Started by upstream project "BIOFORMATS-test-repo" build number 289
originally caused by:
Started by upstream project "Trigger" build number 308
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7
[BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins11266872974110075637.sh
+ '[' prairie = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_45704_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] 05:49:10,945 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 05:49:10,947 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service.
[testng] 05:49:10,947 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 05:49:10,948 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 05:49:10,948 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 05:49:10,948 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 05:49:10,949 |-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] 05:49:10,949 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 05:49:10,949 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 05:49:10,949 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 05:49:10,949 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 05:49:10,949 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 05:49:11,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 05:49:11,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 05:49:11,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 05:49:11,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 05:49:11,189 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 05:49:11,189 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 05:49:11,189 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 05:49:11,189 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 05:49:11,189 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration.
[testng] 05:49:11,190 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point
[testng] 05:49:11,190 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 241 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-12-13 05:49:11,199] [main] java.version = 1.8.0_342
[testng] 05:49:11,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 05:49:11,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:49:11,244 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-13_05-49-11.log]
[testng] 05:49:11,246 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration.
[testng] [2024-12-13 05:49:11,247] [main] testng.directory = /data
[testng] [2024-12-13 05:49:11,248] [main] testng.configDirectory = /config
[testng] [2024-12-13 05:49:11,258] [main] testng.multiplier = 1.0
[testng] [2024-12-13 05:49:11,259] [main] testng.in-memory = false
[testng] [2024-12-13 05:49:11,259] [main] testng.allow-missing = false
[testng] [2024-12-13 05:49:11,259] [main] user.language = en
[testng] [2024-12-13 05:49:11,259] [main] user.country = ${user.country}
[testng] [2024-12-13 05:49:11,259] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-12-13 05:51:11,944] [main] ----------------------------------------
[testng] [2024-12-13 05:51:11,944] [main] Total files: 714
[testng] [2024-12-13 05:51:11,944] [main] Scan time: 120.684 s (169 ms/file)
[testng] [2024-12-13 05:51:11,945] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 45 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-12-13 05:52:58,546] [pool-1-thread-1] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-001/pollen-001.xml:
[testng] 05:52:58,546 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 05:52:58,546 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:52:58,547 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-13_05-52-58.log]
[testng] 05:52:58,548 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1396f208 - End of configuration.
[testng] [2024-12-13 05:52:59,932] [pool-1-thread-12] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertynotchecked-001/TSeries-invertxchecked_invertynotchecked-001.xml:
[testng] 05:52:59,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 05:52:59,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:52:59,933 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-13_05-52-59.log]
[testng] 05:52:59,934 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1dcb0243 - End of configuration.
[testng] [2024-12-13 05:53:01,361] [pool-1-thread-11] Initializing /data/pam/TSeries-09022010-171/TSeries-09022010-171.xml:
[testng] 05:53:01,362 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 05:53:01,362 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:53:01,362 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-13_05-53-01.log]
[testng] 05:53:01,363 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d0142e5 - End of configuration.
[testng] [2024-12-13 05:53:02,809] [pool-1-thread-10] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-005/pollen-005.xml:
[testng] 05:53:02,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 05:53:02,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:53:02,810 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-13_05-53-02.log]
[testng] 05:53:02,811 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d28030e - End of configuration.
[testng] [2024-12-13 05:53:04,202] [pool-1-thread-9] Initializing /data/julie/bill-bement/3/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] 05:53:04,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 05:53:04,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:53:04,203 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-13_05-53-04.log]
[testng] 05:53:04,203 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c2be541 - End of configuration.
[testng] [2024-12-13 05:53:05,639] [pool-1-thread-8] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertychecked-001/TSeries-invertxnotchecked_invertychecked-001.xml:
[testng] 05:53:05,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 05:53:05,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:53:05,640 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-13_05-53-05.log]
[testng] 05:53:05,640 |-INFO in ch.qos.logback.core.sift.SiftProcessor@589bca9b - End of configuration.
[testng] [2024-12-13 05:53:07,132] [pool-1-thread-7] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-006/TSeries-pollendouble-006.xml:
[testng] 05:53:07,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 05:53:07,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:53:07,133 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-13_05-53-07.log]
[testng] 05:53:07,133 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63c11b74 - End of configuration.
[testng] [2024-12-13 05:53:08,598] [pool-1-thread-6] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollendouble-003/ZSeries-pollendouble-003.xml:
[testng] 05:53:08,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 05:53:08,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:53:08,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-13_05-53-08.log]
[testng] 05:53:08,599 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60af1ec4 - End of configuration.
[testng] [2024-12-13 05:53:10,083] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollentriple-002/ZSeries-pollentriple-002.xml:
[testng] 05:53:10,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 05:53:10,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:53:10,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-13_05-53-10.log]
[testng] 05:53:10,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@453cd5c8 - End of configuration.
[testng] [2024-12-13 05:53:11,592] [pool-1-thread-4] Initializing /data/misc/Ultima ver 2.5 test data sets/ZSeries-pollen-001/ZSeries-pollen-001.xml:
[testng] 05:53:11,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 05:53:11,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:53:11,593 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-13_05-53-11.log]
[testng] 05:53:11,593 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c1e7bcb - End of configuration.
[testng] [2024-12-13 05:53:13,060] [pool-1-thread-3] Initializing /data/julie/bill-bement/5/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] 05:53:13,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 05:53:13,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:53:13,061 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-13_05-53-13.log]
[testng] 05:53:13,062 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e8e0760 - End of configuration.
[testng] [2024-12-13 05:53:14,487] [pool-1-thread-2] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-003/TSeries-10092012-1446-003.xml:
[testng] 05:53:14,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 05:53:14,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:53:14,488 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-13_05-53-14.log]
[testng] 05:53:14,489 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e03be7f - End of configuration.
[testng] [2024-12-13 05:53:56,717] [pool-1-thread-3] Initializing /data/julie/testslide6 2/testslide6 2.xml:
[testng] [2024-12-13 05:53:58,879] [pool-1-thread-9] Initializing /data/julie/sample1-010/References/sample1-010_ImageWindow1Ch2-TSeriesReference.tif:
[testng] [2024-12-13 05:54:04,198] [pool-1-thread-1] Initializing /data/julie/sample1-010/sample1-010.xml:
[testng] [2024-12-13 05:54:06,129] [pool-1-thread-10] Initializing /data/julie/bill-bement/4/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] [2024-12-13 05:54:19,330] [pool-1-thread-9] Initializing /data/pam/SingleImage-09022010/SingleImage-09022010.xml:
[testng] [2024-12-13 05:54:43,263] [pool-1-thread-3] Initializing /data/joe/x,y inversion test/SingleImage-07312012-1639-099/SingleImage-07312012-1639-099.xml:
[testng] [2024-12-13 05:54:45,506] [pool-1-thread-10] Initializing /data/marta/SingleImage-09272011-0856-001/SingleImage-09272011-0856-001.xml:
[testng] [2024-12-13 05:54:48,524] [pool-1-thread-8] Initializing /data/joe/x,y inversion test/TSeries-invertxchecked_invertychecked-001/TSeries-invertxchecked_invertychecked-001.xml:
[testng] [2024-12-13 05:54:50,826] [pool-1-thread-12] Initializing /data/misc/Ultima ver 2.5 test data sets/TSeries-pollendouble-004/TSeries-pollendouble-004.xml:
[testng] [2024-12-13 05:54:53,096] [pool-1-thread-9] Initializing /data/joe/x,y inversion test/TSeries-invertxnotchecked_invertynotchecked-001/TSeries-invertxnotchecked_invertynotchecked-001.xml:
[testng] [2024-12-13 05:55:05,341] [pool-1-thread-4] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow1Ch4-TSeriesReference.tif:
[testng] [2024-12-13 05:55:17,957] [pool-1-thread-3] Initializing /data/kristin/sampleset-001/References/sampleset-001_ImageWindow2Ch3-TSeriesReference.tif:
[testng] [2024-12-13 05:55:21,136] [pool-1-thread-10] Initializing /data/joe/x,y inversion test/1mg-dish1-wide-003/1mg-dish1-wide-003.xml:
[testng] [2024-12-13 05:55:26,680] [pool-1-thread-4] Initializing /data/pam/ZSeries-09022010-356/ZSeries-09022010-356.xml:
[testng] [2024-12-13 05:55:37,219] [pool-1-thread-3] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-003/pollen-003.xml:
[testng] [2024-12-13 05:55:39,473] [pool-1-thread-7] Initializing /data/julie/sample1-010/sample1-010movie.avi:
[testng] [2024-12-13 05:55:44,953] [pool-1-thread-7] Initializing /data/kristin/sampleset-001/sampleset-001.xml:
[testng] [2024-12-13 05:56:10,624] [pool-1-thread-3] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-005/TSeries-10092012-1446-005.xml:
[testng] [2024-12-13 05:56:21,164] [pool-1-thread-8] Initializing /data/julie/bill-bement/3/TSeries-10092012-1446-001/TSeries-10092012-1446-001.xml:
[testng] [2024-12-13 05:56:23,327] [pool-1-thread-9] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-373/ZSeries-09292010-1520-373.xml:
[testng] [2024-12-13 05:56:29,741] [pool-1-thread-6] Initializing /data/julie/bill-bement/6/TSeries-10092012-1446-006/TSeries-10092012-1446-006.xml:
[testng] [2024-12-13 05:57:00,836] [pool-1-thread-4] Initializing /data/joe/TSeries-03232012-0934-006/TSeries-03232012-0934-006.xml:
[testng] [2024-12-13 05:57:05,508] [pool-1-thread-11] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-008/pollenB-008.xml:
[testng] [2024-12-13 05:57:16,868] [pool-1-thread-12] Initializing /data/julie/bill-bement/5/TSeries-10092012-1446-004/TSeries-10092012-1446-004.xml:
[testng] [2024-12-13 05:57:44,660] [pool-1-thread-11] Initializing /data/misc/Ultima ver 2.5 test data sets/pollen-002/pollen-002.xml:
[testng] [2024-12-13 05:57:46,983] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-007/pollenB-007.xml:
[testng] [2024-12-13 05:58:19,259] [pool-1-thread-5] Initializing /data/misc/Ultima ver 2.5 test data sets/pollenB-006/pollenB-006.xml:
[testng] [2024-12-13 05:58:31,051] [pool-1-thread-11] Initializing /data/pam/092910-psf/ZSeries-09292010-1520-372/ZSeries-09292010-1520-372.xml:
[testng] [2024-12-13 05:58:33,376] [pool-1-thread-12] Initializing /data/julie/test slide 1_3/test slide 1_3.xml:
[testng] [2024-12-13 05:58:52,986] [pool-1-thread-5] Initializing /data/pam/TSeries-09022010-170/TSeries-09022010-170.xml:
[testng] [2024-12-13 05:59:13,204] [pool-1-thread-1] Initializing /data/julie/bill-bement/4/TSeries-10092012-1446-002/TSeries-10092012-1446-002.xml:
[testng] [2024-12-13 05:59:20,033] [pool-1-thread-12] Initializing /data/julie/bill-bement/6/SingleImage-10092012-1446-028/SingleImage-10092012-1446-028.xml:
[testng] [2024-12-13 05:59:50,139] [pool-1-thread-5] 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: 56 minutes 47 seconds
Finished: SUCCESS