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Started by upstream project "BIOFORMATS-test-repo" build number 273 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins6298039980735843390.sh + '[' prairie = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43078_merge_ci -v /uod/idr/repos/curated/prairie:/data -v /uod/idr-scratch/merge-ci/curated/prairie:/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] 10:15:46,367 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 10:15:46,368 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 10:15:46,368 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:15:46,369 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:15:46,369 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 10:15:46,370 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 10:15:46,370 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 10:15:46,370 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:15:46,370 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:15:46,371 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 10:15:46,371 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 10:15:46,371 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 10:15:46,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 10:15:46,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 10:15:46,612 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 10:15:46,612 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 10:15:46,619 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 10:15:46,619 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 10:15:46,620 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 10:15:46,620 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 10:15:46,620 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 10:15:46,621 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 10:15:46,621 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 251 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-29 10:15:46,630] [main] java.version = 1.8.0_342 [testng] 10:15:46,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 10:15:46,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:15:46,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-29_10-15-46.log] [testng] 10:15:46,677 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-29 10:15:46,679] [main] testng.directory = /data [testng] [2024-11-29 10:15:46,679] [main] testng.configDirectory = /config [testng] [2024-11-29 10:15:46,691] [main] testng.multiplier = 1.0 [testng] [2024-11-29 10:15:46,691] [main] testng.in-memory = false [testng] [2024-11-29 10:15:46,691] [main] testng.allow-missing = false [testng] [2024-11-29 10:15:46,691] [main] user.language = en [testng] [2024-11-29 10:15:46,691] [main] user.country = ${user.country} [testng] [2024-11-29 10:15:46,691] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-29 10:17:19,983] [main] ---------------------------------------- [testng] [2024-11-29 10:17:19,984] [main] Total files: 714 [testng] [2024-11-29 10:17:19,984] [main] Scan time: 93.292 s (130 ms/file) [testng] [2024-11-29 10:17:19,984] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 45 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-29 10:18:15,136] [pool-1-thread-1] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-001/pollen-001.xml: [testng] 10:18:15,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:18:15,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:15,137 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-29_10-18-15.log] [testng] 10:18:15,138 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7590b0ab - End of configuration. [testng] [2024-11-29 10:18:16,269] [pool-1-thread-12] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertynotchecked-001/TSeries-invertxchecked_invertynotchecked-001.xml: [testng] 10:18:16,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:18:16,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:16,270 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-29_10-18-16.log] [testng] 10:18:16,270 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3567dfb0 - End of configuration. [testng] [2024-11-29 10:18:17,421] [pool-1-thread-11] Initializing /data/pam/TSeries-09022010-171/TSeries-09022010-171.xml: [testng] 10:18:17,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:18:17,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:17,422 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-29_10-18-17.log] [testng] 10:18:17,423 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b1c1965 - End of configuration. [testng] [2024-11-29 10:18:18,451] [pool-1-thread-10] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-005/pollen-005.xml: [testng] 10:18:18,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:18:18,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:18,452 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-29_10-18-18.log] [testng] 10:18:18,453 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71bdecfc - End of configuration. [testng] [2024-11-29 10:18:19,635] [pool-1-thread-9] Initializing /data/julie/bill-bement/3/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml: [testng] 10:18:19,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:18:19,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:19,635 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-29_10-18-19.log] [testng] 10:18:19,636 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5579a1e4 - End of configuration. [testng] [2024-11-29 10:18:20,838] [pool-1-thread-8] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertychecked-001/TSeries-invertxnotchecked_invertychecked-001.xml: [testng] 10:18:20,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:18:20,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:20,839 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-29_10-18-20.log] [testng] 10:18:20,839 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a50c3dc - End of configuration. [testng] [2024-11-29 10:18:21,998] [pool-1-thread-7] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-006/TSeries-pollendouble-006.xml: [testng] 10:18:21,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:18:21,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:21,999 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-29_10-18-21.log] [testng] 10:18:21,999 |-INFO in ch.qos.logback.core.sift.SiftProcessor@589ecad - End of configuration. [testng] [2024-11-29 10:18:23,099] [pool-1-thread-6] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollendouble-003/ZSeries-pollendouble-003.xml: [testng] 10:18:23,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:18:23,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:23,100 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-29_10-18-23.log] [testng] 10:18:23,101 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f84242e - End of configuration. [testng] [2024-11-29 10:18:24,204] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollentriple-002/ZSeries-pollentriple-002.xml: [testng] 10:18:24,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:18:24,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:24,205 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-29_10-18-24.log] [testng] 10:18:24,205 |-INFO in ch.qos.logback.core.sift.SiftProcessor@589bca9b - End of configuration. [testng] [2024-11-29 10:18:25,366] [pool-1-thread-4] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollen-001/ZSeries-pollen-001.xml: [testng] 10:18:25,366 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:18:25,366 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:25,366 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-29_10-18-25.log] [testng] 10:18:25,367 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48a0dc0 - End of configuration. [testng] [2024-11-29 10:18:26,518] [pool-1-thread-3] Initializing /data/julie/bill-bement/5/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml: [testng] 10:18:26,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:18:26,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:26,519 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-29_10-18-26.log] [testng] 10:18:26,519 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4da01a25 - End of configuration. [testng] [2024-11-29 10:18:27,460] [pool-1-thread-2] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-003/TSeries-10092012-1446-003.xml: [testng] 10:18:27,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:18:27,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:27,461 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-29_10-18-27.log] [testng] 10:18:27,462 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37f6fc4c - End of configuration. [testng] [2024-11-29 10:18:55,752] [pool-1-thread-9] Initializing /data/julie/testslide6 2/testslide6 2.xml: [testng] [2024-11-29 10:18:57,204] [pool-1-thread-3] Initializing /data/julie/sample1-010/References/sample1-010_ImageWindow1Ch2-TSeriesReference.tif: [testng] [2024-11-29 10:19:00,919] [pool-1-thread-10] Initializing /data/julie/sample1-010/sample1-010.xml: [testng] [2024-11-29 10:19:02,303] [pool-1-thread-1] Initializing /data/julie/bill-bement/4/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml: [testng] [2024-11-29 10:19:11,996] [pool-1-thread-3] Initializing /data/pam/SingleImage-09022010/SingleImage-09022010.xml: [testng] [2024-11-29 10:19:27,932] [pool-1-thread-9] Initializing /data/joe/x,y inversion test/SingleImage-07312012-1639-099/SingleImage-07312012-1639-099.xml: [testng] [2024-11-29 10:19:29,532] [pool-1-thread-1] Initializing /data/marta/SingleImage-09272011-0856-001/SingleImage-09272011-0856-001.xml: [testng] [2024-11-29 10:19:31,467] [pool-1-thread-8] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertychecked-001/TSeries-invertxchecked_invertychecked-001.xml: [testng] [2024-11-29 10:19:32,971] [pool-1-thread-12] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-004/TSeries-pollendouble-004.xml: [testng] [2024-11-29 10:19:34,539] [pool-1-thread-3] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertynotchecked-001/TSeries-invertxnotchecked_invertynotchecked-001.xml: [testng] [2024-11-29 10:19:42,608] [pool-1-thread-4] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow1Ch4-TSeriesReference.tif: [testng] [2024-11-29 10:19:51,232] [pool-1-thread-9] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow2Ch3-TSeriesReference.tif: [testng] [2024-11-29 10:19:53,222] [pool-1-thread-1] Initializing /data/joe/x,y inversion test/1mg-dish1-wide-003/1mg-dish1-wide-003.xml: [testng] [2024-11-29 10:19:56,963] [pool-1-thread-4] Initializing /data/pam/ZSeries-09022010-356/ZSeries-09022010-356.xml: [testng] [2024-11-29 10:20:05,819] [pool-1-thread-7] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-003/pollen-003.xml: [testng] [2024-11-29 10:20:07,362] [pool-1-thread-9] Initializing /data/julie/sample1-010/sample1-010movie.avi: [testng] [2024-11-29 10:20:11,386] [pool-1-thread-9] Initializing /data/kristin/sampleset-001/sampleset-001.xml: [testng] [2024-11-29 10:20:28,938] [pool-1-thread-7] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-005/TSeries-10092012-1446-005.xml: [testng] [2024-11-29 10:20:36,140] [pool-1-thread-3] Initializing /data/julie/bill-bement/3/TSeries-10092012-1446-001/TSeries-10092012-1446-001.xml: [testng] [2024-11-29 10:20:37,717] [pool-1-thread-8] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-373/ZSeries-09292010-1520-373.xml: [testng] [2024-11-29 10:20:41,017] [pool-1-thread-6] Initializing /data/julie/bill-bement/6/TSeries-10092012-1446-006/TSeries-10092012-1446-006.xml: [testng] [2024-11-29 10:21:02,981] [pool-1-thread-4] Initializing /data/joe/TSeries-03232012-0934-006/TSeries-03232012-0934-006.xml: [testng] [2024-11-29 10:21:09,765] [pool-1-thread-11] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-008/pollenB-008.xml: [testng] [2024-11-29 10:21:17,988] [pool-1-thread-12] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-004/TSeries-10092012-1446-004.xml: [testng] [2024-11-29 10:21:38,547] [pool-1-thread-11] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-002/pollen-002.xml: [testng] [2024-11-29 10:21:40,172] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-007/pollenB-007.xml: [testng] [2024-11-29 10:22:03,534] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-006/pollenB-006.xml: [testng] [2024-11-29 10:22:12,099] [pool-1-thread-11] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-372/ZSeries-09292010-1520-372.xml: [testng] [2024-11-29 10:22:13,858] [pool-1-thread-12] Initializing /data/julie/test slide 1_3/test slide 1_3.xml: [testng] [2024-11-29 10:22:28,768] [pool-1-thread-5] Initializing /data/pam/TSeries-09022010-170/TSeries-09022010-170.xml: [testng] [2024-11-29 10:22:44,246] [pool-1-thread-10] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-002/TSeries-10092012-1446-002.xml: [testng] [2024-11-29 10:22:49,193] [pool-1-thread-12] Initializing /data/julie/bill-bement/6/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml: [testng] [2024-11-29 10:23:12,125] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-004/pollen-004.xml: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2385, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 33 minutes 54 seconds Finished: SUCCESS