Started by upstream project "BIOFORMATS-test-repo" build number 234
originally caused by:
Started by upstream project "Trigger" build number 259
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9
[BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins8162215909296408804.sh
+ '[' prairie = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_36811_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] 03:30:40,781 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 03:30:40,782 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service.
[testng] 03:30:40,782 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 03:30:40,783 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 03:30:40,784 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 03:30:40,784 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 03:30:40,784 |-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] 03:30:40,784 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 03:30:40,785 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 03:30:40,785 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 03:30:40,785 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 03:30:40,785 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 03:30:40,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 03:30:40,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 03:30:41,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 03:30:41,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 03:30:41,029 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 03:30:41,029 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 03:30:41,029 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 03:30:41,029 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 03:30:41,030 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration.
[testng] 03:30:41,030 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point
[testng] 03:30:41,030 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 245 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-25 03:30:41,040] [main] java.version = 1.8.0_342
[testng] 03:30:41,043 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 03:30:41,043 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:30:41,085 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-25_03-30-41.log]
[testng] 03:30:41,086 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration.
[testng] [2024-10-25 03:30:41,088] [main] testng.directory = /data
[testng] [2024-10-25 03:30:41,088] [main] testng.configDirectory = /config
[testng] [2024-10-25 03:30:41,100] [main] testng.multiplier = 1.0
[testng] [2024-10-25 03:30:41,100] [main] testng.in-memory = false
[testng] [2024-10-25 03:30:41,100] [main] testng.allow-missing = false
[testng] [2024-10-25 03:30:41,100] [main] user.language = en
[testng] [2024-10-25 03:30:41,100] [main] user.country = ${user.country}
[testng] [2024-10-25 03:30:41,100] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-10-25 03:31:17,061] [main] ----------------------------------------
[testng] [2024-10-25 03:31:17,061] [main] Total files: 714
[testng] [2024-10-25 03:31:17,061] [main] Scan time: 35.961 s (50 ms/file)
[testng] [2024-10-25 03:31:17,061] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 45 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-25 03:31:33,797] [pool-1-thread-1] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-001/pollen-001.xml:
[testng] 03:31:33,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 03:31:33,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:31:33,798 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-25_03-31-33.log]
[testng] 03:31:33,799 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e97564b - End of configuration.
[testng] [2024-10-25 03:31:34,065] [pool-1-thread-12] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertynotchecked-001/TSeries-invertxchecked_invertynotchecked-001.xml:
[testng] 03:31:34,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 03:31:34,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:31:34,068 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-25_03-31-34.log]
[testng] 03:31:34,070 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18a07eee - End of configuration.
[testng] [2024-10-25 03:31:34,384] [pool-1-thread-11] Initializing /data/pam/TSeries-09022010-171/TSeries-09022010-171.xml:
[testng] 03:31:34,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 03:31:34,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:31:34,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-25_03-31-34.log]
[testng] 03:31:34,386 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5cb06368 - End of configuration.
[testng] [2024-10-25 03:31:34,841] [pool-1-thread-10] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-005/pollen-005.xml:
[testng] 03:31:34,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 03:31:34,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:31:34,842 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-25_03-31-34.log]
[testng] 03:31:34,843 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a5281cc - End of configuration.
[testng] [2024-10-25 03:31:35,234] [pool-1-thread-9] Initializing /data/julie/bill-bement/3/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] 03:31:35,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 03:31:35,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:31:35,235 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-25_03-31-35.log]
[testng] 03:31:35,235 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16916161 - End of configuration.
[testng] [2024-10-25 03:31:35,573] [pool-1-thread-8] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertychecked-001/TSeries-invertxnotchecked_invertychecked-001.xml:
[testng] 03:31:35,573 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 03:31:35,573 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:31:35,574 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-25_03-31-35.log]
[testng] 03:31:35,574 |-INFO in ch.qos.logback.core.sift.SiftProcessor@478b29ef - End of configuration.
[testng] [2024-10-25 03:31:35,946] [pool-1-thread-7] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-006/TSeries-pollendouble-006.xml:
[testng] 03:31:35,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 03:31:35,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:31:35,947 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-25_03-31-35.log]
[testng] 03:31:35,948 |-INFO in ch.qos.logback.core.sift.SiftProcessor@277c7b21 - End of configuration.
[testng] [2024-10-25 03:31:36,300] [pool-1-thread-6] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollendouble-003/ZSeries-pollendouble-003.xml:
[testng] 03:31:36,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 03:31:36,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:31:36,301 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-25_03-31-36.log]
[testng] 03:31:36,301 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4816112f - End of configuration.
[testng] [2024-10-25 03:31:36,671] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollentriple-002/ZSeries-pollentriple-002.xml:
[testng] 03:31:36,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 03:31:36,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:31:36,672 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-25_03-31-36.log]
[testng] 03:31:36,673 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1207fa2e - End of configuration.
[testng] [2024-10-25 03:31:36,980] [pool-1-thread-4] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollen-001/ZSeries-pollen-001.xml:
[testng] 03:31:36,980 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 03:31:36,980 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:31:36,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-25_03-31-36.log]
[testng] 03:31:36,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@290b59ba - End of configuration.
[testng] [2024-10-25 03:31:37,276] [pool-1-thread-3] Initializing /data/julie/bill-bement/5/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] 03:31:37,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 03:31:37,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:31:37,277 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-25_03-31-37.log]
[testng] 03:31:37,278 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b962a0b - End of configuration.
[testng] [2024-10-25 03:31:37,528] [pool-1-thread-2] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-003/TSeries-10092012-1446-003.xml:
[testng] 03:31:37,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 03:31:37,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:31:37,529 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-25_03-31-37.log]
[testng] 03:31:37,530 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5763684b - End of configuration.
[testng] [2024-10-25 03:31:50,592] [pool-1-thread-3] Initializing /data/julie/testslide6 2/testslide6 2.xml:
[testng] [2024-10-25 03:31:51,161] [pool-1-thread-9] Initializing /data/julie/sample1-010/References/sample1-010_ImageWindow1Ch2-TSeriesReference.tif:
[testng] [2024-10-25 03:31:51,957] [pool-1-thread-10] Initializing /data/julie/sample1-010/sample1-010.xml:
[testng] [2024-10-25 03:31:52,747] [pool-1-thread-1] Initializing /data/julie/bill-bement/4/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] [2024-10-25 03:31:56,867] [pool-1-thread-9] Initializing /data/pam/SingleImage-09022010/SingleImage-09022010.xml:
[testng] [2024-10-25 03:32:02,932] [pool-1-thread-3] Initializing /data/joe/x,y inversion test/SingleImage-07312012-1639-099/SingleImage-07312012-1639-099.xml:
[testng] [2024-10-25 03:32:03,443] [pool-1-thread-1] Initializing /data/marta/SingleImage-09272011-0856-001/SingleImage-09272011-0856-001.xml:
[testng] [2024-10-25 03:32:04,765] [pool-1-thread-12] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertychecked-001/TSeries-invertxchecked_invertychecked-001.xml:
[testng] [2024-10-25 03:32:05,280] [pool-1-thread-8] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-004/TSeries-pollendouble-004.xml:
[testng] [2024-10-25 03:32:05,711] [pool-1-thread-9] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertynotchecked-001/TSeries-invertxnotchecked_invertynotchecked-001.xml:
[testng] [2024-10-25 03:32:08,440] [pool-1-thread-4] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow1Ch4-TSeriesReference.tif:
[testng] [2024-10-25 03:32:11,375] [pool-1-thread-3] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow2Ch3-TSeriesReference.tif:
[testng] [2024-10-25 03:32:12,133] [pool-1-thread-1] Initializing /data/joe/x,y inversion test/1mg-dish1-wide-003/1mg-dish1-wide-003.xml:
[testng] [2024-10-25 03:32:13,155] [pool-1-thread-4] Initializing /data/pam/ZSeries-09022010-356/ZSeries-09022010-356.xml:
[testng] [2024-10-25 03:32:15,905] [pool-1-thread-7] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-003/pollen-003.xml:
[testng] [2024-10-25 03:32:16,812] [pool-1-thread-3] Initializing /data/julie/sample1-010/sample1-010movie.avi:
[testng] [2024-10-25 03:32:18,480] [pool-1-thread-3] Initializing /data/kristin/sampleset-001/sampleset-001.xml:
[testng] [2024-10-25 03:32:24,441] [pool-1-thread-7] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-005/TSeries-10092012-1446-005.xml:
[testng] [2024-10-25 03:32:28,095] [pool-1-thread-12] Initializing /data/julie/bill-bement/3/TSeries-10092012-1446-001/TSeries-10092012-1446-001.xml:
[testng] [2024-10-25 03:32:28,749] [pool-1-thread-6] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-373/ZSeries-09292010-1520-373.xml:
[testng] [2024-10-25 03:32:29,295] [pool-1-thread-9] Initializing /data/julie/bill-bement/6/TSeries-10092012-1446-006/TSeries-10092012-1446-006.xml:
[testng] [2024-10-25 03:32:36,495] [pool-1-thread-4] Initializing /data/joe/TSeries-03232012-0934-006/TSeries-03232012-0934-006.xml:
[testng] [2024-10-25 03:32:38,804] [pool-1-thread-11] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-008/pollenB-008.xml:
[testng] [2024-10-25 03:32:41,519] [pool-1-thread-8] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-004/TSeries-10092012-1446-004.xml:
[testng] [2024-10-25 03:32:47,181] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-002/pollen-002.xml:
[testng] [2024-10-25 03:32:48,563] [pool-1-thread-11] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-007/pollenB-007.xml:
[testng] [2024-10-25 03:32:57,278] [pool-1-thread-11] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-006/pollenB-006.xml:
[testng] [2024-10-25 03:32:59,518] [pool-1-thread-5] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-372/ZSeries-09292010-1520-372.xml:
[testng] [2024-10-25 03:33:01,235] [pool-1-thread-8] Initializing /data/julie/test slide 1_3/test slide 1_3.xml:
[testng] [2024-10-25 03:33:05,485] [pool-1-thread-11] Initializing /data/pam/TSeries-09022010-170/TSeries-09022010-170.xml:
[testng] [2024-10-25 03:33:13,422] [pool-1-thread-10] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-002/TSeries-10092012-1446-002.xml:
[testng] [2024-10-25 03:33:13,998] [pool-1-thread-8] Initializing /data/julie/bill-bement/6/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] [2024-10-25 03:33:21,701] [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: 14 minutes 2 seconds
Finished: SUCCESS