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Started by upstream project "BIOFORMATS-test-repo" build number 38 originally caused by: Started by upstream project "Trigger" build number 44 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/jenkins3804566060288607357.sh + '[' microct = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_5234_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] 09:06:05,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 09:06:05,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 09:06:05,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 09:06:05,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 09:06:05,973 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 09:06:05,973 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 09:06:05,974 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 09:06:05,975 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 09:06:05,975 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5c30a9b0 - End of configuration. [testng] 09:06:05,977 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@7a69b07 - Registering current configuration as safe fallback point [testng] 09:06:05,977 |-INFO in ch.qos.logback.classic.util.ContextInitializer@5e82df6a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 457 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-19 09:06:05,995] [main] java.version = 1.8.0_342 [testng] 09:06:06,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:06:06,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:06:06,091 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-19_09-06-06.log] [testng] 09:06:06,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-19 09:06:06,096] [main] testng.directory = /data [testng] [2024-04-19 09:06:06,096] [main] testng.configDirectory = /config [testng] [2024-04-19 09:06:06,115] [main] testng.multiplier = 1.0 [testng] [2024-04-19 09:06:06,116] [main] testng.in-memory = false [testng] [2024-04-19 09:06:06,116] [main] testng.allow-missing = false [testng] [2024-04-19 09:06:06,116] [main] user.language = en [testng] [2024-04-19 09:06:06,116] [main] user.country = ${user.country} [testng] [2024-04-19 09:06:06,116] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-19 09:06:07,799] [main] ---------------------------------------- [testng] [2024-04-19 09:06:07,799] [main] Total files: 53 [testng] [2024-04-19 09:06:07,799] [main] Scan time: 1.683 s (31 ms/file) [testng] [2024-04-19 09:06:07,799] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 53 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-19 09:06:38,113] [pool-1-thread-1] Initializing /data/samples/hox-wt-2005050901-humerus/hox-wt-20050509-01-humerus.vff: [testng] 09:06:38,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 09:06:38,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:06:38,116 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-19_09-06-38.log] [testng] 09:06:38,117 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ae97074 - End of configuration. [testng] [2024-04-19 09:06:38,315] [pool-1-thread-12] Initializing /data/samples/how-wt-2005043001-humerus/how-wt-2005043001-humerus.vff: [testng] 09:06:38,316 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 09:06:38,316 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:06:38,317 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-19_09-06-38.log] [testng] 09:06:38,317 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42dda8fa - End of configuration. [testng] [2024-04-19 09:06:38,780] [pool-1-thread-11] Initializing /data/samples/orig.Mouse_Hand_2004010900/Mouse_Hand_2004010900.vff: [testng] 09:06:38,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 09:06:38,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:06:38,781 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-19_09-06-38.log] [testng] 09:06:38,781 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40ff437c - End of configuration. [testng] [2024-04-19 09:06:39,402] [pool-1-thread-10] Initializing /data/samples/hox-wt-2005050501-hand/hox-wt-20050505-01-hand.vff: [testng] 09:06:39,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 09:06:39,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:06:39,403 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-19_09-06-39.log] [testng] 09:06:39,404 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23628b26 - End of configuration. [testng] [2024-04-19 09:06:39,993] [pool-1-thread-9] Initializing /data/samples/Pepper_2003112000/Pepper_2003112000.vff: [testng] 09:06:39,993 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 09:06:39,993 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:06:39,994 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-19_09-06-39.log] [testng] 09:06:39,994 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58da87ab - End of configuration. [testng] [2024-04-19 09:06:40,709] [pool-1-thread-8] Initializing /data/samples/hox_wt_2005041401/hox-wt-04142005.vff: [testng] 09:06:40,710 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 09:06:40,710 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:06:40,710 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-19_09-06-40.log] [testng] 09:06:40,710 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ce1f0e1 - End of configuration. [testng] [2024-04-19 09:06:41,690] [pool-1-thread-7] Initializing /data/samples/hox_wt_2005040401/hox-wt-04042005-a.vff: [testng] 09:06:41,690 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 09:06:41,690 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:06:41,691 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-19_09-06-41.log] [testng] 09:06:41,691 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ccf3057 - End of configuration. [testng] [2024-04-19 09:06:42,169] [pool-1-thread-6] Initializing /data/samples/hox-wt-2005042701-humerus/hox-wt-2005042701-humerus.vff: [testng] 09:06:42,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 09:06:42,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:06:42,170 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-19_09-06-42.log] [testng] 09:06:42,171 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51fb89f1 - End of configuration. [testng] [2024-04-19 09:06:42,638] [pool-1-thread-5] Initializing /data/samples/hox-wt-2005050904-hand/hox-wt-20050509-04-hand.vff: [testng] 09:06:42,638 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 09:06:42,638 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:06:42,639 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-19_09-06-42.log] [testng] 09:06:42,639 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4979bb79 - End of configuration. [testng] [2024-04-19 09:06:42,982] [pool-1-thread-4] Initializing /data/samples/Chick_Embryo_2003121201/Chick_Embryo_2003121201.vff: [testng] 09:06:42,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 09:06:42,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:06:42,983 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-19_09-06-42.log] [testng] 09:06:42,983 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7da43f0f - End of configuration. [testng] [2024-04-19 09:06:43,652] [pool-1-thread-3] Initializing /data/samples/hox-wt-2005050901-hand/hox-wt-20050509-01-hand.vff: [testng] 09:06:43,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 09:06:43,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:06:43,653 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-19_09-06-43.log] [testng] 09:06:43,653 |-INFO in ch.qos.logback.core.sift.SiftProcessor@634f368c - End of configuration. [testng] [2024-04-19 09:06:44,384] [pool-1-thread-2] Initializing /data/samples/hox-wt-2005042601-hand/hox-wt-2005042601-hand.vff: [testng] 09:06:44,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 09:06:44,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:06:44,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-19_09-06-44.log] [testng] 09:06:44,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@254684c1 - End of configuration. [testng] [2024-04-19 09:07:19,012] [pool-1-thread-5] Initializing /data/samples/hox-wt-2005050904-humerus/hox-wt-20050509-04-humerus.vff: [testng] [2024-04-19 09:07:22,682] [pool-1-thread-6] Initializing /data/samples/hox-wt-2005050903-humerus/hox-wt-20050509-03-humerus.vff: [testng] [2024-04-19 09:07:24,994] [pool-1-thread-1] Initializing /data/samples/hox_wt_2005041101/hox-wt-04112005-a.vff: [testng] [2024-04-19 09:07:27,030] [pool-1-thread-12] Initializing /data/samples/hox-wt-2005050801-humerus/hox-wt-20050508-01-humerus.vff: [testng] [2024-04-19 09:07:28,694] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005050902-hand/hox-wt-20050509-02-hand.vff: [testng] [2024-04-19 09:07:30,406] [pool-1-thread-10] Initializing /data/samples/hox_wt_2005040501/hox-wt-04052005-a.vff: [testng] [2024-04-19 09:07:31,461] [pool-1-thread-2] Initializing /data/samples/hox_wt_2005040701/hox-wt-04072005-a.vff: [testng] [2024-04-19 09:07:31,952] [pool-1-thread-3] Initializing /data/samples/hox-wt-2005042201-hand/hox-wt-2005042201-hand.vff: [testng] [2024-04-19 09:07:32,571] [pool-1-thread-7] Initializing /data/samples/hox-wt-2005042601-humerus/hox-wt-2005042601-humerus.vff: [testng] [2024-04-19 09:07:53,223] [pool-1-thread-11] Initializing /data/samples/hox-wt-2005050201-humerus/hox-wt-20050502-01-humerus.vff: [testng] [2024-04-19 09:07:55,014] [pool-1-thread-9] Initializing /data/samples/Chick_Embryo_2003121700/Chick_Embryo_2003121700.vff: [testng] [2024-04-19 09:08:09,767] [pool-1-thread-4] Initializing /data/samples/hox-wt-2005050201-hand/hox-wt-20050502-01-hand.vff: [testng] [2024-04-19 09:08:12,960] [pool-1-thread-5] Initializing /data/samples/hox_wt_2005041201/hox-wt-04122005.vff: [testng] [2024-04-19 09:08:15,098] [pool-1-thread-12] Initializing /data/samples/hox-wt-2005042301-hand/hox-wt-2005042301-hand.vff: [testng] [2024-04-19 09:08:16,275] [pool-1-thread-8] Initializing /data/samples/hox-wt-2005042101-humerus/hox-wt-2005042101-humerus.vff: [testng] [2024-04-19 09:08:17,013] [pool-1-thread-6] Initializing /data/samples/hox-wt-2005050903-hand/hox-wt-20050509-03-hand.vff: [testng] [2024-04-19 09:08:17,583] [pool-1-thread-10] Initializing /data/samples/Ping_1_2003112001/Ping_1_2003112001.vff: [testng] [2024-04-19 09:08:18,335] [pool-1-thread-7] Initializing /data/samples/hox_wt_2005041301/hox-wt-04132005.vff: [testng] [2024-04-19 09:08:18,955] [pool-1-thread-3] Initializing /data/samples/hox-wt-2005050801-hand/hox-wt-20050508-01-hand.vff: [testng] [2024-04-19 09:08:29,414] [pool-1-thread-2] Initializing /data/samples/Hersheys_Kiss_2003120100/Hersheys_Kiss_2003120100.vff: [testng] [2024-04-19 09:08:32,533] [pool-1-thread-1] Initializing /data/samples/hox-wt-2005042301-humerus/hox-wt-2005042301-humerus.vff: [testng] [2024-04-19 09:08:41,895] [pool-1-thread-11] Initializing /data/samples/hox_wt_2005042701/hox-wt-2005042701-hand.vff: [testng] [2024-04-19 09:08:55,013] [pool-1-thread-8] Initializing /data/samples/Mouse_ankle_2003091500/AnkleJoint21umvoxels.vff: [testng] [2024-04-19 09:08:57,945] [pool-1-thread-4] Initializing /data/samples/Chick_Embryo_2003121200/Chick_Embryo_2003121200.vff: [testng] [2024-04-19 09:09:01,867] [pool-1-thread-12] Initializing /data/samples/how-wt-2005043001/how-wt-2005043001-hand.vff: [testng] [2024-04-19 09:09:03,972] [pool-1-thread-6] Initializing /data/samples/Mouse_Hand_2004010900/Mouse_Hand_2004010900.vff: [testng] [2024-04-19 09:09:05,858] [pool-1-thread-5] Initializing /data/samples/hox-wt-2005050902-humerus/hox-wt-20050509-02-humerus.vff: [testng] [2024-04-19 09:09:07,422] [pool-1-thread-3] Initializing /data/samples/Mouse_Hand_2004011200/Mouse_Hand_2004011200.vff: [testng] [2024-04-19 09:09:10,575] [pool-1-thread-7] Initializing /data/samples/hox-wt-2005050501-humerus/hox-wt-20050505-01-humerus.vff: [testng] [2024-04-19 09:09:11,930] [pool-1-thread-10] Initializing /data/samples/Mouse_Hand_2004010700/Mouse_Hand_2004010700.vff: [testng] [2024-04-19 09:09:13,850] [pool-1-thread-9] Initializing /data/samples/Bat_Small_2003092500/Bat_Small_2003092500.vff: [testng] [2024-04-19 09:09:16,052] [pool-1-thread-1] Initializing /data/samples/hox-wt-2005042201-humerus/hox-wt-2005042201-humerus.vff: [testng] [2024-04-19 09:09:35,891] [pool-1-thread-2] Initializing /data/samples/Ping_1_2003112002/Ping_1_2003112002.vff: [testng] [2024-04-19 09:09:47,548] [pool-1-thread-8] Initializing /data/samples/hox_wt_2005041501/hox-wt-04152005.vff: [testng] [2024-04-19 09:09:50,755] [pool-1-thread-11] Initializing /data/samples/mouse_skull_93um/mouse_skull_93um.vff: [testng] [2024-04-19 09:09:52,426] [pool-1-thread-7] Initializing /data/samples/Ping_1_2003112000/Ping_1_2003112000.vff: [testng] [2024-04-19 09:09:57,461] [pool-1-thread-12] Initializing /data/samples/Bat_Large_2003092500/Bat_Large_2003092500.vff: [testng] [2024-04-19 09:10:02,502] [pool-1-thread-1] Initializing /data/samples/hox-wt-2005042101-hand/hox-wt-2005042101-hand.vff: [testng] [2024-04-19 09:10:04,872] [pool-1-thread-5] Initializing /data/samples/Mouse_Hand_2004010701/Mouse_Hand_2004010701.vff: [testng] [2024-04-19 09:10:19,739] [pool-1-thread-9] Initializing /data/samples/Almond_Kiss_2003112600/Almond_Kiss_2003112600.vff: [testng] [2024-04-19 09:10:25,024] [pool-1-thread-10] 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 58 seconds Finished: SUCCESS