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Started by upstream project "BIOFORMATS-test-repo" build number 264 originally caused by: Started by upstream project "Trigger" build number 287 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins7996515917855320171.sh + '[' prairie = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41731_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] 03:49:58,887 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:49:58,888 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 03:49:58,888 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:49:58,889 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:49:58,890 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:49:58,890 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:49:58,890 |-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] 03:49:58,890 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:49:58,891 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:49:58,891 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:49:58,891 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:49:58,891 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:49:59,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:49:59,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:49:59,168 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:49:59,168 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:49:59,177 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:49:59,177 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:49:59,177 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:49:59,178 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:49:59,178 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 03:49:59,179 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 03:49:59,179 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 288 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-22 03:49:59,190] [main] java.version = 1.8.0_342 [testng] 03:49:59,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:49:59,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:59,241 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-22_03-49-59.log] [testng] 03:49:59,243 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-22 03:49:59,245] [main] testng.directory = /data [testng] [2024-11-22 03:49:59,245] [main] testng.configDirectory = /config [testng] [2024-11-22 03:49:59,259] [main] testng.multiplier = 1.0 [testng] [2024-11-22 03:49:59,259] [main] testng.in-memory = false [testng] [2024-11-22 03:49:59,259] [main] testng.allow-missing = false [testng] [2024-11-22 03:49:59,259] [main] user.language = en [testng] [2024-11-22 03:49:59,259] [main] user.country = ${user.country} [testng] [2024-11-22 03:49:59,259] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-22 03:50:49,194] [main] ---------------------------------------- [testng] [2024-11-22 03:50:49,194] [main] Total files: 714 [testng] [2024-11-22 03:50:49,194] [main] Scan time: 49.935 s (69 ms/file) [testng] [2024-11-22 03:50:49,195] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 45 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-22 03:51:16,184] [pool-1-thread-1] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-001/pollen-001.xml: [testng] 03:51:16,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:51:16,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:16,187 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-22_03-51-16.log] [testng] 03:51:16,188 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ed0f2a9 - End of configuration. [testng] [2024-11-22 03:51:16,648] [pool-1-thread-12] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertynotchecked-001/TSeries-invertxchecked_invertynotchecked-001.xml: [testng] 03:51:16,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:51:16,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:16,649 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-22_03-51-16.log] [testng] 03:51:16,650 |-INFO in ch.qos.logback.core.sift.SiftProcessor@578dfcdb - End of configuration. [testng] [2024-11-22 03:51:17,087] [pool-1-thread-11] Initializing /data/pam/TSeries-09022010-171/TSeries-09022010-171.xml: [testng] 03:51:17,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:51:17,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:17,088 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-22_03-51-17.log] [testng] 03:51:17,088 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33f6cf9a - End of configuration. [testng] [2024-11-22 03:51:17,538] [pool-1-thread-10] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-005/pollen-005.xml: [testng] 03:51:17,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:51:17,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:17,539 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-22_03-51-17.log] [testng] 03:51:17,539 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7152bfec - End of configuration. [testng] [2024-11-22 03:51:17,947] [pool-1-thread-9] Initializing /data/julie/bill-bement/3/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml: [testng] 03:51:17,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:51:17,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:17,948 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-22_03-51-17.log] [testng] 03:51:17,948 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e4d4efd - End of configuration. [testng] [2024-11-22 03:51:18,340] [pool-1-thread-8] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertychecked-001/TSeries-invertxnotchecked_invertychecked-001.xml: [testng] 03:51:18,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:51:18,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:18,341 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-22_03-51-18.log] [testng] 03:51:18,341 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e1016f2 - End of configuration. [testng] [2024-11-22 03:51:18,748] [pool-1-thread-7] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-006/TSeries-pollendouble-006.xml: [testng] 03:51:18,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:51:18,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:18,757 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-22_03-51-18.log] [testng] 03:51:18,757 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c1996d - End of configuration. [testng] [2024-11-22 03:51:19,179] [pool-1-thread-6] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollendouble-003/ZSeries-pollendouble-003.xml: [testng] 03:51:19,180 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:51:19,180 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:19,180 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-22_03-51-19.log] [testng] 03:51:19,181 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e392600 - End of configuration. [testng] [2024-11-22 03:51:19,598] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollentriple-002/ZSeries-pollentriple-002.xml: [testng] 03:51:19,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:51:19,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:19,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-22_03-51-19.log] [testng] 03:51:19,599 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b12301a - End of configuration. [testng] [2024-11-22 03:51:20,034] [pool-1-thread-4] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollen-001/ZSeries-pollen-001.xml: [testng] 03:51:20,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:51:20,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:20,034 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-22_03-51-20.log] [testng] 03:51:20,035 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b6e3da1 - End of configuration. [testng] [2024-11-22 03:51:20,477] [pool-1-thread-3] Initializing /data/julie/bill-bement/5/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml: [testng] 03:51:20,477 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:51:20,477 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:20,478 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-22_03-51-20.log] [testng] 03:51:20,478 |-INFO in ch.qos.logback.core.sift.SiftProcessor@648686fc - End of configuration. [testng] [2024-11-22 03:51:20,902] [pool-1-thread-2] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-003/TSeries-10092012-1446-003.xml: [testng] 03:51:20,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:51:20,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:20,903 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-22_03-51-20.log] [testng] 03:51:20,904 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bb4c108 - End of configuration. [testng] [2024-11-22 03:51:37,818] [pool-1-thread-3] Initializing /data/julie/testslide6 2/testslide6 2.xml: [testng] [2024-11-22 03:51:38,719] [pool-1-thread-9] Initializing /data/julie/sample1-010/References/sample1-010_ImageWindow1Ch2-TSeriesReference.tif: [testng] [2024-11-22 03:51:39,916] [pool-1-thread-10] Initializing /data/julie/sample1-010/sample1-010.xml: [testng] [2024-11-22 03:51:40,704] [pool-1-thread-1] Initializing /data/julie/bill-bement/4/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml: [testng] [2024-11-22 03:51:47,587] [pool-1-thread-9] Initializing /data/pam/SingleImage-09022010/SingleImage-09022010.xml: [testng] [2024-11-22 03:51:56,343] [pool-1-thread-1] Initializing /data/joe/x,y inversion test/SingleImage-07312012-1639-099/SingleImage-07312012-1639-099.xml: [testng] [2024-11-22 03:51:58,433] [pool-1-thread-8] Initializing /data/marta/SingleImage-09272011-0856-001/SingleImage-09272011-0856-001.xml: [testng] [2024-11-22 03:51:59,377] [pool-1-thread-3] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertychecked-001/TSeries-invertxchecked_invertychecked-001.xml: [testng] [2024-11-22 03:52:00,233] [pool-1-thread-12] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-004/TSeries-pollendouble-004.xml: [testng] [2024-11-22 03:52:01,107] [pool-1-thread-9] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertynotchecked-001/TSeries-invertxnotchecked_invertynotchecked-001.xml: [testng] [2024-11-22 03:52:05,792] [pool-1-thread-4] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow1Ch4-TSeriesReference.tif: [testng] [2024-11-22 03:52:10,836] [pool-1-thread-1] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow2Ch3-TSeriesReference.tif: [testng] [2024-11-22 03:52:14,191] [pool-1-thread-4] Initializing /data/joe/x,y inversion test/1mg-dish1-wide-003/1mg-dish1-wide-003.xml: [testng] [2024-11-22 03:52:15,150] [pool-1-thread-8] Initializing /data/pam/ZSeries-09022010-356/ZSeries-09022010-356.xml: [testng] [2024-11-22 03:52:19,823] [pool-1-thread-1] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-003/pollen-003.xml: [testng] [2024-11-22 03:52:20,737] [pool-1-thread-7] Initializing /data/julie/sample1-010/sample1-010movie.avi: [testng] [2024-11-22 03:52:23,289] [pool-1-thread-7] Initializing /data/kristin/sampleset-001/sampleset-001.xml: [testng] [2024-11-22 03:52:33,282] [pool-1-thread-1] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-005/TSeries-10092012-1446-005.xml: [testng] [2024-11-22 03:52:38,379] [pool-1-thread-9] Initializing /data/julie/bill-bement/3/TSeries-10092012-1446-001/TSeries-10092012-1446-001.xml: [testng] [2024-11-22 03:52:39,276] [pool-1-thread-3] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-373/ZSeries-09292010-1520-373.xml: [testng] [2024-11-22 03:52:40,129] [pool-1-thread-6] Initializing /data/julie/bill-bement/6/TSeries-10092012-1446-006/TSeries-10092012-1446-006.xml: [testng] [2024-11-22 03:52:52,414] [pool-1-thread-8] Initializing /data/joe/TSeries-03232012-0934-006/TSeries-03232012-0934-006.xml: [testng] [2024-11-22 03:52:55,201] [pool-1-thread-11] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-008/pollenB-008.xml: [testng] [2024-11-22 03:52:59,814] [pool-1-thread-12] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-004/TSeries-10092012-1446-004.xml: [testng] [2024-11-22 03:53:11,117] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-002/pollen-002.xml: [testng] [2024-11-22 03:53:12,026] [pool-1-thread-11] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-007/pollenB-007.xml: [testng] [2024-11-22 03:53:25,431] [pool-1-thread-11] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-006/pollenB-006.xml: [testng] [2024-11-22 03:53:30,282] [pool-1-thread-5] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-372/ZSeries-09292010-1520-372.xml: [testng] [2024-11-22 03:53:32,118] [pool-1-thread-12] Initializing /data/julie/test slide 1_3/test slide 1_3.xml: [testng] [2024-11-22 03:53:40,947] [pool-1-thread-11] Initializing /data/pam/TSeries-09022010-170/TSeries-09022010-170.xml: [testng] [2024-11-22 03:53:50,162] [pool-1-thread-10] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-002/TSeries-10092012-1446-002.xml: [testng] [2024-11-22 03:53:53,037] [pool-1-thread-12] Initializing /data/julie/bill-bement/6/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml: [testng] [2024-11-22 03:54:05,368] [pool-1-thread-11] 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: 42 minutes 26 seconds Finished: SUCCESS