Started by upstream project "BIOFORMATS-test-repo" build number 249
originally caused by:
Started by upstream project "Trigger" build number 273
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/jenkins8939890990705374638.sh
+ '[' prairie = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_39271_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] 03:48:22,967 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 03:48:22,969 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service.
[testng] 03:48:22,969 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 03:48:22,970 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 03:48:22,970 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 03:48:22,970 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 03:48:22,971 |-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] 03:48:22,971 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 03:48:22,971 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 03:48:22,971 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 03:48:22,971 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 03:48:22,972 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 03:48:23,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 03:48:23,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 03:48:23,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 03:48:23,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 03:48:23,226 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 03:48:23,226 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 03:48:23,226 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 03:48:23,227 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 03:48:23,227 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration.
[testng] 03:48:23,227 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point
[testng] 03:48:23,227 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 256 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-08 03:48:23,237] [main] java.version = 1.8.0_342
[testng] 03:48:23,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 03:48:23,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:48:23,284 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-08_03-48-23.log]
[testng] 03:48:23,285 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration.
[testng] [2024-11-08 03:48:23,287] [main] testng.directory = /data
[testng] [2024-11-08 03:48:23,287] [main] testng.configDirectory = /config
[testng] [2024-11-08 03:48:23,300] [main] testng.multiplier = 1.0
[testng] [2024-11-08 03:48:23,300] [main] testng.in-memory = false
[testng] [2024-11-08 03:48:23,300] [main] testng.allow-missing = false
[testng] [2024-11-08 03:48:23,300] [main] user.language = en
[testng] [2024-11-08 03:48:23,300] [main] user.country = ${user.country}
[testng] [2024-11-08 03:48:23,300] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-11-08 03:49:31,866] [main] ----------------------------------------
[testng] [2024-11-08 03:49:31,867] [main] Total files: 714
[testng] [2024-11-08 03:49:31,867] [main] Scan time: 68.566 s (96 ms/file)
[testng] [2024-11-08 03:49:31,867] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 45 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-08 03:49:52,705] [pool-1-thread-1] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-001/pollen-001.xml:
[testng] 03:49:52,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 03:49:52,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:49:52,707 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-08_03-49-52.log]
[testng] 03:49:52,708 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b09b60a - End of configuration.
[testng] [2024-11-08 03:49:53,023] [pool-1-thread-12] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertynotchecked-001/TSeries-invertxchecked_invertynotchecked-001.xml:
[testng] 03:49:53,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 03:49:53,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:49:53,024 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-08_03-49-53.log]
[testng] 03:49:53,025 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b685b20 - End of configuration.
[testng] [2024-11-08 03:49:53,383] [pool-1-thread-11] Initializing /data/pam/TSeries-09022010-171/TSeries-09022010-171.xml:
[testng] 03:49:53,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 03:49:53,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:49:53,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-08_03-49-53.log]
[testng] 03:49:53,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d189e47 - End of configuration.
[testng] [2024-11-08 03:49:53,761] [pool-1-thread-10] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-005/pollen-005.xml:
[testng] 03:49:53,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 03:49:53,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:49:53,762 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-08_03-49-53.log]
[testng] 03:49:53,762 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37e26438 - End of configuration.
[testng] [2024-11-08 03:49:54,123] [pool-1-thread-9] Initializing /data/julie/bill-bement/3/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] 03:49:54,123 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 03:49:54,123 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:49:54,124 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-08_03-49-54.log]
[testng] 03:49:54,124 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cb23d5e - End of configuration.
[testng] [2024-11-08 03:49:54,535] [pool-1-thread-8] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertychecked-001/TSeries-invertxnotchecked_invertychecked-001.xml:
[testng] 03:49:54,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 03:49:54,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:49:54,535 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-08_03-49-54.log]
[testng] 03:49:54,536 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2bfbf8ec - End of configuration.
[testng] [2024-11-08 03:49:54,960] [pool-1-thread-7] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-006/TSeries-pollendouble-006.xml:
[testng] 03:49:54,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 03:49:54,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:49:54,961 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-08_03-49-54.log]
[testng] 03:49:54,961 |-INFO in ch.qos.logback.core.sift.SiftProcessor@276cd805 - End of configuration.
[testng] [2024-11-08 03:49:55,354] [pool-1-thread-6] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollendouble-003/ZSeries-pollendouble-003.xml:
[testng] 03:49:55,354 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 03:49:55,354 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:49:55,355 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-08_03-49-55.log]
[testng] 03:49:55,355 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6409237 - End of configuration.
[testng] [2024-11-08 03:49:55,779] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollentriple-002/ZSeries-pollentriple-002.xml:
[testng] 03:49:55,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 03:49:55,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:49:55,780 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-08_03-49-55.log]
[testng] 03:49:55,781 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d5176d4 - End of configuration.
[testng] [2024-11-08 03:49:56,154] [pool-1-thread-4] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollen-001/ZSeries-pollen-001.xml:
[testng] 03:49:56,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 03:49:56,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:49:56,155 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-08_03-49-56.log]
[testng] 03:49:56,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4170ee29 - End of configuration.
[testng] [2024-11-08 03:49:56,557] [pool-1-thread-3] Initializing /data/julie/bill-bement/5/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] 03:49:56,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 03:49:56,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:49:56,557 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-08_03-49-56.log]
[testng] 03:49:56,558 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c981d7a - End of configuration.
[testng] [2024-11-08 03:49:56,915] [pool-1-thread-2] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-003/TSeries-10092012-1446-003.xml:
[testng] 03:49:56,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 03:49:56,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:49:56,916 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-08_03-49-56.log]
[testng] 03:49:56,916 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bf7be4 - End of configuration.
[testng] [2024-11-08 03:50:14,195] [pool-1-thread-9] Initializing /data/julie/testslide6 2/testslide6 2.xml:
[testng] [2024-11-08 03:50:15,181] [pool-1-thread-3] Initializing /data/julie/sample1-010/References/sample1-010_ImageWindow1Ch2-TSeriesReference.tif:
[testng] [2024-11-08 03:50:16,441] [pool-1-thread-1] Initializing /data/julie/sample1-010/sample1-010.xml:
[testng] [2024-11-08 03:50:17,258] [pool-1-thread-10] Initializing /data/julie/bill-bement/4/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] [2024-11-08 03:50:24,749] [pool-1-thread-3] Initializing /data/pam/SingleImage-09022010/SingleImage-09022010.xml:
[testng] [2024-11-08 03:50:33,477] [pool-1-thread-10] Initializing /data/joe/x,y inversion test/SingleImage-07312012-1639-099/SingleImage-07312012-1639-099.xml:
[testng] [2024-11-08 03:50:36,492] [pool-1-thread-12] Initializing /data/marta/SingleImage-09272011-0856-001/SingleImage-09272011-0856-001.xml:
[testng] [2024-11-08 03:50:37,328] [pool-1-thread-8] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertychecked-001/TSeries-invertxchecked_invertychecked-001.xml:
[testng] [2024-11-08 03:50:38,152] [pool-1-thread-9] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-004/TSeries-pollendouble-004.xml:
[testng] [2024-11-08 03:50:38,881] [pool-1-thread-3] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertynotchecked-001/TSeries-invertxnotchecked_invertynotchecked-001.xml:
[testng] [2024-11-08 03:50:43,301] [pool-1-thread-4] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow1Ch4-TSeriesReference.tif:
[testng] [2024-11-08 03:50:48,263] [pool-1-thread-10] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow2Ch3-TSeriesReference.tif:
[testng] [2024-11-08 03:50:51,469] [pool-1-thread-4] Initializing /data/joe/x,y inversion test/1mg-dish1-wide-003/1mg-dish1-wide-003.xml:
[testng] [2024-11-08 03:50:54,240] [pool-1-thread-12] Initializing /data/pam/ZSeries-09022010-356/ZSeries-09022010-356.xml:
[testng] [2024-11-08 03:50:56,987] [pool-1-thread-7] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-003/pollen-003.xml:
[testng] [2024-11-08 03:50:57,840] [pool-1-thread-10] Initializing /data/julie/sample1-010/sample1-010movie.avi:
[testng] [2024-11-08 03:51:00,271] [pool-1-thread-10] Initializing /data/kristin/sampleset-001/sampleset-001.xml:
[testng] [2024-11-08 03:51:10,673] [pool-1-thread-7] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-005/TSeries-10092012-1446-005.xml:
[testng] [2024-11-08 03:51:15,602] [pool-1-thread-6] Initializing /data/julie/bill-bement/3/TSeries-10092012-1446-001/TSeries-10092012-1446-001.xml:
[testng] [2024-11-08 03:51:16,480] [pool-1-thread-8] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-373/ZSeries-09292010-1520-373.xml:
[testng] [2024-11-08 03:51:17,337] [pool-1-thread-3] Initializing /data/julie/bill-bement/6/TSeries-10092012-1446-006/TSeries-10092012-1446-006.xml:
[testng] [2024-11-08 03:51:31,871] [pool-1-thread-12] Initializing /data/joe/TSeries-03232012-0934-006/TSeries-03232012-0934-006.xml:
[testng] [2024-11-08 03:51:33,849] [pool-1-thread-11] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-008/pollenB-008.xml:
[testng] [2024-11-08 03:51:38,688] [pool-1-thread-9] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-004/TSeries-10092012-1446-004.xml:
[testng] [2024-11-08 03:51:47,954] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-002/pollen-002.xml:
[testng] [2024-11-08 03:51:50,810] [pool-1-thread-11] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-007/pollenB-007.xml:
[testng] [2024-11-08 03:52:04,229] [pool-1-thread-11] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-006/pollenB-006.xml:
[testng] [2024-11-08 03:52:06,907] [pool-1-thread-5] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-372/ZSeries-09292010-1520-372.xml:
[testng] [2024-11-08 03:52:09,712] [pool-1-thread-9] Initializing /data/julie/test slide 1_3/test slide 1_3.xml:
[testng] [2024-11-08 03:52:17,642] [pool-1-thread-11] Initializing /data/pam/TSeries-09022010-170/TSeries-09022010-170.xml:
[testng] [2024-11-08 03:52:26,574] [pool-1-thread-1] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-002/TSeries-10092012-1446-002.xml:
[testng] [2024-11-08 03:52:29,487] [pool-1-thread-9] Initializing /data/julie/bill-bement/6/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] [2024-11-08 03:52:42,897] [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: 39 minutes 54 seconds
Finished: SUCCESS