Started by upstream project "BIOFORMATS-test-repo" build number 59
originally caused by:
Started by upstream project "Trigger" build number 66
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4
[BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins8177362573101262481.sh
+ '[' prairie = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_8784_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] 02:18:30,455 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:18:30,456 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service.
[testng] 02:18:30,457 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:18:30,458 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:18:30,458 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:18:30,458 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:18:30,459 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 02:18:30,459 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:18:30,459 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:18:30,459 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:18:30,460 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:18:30,460 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:18:30,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:18:30,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:18:30,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:18:30,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:18:30,767 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:18:30,767 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:18:30,767 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:18:30,768 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:18:30,768 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration.
[testng] 02:18:30,769 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point
[testng] 02:18:30,769 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 310 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-05-10 02:18:30,780] [main] java.version = 1.8.0_342
[testng] 02:18:30,784 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:18:30,784 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:30,834 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-10_02-18-30.log]
[testng] 02:18:30,836 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration.
[testng] [2024-05-10 02:18:30,838] [main] testng.directory = /data
[testng] [2024-05-10 02:18:30,839] [main] testng.configDirectory = /config
[testng] [2024-05-10 02:18:30,852] [main] testng.multiplier = 1.0
[testng] [2024-05-10 02:18:30,853] [main] testng.in-memory = false
[testng] [2024-05-10 02:18:30,853] [main] testng.allow-missing = false
[testng] [2024-05-10 02:18:30,853] [main] user.language = en
[testng] [2024-05-10 02:18:30,853] [main] user.country = ${user.country}
[testng] [2024-05-10 02:18:30,853] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-05-10 02:18:41,991] [main] ----------------------------------------
[testng] [2024-05-10 02:18:41,992] [main] Total files: 714
[testng] [2024-05-10 02:18:41,992] [main] Scan time: 11.138 s (15 ms/file)
[testng] [2024-05-10 02:18:41,992] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 45 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-05-10 02:18:47,183] [pool-1-thread-1] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-002/pollen-002.xml:
[testng] 02:18:47,184 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:18:47,184 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:47,186 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-10_02-18-47.log]
[testng] 02:18:47,186 |-INFO in ch.qos.logback.core.sift.SiftProcessor@255e21ad - End of configuration.
[testng] [2024-05-10 02:18:47,237] [pool-1-thread-12] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertychecked-001/TSeries-invertxnotchecked_invertychecked-001.xml:
[testng] 02:18:47,237 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:18:47,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:47,239 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-10_02-18-47.log]
[testng] 02:18:47,239 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69e3790f - End of configuration.
[testng] [2024-05-10 02:18:47,282] [pool-1-thread-11] Initializing /data/pam/ZSeries-09022010-356/ZSeries-09022010-356.xml:
[testng] 02:18:47,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:18:47,283 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:47,283 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-10_02-18-47.log]
[testng] 02:18:47,284 |-INFO in ch.qos.logback.core.sift.SiftProcessor@445b3fbb - End of configuration.
[testng] [2024-05-10 02:18:47,313] [pool-1-thread-10] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-006/pollenB-006.xml:
[testng] 02:18:47,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:18:47,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:47,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-10_02-18-47.log]
[testng] 02:18:47,315 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44439959 - End of configuration.
[testng] [2024-05-10 02:18:47,336] [pool-1-thread-9] Initializing /data/julie/bill-bement/3/TSeries-10092012-1446-001/TSeries-10092012-1446-001.xml:
[testng] 02:18:47,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:18:47,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:47,337 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-10_02-18-47.log]
[testng] 02:18:47,337 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34fda6ad - End of configuration.
[testng] [2024-05-10 02:18:47,505] [pool-1-thread-8] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertynotchecked-001/TSeries-invertxnotchecked_invertynotchecked-001.xml:
[testng] 02:18:47,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:18:47,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:47,506 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-10_02-18-47.log]
[testng] 02:18:47,507 |-INFO in ch.qos.logback.core.sift.SiftProcessor@479c1285 - End of configuration.
[testng] [2024-05-10 02:18:47,545] [pool-1-thread-7] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollen-001/ZSeries-pollen-001.xml:
[testng] 02:18:47,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:18:47,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:47,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-10_02-18-47.log]
[testng] 02:18:47,547 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30c8629b - End of configuration.
[testng] [2024-05-10 02:18:47,581] [pool-1-thread-6] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollentriple-002/ZSeries-pollentriple-002.xml:
[testng] 02:18:47,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:18:47,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:47,583 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-10_02-18-47.log]
[testng] 02:18:47,583 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c16df15 - End of configuration.
[testng] [2024-05-10 02:18:47,608] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-001/pollen-001.xml:
[testng] 02:18:47,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:18:47,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:47,609 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-10_02-18-47.log]
[testng] 02:18:47,610 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b0c4ff3 - End of configuration.
[testng] [2024-05-10 02:18:47,637] [pool-1-thread-4] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollendouble-003/ZSeries-pollendouble-003.xml:
[testng] 02:18:47,637 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:18:47,637 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:47,638 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-10_02-18-47.log]
[testng] 02:18:47,638 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63b1fe05 - End of configuration.
[testng] [2024-05-10 02:18:47,662] [pool-1-thread-3] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-004/TSeries-10092012-1446-004.xml:
[testng] 02:18:47,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:18:47,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:47,663 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-10_02-18-47.log]
[testng] 02:18:47,664 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41cadf98 - End of configuration.
[testng] [2024-05-10 02:18:47,693] [pool-1-thread-2] Initializing /data/julie/bill-bement/5/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] 02:18:47,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:18:47,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:47,695 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-10_02-18-47.log]
[testng] 02:18:47,695 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b22461c - End of configuration.
[testng] [2024-05-10 02:18:50,189] [pool-1-thread-2] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow1Ch4-TSeriesReference.tif:
[testng] [2024-05-10 02:18:50,219] [pool-1-thread-10] Initializing /data/pam/TSeries-09022010-170/TSeries-09022010-170.xml:
[testng] [2024-05-10 02:18:50,240] [pool-1-thread-1] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-002/TSeries-10092012-1446-002.xml:
[testng] [2024-05-10 02:18:50,265] [pool-1-thread-5] Initializing /data/julie/sample1-010/sample1-010movie.avi:
[testng] [2024-05-10 02:18:50,293] [pool-1-thread-11] Initializing /data/julie/sample1-010/sample1-010.xml:
[testng] [2024-05-10 02:18:50,646] [pool-1-thread-7] Initializing /data/joe/TSeries-03232012-0934-006/TSeries-03232012-0934-006.xml:
[testng] [2024-05-10 02:18:51,222] [pool-1-thread-5] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertychecked-001/TSeries-invertxchecked_invertychecked-001.xml:
[testng] [2024-05-10 02:18:51,633] [pool-1-thread-2] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-004/TSeries-pollendouble-004.xml:
[testng] [2024-05-10 02:18:51,984] [pool-1-thread-10] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertynotchecked-001/TSeries-invertxchecked_invertynotchecked-001.xml:
[testng] [2024-05-10 02:18:52,299] [pool-1-thread-3] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-006/TSeries-pollendouble-006.xml:
[testng] [2024-05-10 02:18:52,706] [pool-1-thread-4] Initializing /data/julie/bill-bement/3/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] [2024-05-10 02:18:53,292] [pool-1-thread-1] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow2Ch3-TSeriesReference.tif:
[testng] [2024-05-10 02:18:53,327] [pool-1-thread-4] Initializing /data/kristin/sampleset-001/sampleset-001.xml:
[testng] [2024-05-10 02:18:53,488] [pool-1-thread-12] Initializing /data/joe/x,y inversion test/SingleImage-07312012-1639-099/SingleImage-07312012-1639-099.xml:
[testng] [2024-05-10 02:18:53,595] [pool-1-thread-8] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-004/pollen-004.xml:
[testng] [2024-05-10 02:18:53,985] [pool-1-thread-6] Initializing /data/julie/test slide 1_3/test slide 1_3.xml:
[testng] [2024-05-10 02:18:54,006] [pool-1-thread-1] Initializing /data/marta/SingleImage-09272011-0856-001/SingleImage-09272011-0856-001.xml:
[testng] [2024-05-10 02:18:54,034] [pool-1-thread-12] Initializing /data/julie/bill-bement/6/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] [2024-05-10 02:18:54,234] [pool-1-thread-8] Initializing /data/julie/bill-bement/4/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] [2024-05-10 02:18:54,500] [pool-1-thread-2] Initializing /data/pam/SingleImage-09022010/SingleImage-09022010.xml:
[testng] [2024-05-10 02:18:54,535] [pool-1-thread-12] Initializing /data/julie/sample1-010/References/sample1-010_ImageWindow1Ch2-TSeriesReference.tif:
[testng] [2024-05-10 02:18:54,751] [pool-1-thread-8] Initializing /data/joe/x,y inversion test/1mg-dish1-wide-003/1mg-dish1-wide-003.xml:
[testng] [2024-05-10 02:18:54,844] [pool-1-thread-1] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-372/ZSeries-09292010-1520-372.xml:
[testng] [2024-05-10 02:18:54,965] [pool-1-thread-6] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-005/TSeries-10092012-1446-005.xml:
[testng] [2024-05-10 02:18:55,180] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-003/pollen-003.xml:
[testng] [2024-05-10 02:18:55,235] [pool-1-thread-3] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-008/pollenB-008.xml:
[testng] [2024-05-10 02:18:55,346] [pool-1-thread-2] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-007/pollenB-007.xml:
[testng] [2024-05-10 02:18:55,423] [pool-1-thread-10] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-373/ZSeries-09292010-1520-373.xml:
[testng] [2024-05-10 02:18:55,581] [pool-1-thread-12] Initializing /data/julie/testslide6 2/testslide6 2.xml:
[testng] [2024-05-10 02:18:55,731] [pool-1-thread-5] Initializing /data/pam/TSeries-09022010-171/TSeries-09022010-171.xml:
[testng] [2024-05-10 02:18:55,892] [pool-1-thread-2] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-003/TSeries-10092012-1446-003.xml:
[testng] [2024-05-10 02:18:56,100] [pool-1-thread-3] Initializing /data/julie/bill-bement/6/TSeries-10092012-1446-006/TSeries-10092012-1446-006.xml:
[testng] [2024-05-10 02:18:56,430] [pool-1-thread-12] 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 40 seconds
Finished: SUCCESS