.vff: [testng] [2024-06-21 01:27:11,880] [pool-1-thread-5] Initializing /data/samples/hox_wt_2005041301/hox-wt-04132005.vff: [testng] [2024-06-21 01:27:19,387] [pool-1-thread-6] Initializing /data/samples/Mouse_Hand_2004010900/Mouse_Hand_2004010900.vff: [testng] [2024-06-21 01:27:23,376] [pool-1-thread-12] Initializing /data/samples/Chick_Embryo_2003121201/Chick_Embryo_2003121201.vff: [testng] [2024-06-21 01:27:27,427] [pool-1-thread-8] Initializing /data/samples/Pepper_2003112000/Pepper_2003112000.vff: [testng] [2024-06-21 01:27:30,291] [pool-1-thread-11] Initializing /data/samples/Ping_1_2003112002/Ping_1_2003112002.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 5 seconds Finished: SUCCESS