Started by upstream project "BIOFORMATS-test-repo" build number 120
originally caused by:
Started by upstream project "Trigger" build number 137
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/jenkins964256565227276646.sh
+ '[' flex = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_18726_merge_ci -v /uod/idr/repos/curated/flex:/data -v /uod/idr-scratch/merge-ci/curated/flex:/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
[javac] warning: [options] bootstrap class path not set in conjunction with -source 8
[javac] 1 warning
test-automated:
[testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket
[testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket
[testng] File leak detector installed
[testng] 01:30:18,423 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:30:18,424 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 01:30:18,424 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:30:18,425 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:30:18,426 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:30:18,426 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:30:18,427 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:30:18,427 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:30:18,427 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:30:18,428 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:30:18,428 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:30:18,428 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:30:18,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:30:18,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:30:18,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:30:18,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:30:18,665 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:30:18,665 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:30:18,665 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:30:18,665 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:30:18,665 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 01:30:18,666 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 01:30:18,666 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 239 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-07-14 01:30:18,676] [main] java.version = 17.0.2
[testng] 01:30:18,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:30:18,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:30:18,722 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-14_01-30-18.log]
[testng] 01:30:18,724 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-07-14 01:30:18,726] [main] testng.directory = /data
[testng] [2024-07-14 01:30:18,726] [main] testng.configDirectory = /config
[testng] [2024-07-14 01:30:18,736] [main] testng.multiplier = 1.0
[testng] [2024-07-14 01:30:18,737] [main] testng.in-memory = false
[testng] [2024-07-14 01:30:18,737] [main] testng.allow-missing = false
[testng] [2024-07-14 01:30:18,737] [main] user.language = en
[testng] [2024-07-14 01:30:18,737] [main] user.country = ${user.country}
[testng] [2024-07-14 01:30:18,737] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-07-14 01:30:31,450] [main] ----------------------------------------
[testng] [2024-07-14 01:30:31,450] [main] Total files: 791
[testng] [2024-07-14 01:30:31,451] [main] Scan time: 12.713 s (16 ms/file)
[testng] [2024-07-14 01:30:31,451] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 42 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-07-14 01:36:26,033] [pool-1-thread-1] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex:
[testng] 01:36:26,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:36:26,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:26,034 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-14_01-36-26.log]
[testng] 01:36:26,035 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5baf89ba - End of configuration.
[testng] [2024-07-14 01:36:26,074] [pool-1-thread-12] Initializing /data/qa-18096/002002001.flex:
[testng] 01:36:26,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:36:26,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:26,075 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-14_01-36-26.log]
[testng] 01:36:26,076 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4409ab1d - End of configuration.
[testng] [2024-07-14 01:36:26,128] [pool-1-thread-11] Initializing /data/anatole/001004000.flex:
[testng] 01:36:26,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:36:26,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:26,129 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-14_01-36-26.log]
[testng] 01:36:26,129 |-INFO in ch.qos.logback.core.sift.SiftProcessor@85ea298 - End of configuration.
[testng] [2024-07-14 01:36:26,193] [pool-1-thread-10] Initializing /data/qa-7469/002002.flex:
[testng] 01:36:26,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:36:26,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:26,194 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-14_01-36-26.log]
[testng] 01:36:26,194 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a7d87d0 - End of configuration.
[testng] [2024-07-14 01:36:26,233] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex:
[testng] 01:36:26,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:36:26,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:26,234 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-14_01-36-26.log]
[testng] 01:36:26,235 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dc9e566 - End of configuration.
[testng] [2024-07-14 01:36:26,700] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex:
[testng] 01:36:26,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:36:26,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:26,701 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-14_01-36-26.log]
[testng] 01:36:26,701 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44b7b736 - End of configuration.
[testng] [2024-07-14 01:36:27,185] [pool-1-thread-7] Initializing /data/tony/000101400 - from PE sofwatre.tif:
[testng] 01:36:27,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:36:27,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:27,186 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-14_01-36-27.log]
[testng] 01:36:27,186 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d87af9c - End of configuration.
[testng] [2024-07-14 01:36:27,242] [pool-1-thread-6] Initializing /data/tamjid/006003000.flex:
[testng] 01:36:27,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:36:27,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:27,244 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-14_01-36-27.log]
[testng] 01:36:27,244 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ddf9bb6 - End of configuration.
[testng] [2024-07-14 01:36:27,293] [pool-1-thread-5] Initializing /data/tony/003008000.flex:
[testng] 01:36:27,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:36:27,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:27,294 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-14_01-36-27.log]
[testng] 01:36:27,295 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b535d62 - End of configuration.
[testng] [2024-07-14 01:36:27,351] [pool-1-thread-4] Initializing /data/tamjid/006005000.flex:
[testng] 01:36:27,351 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:36:27,351 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:27,352 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-14_01-36-27.log]
[testng] 01:36:27,352 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37e05dad - End of configuration.
[testng] [2024-07-14 01:36:27,383] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex:
[testng] 01:36:27,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:36:27,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:27,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-14_01-36-27.log]
[testng] 01:36:27,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@de6a1c7 - End of configuration.
[testng] [2024-07-14 01:36:27,463] [pool-1-thread-2] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex:
[testng] 01:36:27,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:36:27,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:27,465 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-14_01-36-27.log]
[testng] 01:36:27,465 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5000dd6c - End of configuration.
[testng] [2024-07-14 01:36:29,442] [pool-1-thread-6] Initializing /data/tony/015002000.tiff:
[testng] [2024-07-14 01:36:29,502] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex:
[testng] [2024-07-14 01:36:29,558] [pool-1-thread-10] Initializing /data/tony/001014000 - from flex.tif:
[testng] [2024-07-14 01:36:29,627] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex:
[testng] [2024-07-14 01:36:30,087] [pool-1-thread-12] Initializing /data/tony/test.tiff:
[testng] [2024-07-14 01:36:30,287] [pool-1-thread-3] Initializing /data/qa-17190/002002011.flex:
[testng] [2024-07-14 01:36:30,514] [pool-1-thread-1] Initializing /data/achim/003003000.flex:
[testng] [2024-07-14 01:36:30,902] [pool-1-thread-3] Initializing /data/stephane/006013000.flex:
[testng] [2024-07-14 01:36:30,973] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex:
[testng] [2024-07-14 01:36:31,024] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex:
[testng] [2024-07-14 01:36:31,584] [pool-1-thread-12] Initializing /data/tony/003003000.tiff:
[testng] [2024-07-14 01:36:31,859] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex:
[testng] [2024-07-14 01:36:32,136] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex:
[testng] [2024-07-14 01:36:32,532] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex:
[testng] [2024-07-14 01:36:33,099] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex:
[testng] [2024-07-14 01:36:33,165] [pool-1-thread-5] Initializing /data/ghislain/test.flex:
[testng] [2024-07-14 01:36:33,975] [pool-1-thread-5] Initializing /data/tamjid/006004000.flex:
[testng] [2024-07-14 01:36:34,276] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex:
[testng] [2024-07-14 01:36:34,757] [pool-1-thread-11] Initializing /data/tony/test1.flex:
[testng] [2024-07-14 01:36:34,892] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex:
[testng] [2024-07-14 01:36:35,115] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex:
[testng] [2024-07-14 01:36:35,927] [pool-1-thread-3] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex:
[testng] [2024-07-14 01:36:36,381] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex:
[testng] [2024-07-14 01:36:36,683] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex:
[testng] [2024-07-14 01:36:37,382] [pool-1-thread-4] Initializing /data/public/idr0007/Plate1/001001000.flex:
[testng] [2024-07-14 01:36:38,230] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex:
[testng] [2024-07-14 01:36:39,317] [pool-1-thread-1] Initializing /data/manuel/003003001.flex:
[testng] [2024-07-14 01:36:39,467] [pool-1-thread-11] Initializing /data/tony/001001000_objects.flex:
[testng] [2024-07-14 01:36:40,053] [pool-1-thread-5] Initializing /data/qa-18096/002003001.flex:
[testng] [2024-07-14 01:36:40,118] [pool-1-thread-11] Initializing /data/stephane/002007000.flex:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2226, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 9 minutes 19 seconds
Finished: SUCCESS