Started by upstream project "BIOFORMATS-test-repo" build number 2
originally caused by:
Started by upstream project "Trigger" build number 3
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/jenkins10695455710659865643.sh
+ '[' prairie = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_253_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] 01:34:56,785 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:34:56,787 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service.
[testng] 01:34:56,787 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:34:56,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:34:56,788 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:34:56,788 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:34:56,789 |-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] 01:34:56,789 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:34:56,789 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:34:56,789 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:34:56,789 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:34:56,790 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:34:57,010 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:34:57,010 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:34:57,037 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:34:57,037 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:34:57,044 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:34:57,045 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:34:57,045 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:34:57,045 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:34:57,045 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration.
[testng] 01:34:57,046 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point
[testng] 01:34:57,046 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 257 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-03-15 01:34:57,056] [main] java.version = 1.8.0_342
[testng] 01:34:57,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:34:57,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:34:57,102 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-15_01-34-57.log]
[testng] 01:34:57,104 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration.
[testng] [2024-03-15 01:34:57,105] [main] testng.directory = /data
[testng] [2024-03-15 01:34:57,106] [main] testng.configDirectory = /config
[testng] [2024-03-15 01:34:57,117] [main] testng.multiplier = 1.0
[testng] [2024-03-15 01:34:57,118] [main] testng.in-memory = false
[testng] [2024-03-15 01:34:57,118] [main] testng.allow-missing = false
[testng] [2024-03-15 01:34:57,118] [main] user.language = en
[testng] [2024-03-15 01:34:57,118] [main] user.country = ${user.country}
[testng] [2024-03-15 01:34:57,118] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-03-15 01:35:13,696] [main] ----------------------------------------
[testng] [2024-03-15 01:35:13,696] [main] Total files: 714
[testng] [2024-03-15 01:35:13,696] [main] Scan time: 16.578 s (23 ms/file)
[testng] [2024-03-15 01:35:13,696] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 45 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-03-15 01:35:28,300] [pool-1-thread-1] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-005/pollen-005.xml:
[testng] 01:35:28,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:35:28,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:28,303 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-15_01-35-28.log]
[testng] 01:35:28,303 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51cc87d1 - End of configuration.
[testng] [2024-03-15 01:35:28,546] [pool-1-thread-12] Initializing /data/julie/bill-bement/3/TSeries-10092012-1446-001/TSeries-10092012-1446-001.xml:
[testng] 01:35:28,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:35:28,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:28,548 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-15_01-35-28.log]
[testng] 01:35:28,548 |-INFO in ch.qos.logback.core.sift.SiftProcessor@312567b8 - End of configuration.
[testng] [2024-03-15 01:35:28,901] [pool-1-thread-11] Initializing /data/joe/x,y inversion test/1mg-dish1-wide-003/1mg-dish1-wide-003.xml:
[testng] 01:35:28,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:35:28,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:28,902 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-15_01-35-28.log]
[testng] 01:35:28,903 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57579184 - End of configuration.
[testng] [2024-03-15 01:35:29,250] [pool-1-thread-10] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-372/ZSeries-09292010-1520-372.xml:
[testng] 01:35:29,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:35:29,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:29,252 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-15_01-35-29.log]
[testng] 01:35:29,252 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e501442 - End of configuration.
[testng] [2024-03-15 01:35:29,513] [pool-1-thread-9] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-003/TSeries-10092012-1446-003.xml:
[testng] 01:35:29,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:35:29,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:29,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-15_01-35-29.log]
[testng] 01:35:29,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7963fa52 - End of configuration.
[testng] [2024-03-15 01:35:29,873] [pool-1-thread-8] Initializing /data/julie/bill-bement/4/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] 01:35:29,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:35:29,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:29,874 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-15_01-35-29.log]
[testng] 01:35:29,874 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17da7644 - End of configuration.
[testng] [2024-03-15 01:35:30,037] [pool-1-thread-7] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-001/pollen-001.xml:
[testng] 01:35:30,037 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:35:30,037 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:30,038 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-15_01-35-30.log]
[testng] 01:35:30,038 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72f31c08 - End of configuration.
[testng] [2024-03-15 01:35:30,203] [pool-1-thread-6] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-003/pollen-003.xml:
[testng] 01:35:30,203 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:35:30,203 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:30,204 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-15_01-35-30.log]
[testng] 01:35:30,205 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33d47faf - End of configuration.
[testng] [2024-03-15 01:35:30,395] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-004/pollen-004.xml:
[testng] 01:35:30,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:35:30,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:30,395 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-15_01-35-30.log]
[testng] 01:35:30,396 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ae43a6a - End of configuration.
[testng] [2024-03-15 01:35:30,554] [pool-1-thread-4] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-002/pollen-002.xml:
[testng] 01:35:30,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:35:30,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:30,555 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-15_01-35-30.log]
[testng] 01:35:30,556 |-INFO in ch.qos.logback.core.sift.SiftProcessor@518636f4 - End of configuration.
[testng] [2024-03-15 01:35:30,739] [pool-1-thread-3] Initializing /data/julie/bill-bement/6/TSeries-10092012-1446-006/TSeries-10092012-1446-006.xml:
[testng] 01:35:30,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:35:30,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:30,740 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-15_01-35-30.log]
[testng] 01:35:30,740 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9718666 - End of configuration.
[testng] [2024-03-15 01:35:31,042] [pool-1-thread-2] Initializing /data/julie/bill-bement/6/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] 01:35:31,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:35:31,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:31,043 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-15_01-35-31.log]
[testng] 01:35:31,043 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9ede4c7 - End of configuration.
[testng] [2024-03-15 01:35:37,215] [pool-1-thread-6] Initializing /data/marta/SingleImage-09272011-0856-001/SingleImage-09272011-0856-001.xml:
[testng] [2024-03-15 01:35:38,479] [pool-1-thread-8] Initializing /data/julie/testslide6 2/testslide6 2.xml:
[testng] [2024-03-15 01:35:38,866] [pool-1-thread-2] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-004/TSeries-10092012-1446-004.xml:
[testng] [2024-03-15 01:35:39,257] [pool-1-thread-5] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow1Ch4-TSeriesReference.tif:
[testng] [2024-03-15 01:35:39,822] [pool-1-thread-1] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertychecked-001/TSeries-invertxchecked_invertychecked-001.xml:
[testng] [2024-03-15 01:35:40,297] [pool-1-thread-7] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertynotchecked-001/TSeries-invertxnotchecked_invertynotchecked-001.xml:
[testng] [2024-03-15 01:35:40,810] [pool-1-thread-4] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollendouble-003/ZSeries-pollendouble-003.xml:
[testng] [2024-03-15 01:35:43,590] [pool-1-thread-5] Initializing /data/julie/bill-bement/3/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] [2024-03-15 01:35:45,357] [pool-1-thread-6] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollentriple-002/ZSeries-pollentriple-002.xml:
[testng] [2024-03-15 01:35:48,507] [pool-1-thread-8] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-002/TSeries-10092012-1446-002.xml:
[testng] [2024-03-15 01:35:51,117] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-004/TSeries-pollendouble-004.xml:
[testng] [2024-03-15 01:35:54,577] [pool-1-thread-2] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-006/TSeries-pollendouble-006.xml:
[testng] [2024-03-15 01:35:58,108] [pool-1-thread-1] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertychecked-001/TSeries-invertxnotchecked_invertychecked-001.xml:
[testng] [2024-03-15 01:35:58,506] [pool-1-thread-7] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-007/pollenB-007.xml:
[testng] [2024-03-15 01:36:04,210] [pool-1-thread-7] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow2Ch3-TSeriesReference.tif:
[testng] [2024-03-15 01:36:07,117] [pool-1-thread-7] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollen-001/ZSeries-pollen-001.xml:
[testng] [2024-03-15 01:36:14,724] [pool-1-thread-1] Initializing /data/julie/sample1-010/sample1-010.xml:
[testng] [2024-03-15 01:36:15,876] [pool-1-thread-8] Initializing /data/julie/bill-bement/5/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] [2024-03-15 01:36:16,196] [pool-1-thread-4] Initializing /data/pam/ZSeries-09022010-356/ZSeries-09022010-356.xml:
[testng] [2024-03-15 01:36:16,941] [pool-1-thread-5] Initializing /data/julie/test slide 1_3/test slide 1_3.xml:
[testng] [2024-03-15 01:36:19,594] [pool-1-thread-2] Initializing /data/joe/TSeries-03232012-0934-006/TSeries-03232012-0934-006.xml:
[testng] [2024-03-15 01:36:22,799] [pool-1-thread-8] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertynotchecked-001/TSeries-invertxchecked_invertynotchecked-001.xml:
[testng] [2024-03-15 01:36:24,677] [pool-1-thread-5] Initializing /data/pam/TSeries-09022010-170/TSeries-09022010-170.xml:
[testng] [2024-03-15 01:36:25,819] [pool-1-thread-7] Initializing /data/joe/x,y inversion test/SingleImage-07312012-1639-099/SingleImage-07312012-1639-099.xml:
[testng] [2024-03-15 01:36:31,633] [pool-1-thread-7] Initializing /data/julie/sample1-010/References/sample1-010_ImageWindow1Ch2-TSeriesReference.tif:
[testng] [2024-03-15 01:36:32,107] [pool-1-thread-4] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-006/pollenB-006.xml:
[testng] [2024-03-15 01:36:34,055] [pool-1-thread-6] Initializing /data/pam/SingleImage-09022010/SingleImage-09022010.xml:
[testng] [2024-03-15 01:36:34,818] [pool-1-thread-5] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-373/ZSeries-09292010-1520-373.xml:
[testng] [2024-03-15 01:36:35,232] [pool-1-thread-7] Initializing /data/pam/TSeries-09022010-171/TSeries-09022010-171.xml:
[testng] [2024-03-15 01:36:38,152] [pool-1-thread-4] Initializing /data/kristin/sampleset-001/sampleset-001.xml:
[testng] [2024-03-15 01:36:39,524] [pool-1-thread-8] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-005/TSeries-10092012-1446-005.xml:
[testng] [2024-03-15 01:36:40,133] [pool-1-thread-6] Initializing /data/julie/sample1-010/sample1-010movie.avi:
[testng] [2024-03-15 01:36:41,173] [pool-1-thread-6] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-008/pollenB-008.xml:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2385, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 9 minutes 47 seconds
Finished: SUCCESS