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Started by upstream project "BIOFORMATS-test-repo" build number 133 originally caused by: Started by upstream project "Trigger" build number 153 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/jenkins9344172256482738821.sh + '[' prairie = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_20920_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] 02:22:27,741 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:22:27,743 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 02:22:27,743 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:22:27,744 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:22:27,744 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:22:27,744 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:22:27,744 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:22:27,744 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:22:27,745 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:22:27,745 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:22:27,745 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:22:27,745 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:22:27,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:22:27,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:22:28,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:22:28,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:22:28,023 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:22:28,023 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:22:28,023 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:22:28,023 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:22:28,023 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 02:22:28,024 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 02:22:28,024 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 279 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-26 02:22:28,034] [main] java.version = 1.8.0_342 [testng] 02:22:28,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:22:28,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:28,083 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-26_02-22-28.log] [testng] 02:22:28,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-26 02:22:28,087] [main] testng.directory = /data [testng] [2024-07-26 02:22:28,087] [main] testng.configDirectory = /config [testng] [2024-07-26 02:22:28,100] [main] testng.multiplier = 1.0 [testng] [2024-07-26 02:22:28,100] [main] testng.in-memory = false [testng] [2024-07-26 02:22:28,100] [main] testng.allow-missing = false [testng] [2024-07-26 02:22:28,100] [main] user.language = en [testng] [2024-07-26 02:22:28,100] [main] user.country = ${user.country} [testng] [2024-07-26 02:22:28,100] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-26 02:22:38,979] [main] ---------------------------------------- [testng] [2024-07-26 02:22:38,980] [main] Total files: 714 [testng] [2024-07-26 02:22:38,980] [main] Scan time: 10.879 s (15 ms/file) [testng] [2024-07-26 02:22:38,980] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 45 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-26 02:22:44,283] [pool-1-thread-1] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-002/pollen-002.xml: [testng] 02:22:44,284 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:22:44,284 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:44,285 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-26_02-22-44.log] [testng] 02:22:44,286 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4235f99 - End of configuration. [testng] [2024-07-26 02:22:44,323] [pool-1-thread-12] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertychecked-001/TSeries-invertxnotchecked_invertychecked-001.xml: [testng] 02:22:44,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:22:44,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:44,324 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-26_02-22-44.log] [testng] 02:22:44,324 |-INFO in ch.qos.logback.core.sift.SiftProcessor@166566df - End of configuration. [testng] [2024-07-26 02:22:44,358] [pool-1-thread-11] Initializing /data/pam/ZSeries-09022010-356/ZSeries-09022010-356.xml: [testng] 02:22:44,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:22:44,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:44,359 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-26_02-22-44.log] [testng] 02:22:44,360 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34a71ea - End of configuration. [testng] [2024-07-26 02:22:44,383] [pool-1-thread-10] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-006/pollenB-006.xml: [testng] 02:22:44,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:22:44,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:44,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-26_02-22-44.log] [testng] 02:22:44,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d7fe8b7 - End of configuration. [testng] [2024-07-26 02:22:44,408] [pool-1-thread-9] Initializing /data/julie/bill-bement/3/TSeries-10092012-1446-001/TSeries-10092012-1446-001.xml: [testng] 02:22:44,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:22:44,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:44,409 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-26_02-22-44.log] [testng] 02:22:44,410 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c48957 - End of configuration. [testng] [2024-07-26 02:22:44,563] [pool-1-thread-8] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertynotchecked-001/TSeries-invertxnotchecked_invertynotchecked-001.xml: [testng] 02:22:44,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:22:44,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:44,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-26_02-22-44.log] [testng] 02:22:44,565 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a70c5a9 - End of configuration. [testng] [2024-07-26 02:22:44,600] [pool-1-thread-7] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollen-001/ZSeries-pollen-001.xml: [testng] 02:22:44,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:22:44,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:44,601 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-26_02-22-44.log] [testng] 02:22:44,602 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3fd93799 - End of configuration. [testng] [2024-07-26 02:22:44,627] [pool-1-thread-6] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollentriple-002/ZSeries-pollentriple-002.xml: [testng] 02:22:44,627 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:22:44,627 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:44,628 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-26_02-22-44.log] [testng] 02:22:44,628 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f390dd1 - End of configuration. [testng] [2024-07-26 02:22:44,659] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-001/pollen-001.xml: [testng] 02:22:44,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:22:44,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:44,660 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-26_02-22-44.log] [testng] 02:22:44,660 |-INFO in ch.qos.logback.core.sift.SiftProcessor@462540f - End of configuration. [testng] [2024-07-26 02:22:44,681] [pool-1-thread-4] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollendouble-003/ZSeries-pollendouble-003.xml: [testng] 02:22:44,681 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:22:44,681 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:44,682 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-26_02-22-44.log] [testng] 02:22:44,682 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79ca0e5c - End of configuration. [testng] [2024-07-26 02:22:44,705] [pool-1-thread-3] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-004/TSeries-10092012-1446-004.xml: [testng] 02:22:44,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:22:44,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:44,706 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-26_02-22-44.log] [testng] 02:22:44,706 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ea190ba - End of configuration. [testng] [2024-07-26 02:22:44,739] [pool-1-thread-2] Initializing /data/julie/bill-bement/5/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml: [testng] 02:22:44,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:22:44,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:44,740 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-26_02-22-44.log] [testng] 02:22:44,741 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e1b9a09 - End of configuration. [testng] [2024-07-26 02:22:46,742] [pool-1-thread-2] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow1Ch4-TSeriesReference.tif: [testng] [2024-07-26 02:22:47,019] [pool-1-thread-10] Initializing /data/julie/sample1-010/sample1-010.xml: [testng] [2024-07-26 02:22:47,070] [pool-1-thread-5] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-002/TSeries-10092012-1446-002.xml: [testng] [2024-07-26 02:22:47,102] [pool-1-thread-1] Initializing /data/julie/sample1-010/sample1-010movie.avi: [testng] [2024-07-26 02:22:47,598] [pool-1-thread-11] Initializing /data/pam/TSeries-09022010-170/TSeries-09022010-170.xml: [testng] [2024-07-26 02:22:47,625] [pool-1-thread-7] Initializing /data/joe/TSeries-03232012-0934-006/TSeries-03232012-0934-006.xml: [testng] [2024-07-26 02:22:47,932] [pool-1-thread-1] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertychecked-001/TSeries-invertxchecked_invertychecked-001.xml: [testng] [2024-07-26 02:22:48,077] [pool-1-thread-2] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-004/TSeries-pollendouble-004.xml: [testng] [2024-07-26 02:22:48,376] [pool-1-thread-3] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertynotchecked-001/TSeries-invertxchecked_invertynotchecked-001.xml: [testng] [2024-07-26 02:22:48,817] [pool-1-thread-11] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-006/TSeries-pollendouble-006.xml: [testng] [2024-07-26 02:22:49,319] [pool-1-thread-4] Initializing /data/julie/bill-bement/3/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml: [testng] [2024-07-26 02:22:49,468] [pool-1-thread-5] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow2Ch3-TSeriesReference.tif: [testng] [2024-07-26 02:22:49,661] [pool-1-thread-8] Initializing /data/kristin/sampleset-001/sampleset-001.xml: [testng] [2024-07-26 02:22:49,792] [pool-1-thread-12] Initializing /data/joe/x,y inversion test/SingleImage-07312012-1639-099/SingleImage-07312012-1639-099.xml: [testng] [2024-07-26 02:22:49,924] [pool-1-thread-4] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-004/pollen-004.xml: [testng] [2024-07-26 02:22:50,072] [pool-1-thread-5] Initializing /data/julie/test slide 1_3/test slide 1_3.xml: [testng] [2024-07-26 02:22:50,413] [pool-1-thread-12] Initializing /data/marta/SingleImage-09272011-0856-001/SingleImage-09272011-0856-001.xml: [testng] [2024-07-26 02:22:50,699] [pool-1-thread-4] Initializing /data/julie/bill-bement/6/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml: [testng] [2024-07-26 02:22:50,726] [pool-1-thread-6] Initializing /data/julie/bill-bement/4/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml: [testng] [2024-07-26 02:22:50,973] [pool-1-thread-2] Initializing /data/pam/SingleImage-09022010/SingleImage-09022010.xml: [testng] [2024-07-26 02:22:51,127] [pool-1-thread-5] Initializing /data/julie/sample1-010/References/sample1-010_ImageWindow1Ch2-TSeriesReference.tif: [testng] [2024-07-26 02:22:51,275] [pool-1-thread-4] Initializing /data/joe/x,y inversion test/1mg-dish1-wide-003/1mg-dish1-wide-003.xml: [testng] [2024-07-26 02:22:51,432] [pool-1-thread-6] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-372/ZSeries-09292010-1520-372.xml: [testng] [2024-07-26 02:22:51,582] [pool-1-thread-12] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-005/TSeries-10092012-1446-005.xml: [testng] [2024-07-26 02:22:51,784] [pool-1-thread-1] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-003/pollen-003.xml: [testng] [2024-07-26 02:22:51,815] [pool-1-thread-2] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-008/pollenB-008.xml: [testng] [2024-07-26 02:22:51,837] [pool-1-thread-11] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-007/pollenB-007.xml: [testng] [2024-07-26 02:22:51,985] [pool-1-thread-3] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-373/ZSeries-09292010-1520-373.xml: [testng] [2024-07-26 02:22:52,143] [pool-1-thread-5] Initializing /data/julie/testslide6 2/testslide6 2.xml: [testng] [2024-07-26 02:22:52,520] [pool-1-thread-1] Initializing /data/pam/TSeries-09022010-171/TSeries-09022010-171.xml: [testng] [2024-07-26 02:22:52,646] [pool-1-thread-2] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-003/TSeries-10092012-1446-003.xml: [testng] [2024-07-26 02:22:52,816] [pool-1-thread-11] Initializing /data/julie/bill-bement/6/TSeries-10092012-1446-006/TSeries-10092012-1446-006.xml: [testng] [2024-07-26 02:22:53,296] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-005/pollen-005.xml: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2385, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 1 minute 36 seconds Finished: SUCCESS