Started by upstream project "BIOFORMATS-test-repo" build number 122
originally caused by:
Started by upstream project "Trigger" build number 139
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/jenkins16040598545883426697.sh
+ '[' flex = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_19054_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] WARNING: An illegal reflective access operation has occurred
[testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket
[testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener
[testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
[testng] WARNING: All illegal access operations will be denied in a future release
[testng] File leak detector installed
[testng] 01:31:40,389 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:31:40,391 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 01:31:40,391 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:31:40,392 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:31:40,392 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:31:40,393 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:31:40,393 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:31:40,393 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:31:40,393 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:31:40,394 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:31:40,394 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:31:40,395 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:31:40,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:31:40,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:31:40,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:31:40,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:31:40,614 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:31:40,614 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:31:40,614 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:31:40,615 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:31:40,615 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 01:31:40,616 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 01:31:40,616 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 223 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-07-16 01:31:40,625] [main] java.version = 11.0.16
[testng] 01:31:40,628 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:31:40,628 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:31:40,673 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-16_01-31-40.log]
[testng] 01:31:40,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-07-16 01:31:40,676] [main] testng.directory = /data
[testng] [2024-07-16 01:31:40,677] [main] testng.configDirectory = /config
[testng] [2024-07-16 01:31:40,725] [main] testng.multiplier = 1.0
[testng] [2024-07-16 01:31:40,728] [main] testng.in-memory = false
[testng] [2024-07-16 01:31:40,728] [main] testng.allow-missing = false
[testng] [2024-07-16 01:31:40,728] [main] user.language = en
[testng] [2024-07-16 01:31:40,728] [main] user.country = ${user.country}
[testng] [2024-07-16 01:31:40,728] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-07-16 01:31:53,092] [main] ----------------------------------------
[testng] [2024-07-16 01:31:53,093] [main] Total files: 791
[testng] [2024-07-16 01:31:53,093] [main] Scan time: 12.364 s (15 ms/file)
[testng] [2024-07-16 01:31:53,093] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 42 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-07-16 01:38:00,088] [pool-1-thread-1] Initializing /data/qa-18096/002003001.flex:
[testng] 01:38:00,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:38:00,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:00,091 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-16_01-38-00.log]
[testng] 01:38:00,091 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60def10d - End of configuration.
[testng] [2024-07-16 01:38:00,192] [pool-1-thread-12] Initializing /data/tony/003003000.tiff:
[testng] 01:38:00,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:38:00,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:00,194 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-16_01-38-00.log]
[testng] 01:38:00,194 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2bd173f7 - End of configuration.
[testng] [2024-07-16 01:38:00,386] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex:
[testng] 01:38:00,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:38:00,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:00,388 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-16_01-38-00.log]
[testng] 01:38:00,388 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26ca95a5 - End of configuration.
[testng] [2024-07-16 01:38:01,032] [pool-1-thread-10] Initializing /data/achim/003003000.flex:
[testng] 01:38:01,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:38:01,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:01,033 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-16_01-38-01.log]
[testng] 01:38:01,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75e7fd24 - End of configuration.
[testng] [2024-07-16 01:38:01,112] [pool-1-thread-9] Initializing /data/manuel/003003001.flex:
[testng] 01:38:01,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:38:01,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:01,113 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-16_01-38-01.log]
[testng] 01:38:01,114 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41ac9d44 - End of configuration.
[testng] [2024-07-16 01:38:01,181] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex:
[testng] 01:38:01,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:38:01,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:01,183 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-16_01-38-01.log]
[testng] 01:38:01,183 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4db84aa6 - End of configuration.
[testng] [2024-07-16 01:38:01,213] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex:
[testng] 01:38:01,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:38:01,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:01,214 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-16_01-38-01.log]
[testng] 01:38:01,214 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38de452b - End of configuration.
[testng] [2024-07-16 01:38:01,249] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex:
[testng] 01:38:01,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:38:01,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:01,250 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-16_01-38-01.log]
[testng] 01:38:01,250 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40215639 - End of configuration.
[testng] [2024-07-16 01:38:01,798] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex:
[testng] 01:38:01,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:38:01,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:01,799 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-16_01-38-01.log]
[testng] 01:38:01,800 |-INFO in ch.qos.logback.core.sift.SiftProcessor@401df70b - End of configuration.
[testng] [2024-07-16 01:38:02,334] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex:
[testng] 01:38:02,334 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:38:02,334 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:02,335 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-16_01-38-02.log]
[testng] 01:38:02,335 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e800c9f - End of configuration.
[testng] [2024-07-16 01:38:02,372] [pool-1-thread-3] Initializing /data/tony/003008000.flex:
[testng] 01:38:02,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:38:02,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:02,373 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-16_01-38-02.log]
[testng] 01:38:02,373 |-INFO in ch.qos.logback.core.sift.SiftProcessor@643e733a - End of configuration.
[testng] [2024-07-16 01:38:02,423] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex:
[testng] 01:38:02,423 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:38:02,423 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:02,424 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-16_01-38-02.log]
[testng] 01:38:02,424 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58ea9c89 - End of configuration.
[testng] [2024-07-16 01:38:04,774] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex:
[testng] [2024-07-16 01:38:04,869] [pool-1-thread-1] Initializing /data/tony/001014000 - from flex.tif:
[testng] [2024-07-16 01:38:04,925] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex:
[testng] [2024-07-16 01:38:05,006] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex:
[testng] [2024-07-16 01:38:05,374] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex:
[testng] [2024-07-16 01:38:06,124] [pool-1-thread-7] Initializing /data/tony/test.tiff:
[testng] [2024-07-16 01:38:06,341] [pool-1-thread-9] Initializing /data/qa-17190/002002011.flex:
[testng] [2024-07-16 01:38:06,684] [pool-1-thread-1] Initializing /data/tony/015002000.tiff:
[testng] [2024-07-16 01:38:07,214] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex:
[testng] [2024-07-16 01:38:07,456] [pool-1-thread-7] Initializing /data/qa-18096/002002001.flex:
[testng] [2024-07-16 01:38:07,719] [pool-1-thread-1] Initializing /data/stephane/006013000.flex:
[testng] [2024-07-16 01:38:07,918] [pool-1-thread-10] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex:
[testng] [2024-07-16 01:38:08,308] [pool-1-thread-7] Initializing /data/ghislain/test.flex:
[testng] [2024-07-16 01:38:08,982] [pool-1-thread-9] Initializing /data/tamjid/006004000.flex:
[testng] [2024-07-16 01:38:09,485] [pool-1-thread-7] Initializing /data/tamjid/006005000.flex:
[testng] [2024-07-16 01:38:09,625] [pool-1-thread-12] Initializing /data/qa-2983/004007000.flex:
[testng] [2024-07-16 01:38:09,692] [pool-1-thread-9] Initializing /data/tony/000101400 - from PE sofwatre.tif:
[testng] [2024-07-16 01:38:09,989] [pool-1-thread-3] Initializing /data/tony/test1.flex:
[testng] [2024-07-16 01:38:10,352] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex:
[testng] [2024-07-16 01:38:10,490] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex:
[testng] [2024-07-16 01:38:11,153] [pool-1-thread-9] Initializing /data/stephane/002007000.flex:
[testng] [2024-07-16 01:38:11,540] [pool-1-thread-10] Initializing /data/anatole/001004000.flex:
[testng] [2024-07-16 01:38:11,734] [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] [2024-07-16 01:38:12,177] [pool-1-thread-8] Initializing /data/qa-7469/002002.flex:
[testng] [2024-07-16 01:38:12,874] [pool-1-thread-9] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex:
[testng] [2024-07-16 01:38:13,291] [pool-1-thread-7] Initializing /data/tony/001001000_objects.flex:
[testng] [2024-07-16 01:38:13,346] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex:
[testng] [2024-07-16 01:38:14,097] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex:
[testng] [2024-07-16 01:38:14,708] [pool-1-thread-7] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex:
[testng] [2024-07-16 01:38:14,868] [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]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2226, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 10 minutes 3 seconds
Finished: SUCCESS