Started by upstream project "BIOFORMATS-test-repo" build number 113
originally caused by:
Started by upstream project "Trigger" build number 126
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/jenkins4728872356890160883.sh
+ '[' flex = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_17578_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] 01:31:23,730 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:31:23,733 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 01:31:23,733 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:31:23,734 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:31:23,735 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:31:23,735 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:31:23,735 |-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] 01:31:23,735 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:31:23,736 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:31:23,737 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:31:23,737 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:31:23,737 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:31:23,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:31:23,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:31:24,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:31:24,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:31:24,022 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:31:24,023 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:31:24,023 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:31:24,024 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:31:24,024 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 01:31:24,025 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 01:31:24,025 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 289 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-07-06 01:31:24,036] [main] java.version = 11.0.16
[testng] 01:31:24,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:31:24,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:31:24,092 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-06_01-31-24.log]
[testng] 01:31:24,094 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-07-06 01:31:24,096] [main] testng.directory = /data
[testng] [2024-07-06 01:31:24,097] [main] testng.configDirectory = /config
[testng] [2024-07-06 01:31:24,109] [main] testng.multiplier = 1.0
[testng] [2024-07-06 01:31:24,110] [main] testng.in-memory = false
[testng] [2024-07-06 01:31:24,110] [main] testng.allow-missing = false
[testng] [2024-07-06 01:31:24,110] [main] user.language = en
[testng] [2024-07-06 01:31:24,110] [main] user.country = ${user.country}
[testng] [2024-07-06 01:31:24,111] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-07-06 01:31:40,927] [main] ----------------------------------------
[testng] [2024-07-06 01:31:40,928] [main] Total files: 791
[testng] [2024-07-06 01:31:40,928] [main] Scan time: 16.816 s (21 ms/file)
[testng] [2024-07-06 01:31:40,928] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 42 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-07-06 01:37:12,503] [pool-1-thread-1] Initializing /data/qa-18096/002003001.flex:
[testng] 01:37:12,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:37:12,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:12,507 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-06_01-37-12.log]
[testng] 01:37:12,507 |-INFO in ch.qos.logback.core.sift.SiftProcessor@275685e1 - End of configuration.
[testng] [2024-07-06 01:37:12,569] [pool-1-thread-12] Initializing /data/tony/003003000.tiff:
[testng] 01:37:12,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:37:12,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:12,570 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-06_01-37-12.log]
[testng] 01:37:12,570 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28afa215 - End of configuration.
[testng] [2024-07-06 01:37:12,674] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex:
[testng] 01:37:12,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:37:12,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:12,675 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-06_01-37-12.log]
[testng] 01:37:12,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7442a900 - End of configuration.
[testng] [2024-07-06 01:37:13,239] [pool-1-thread-10] Initializing /data/achim/003003000.flex:
[testng] 01:37:13,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:37:13,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:13,240 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-06_01-37-13.log]
[testng] 01:37:13,240 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c623db9 - End of configuration.
[testng] [2024-07-06 01:37:13,307] [pool-1-thread-9] Initializing /data/manuel/003003001.flex:
[testng] 01:37:13,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:37:13,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:13,308 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-06_01-37-13.log]
[testng] 01:37:13,308 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38a39334 - End of configuration.
[testng] [2024-07-06 01:37:13,356] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex:
[testng] 01:37:13,356 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:37:13,356 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:13,357 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-06_01-37-13.log]
[testng] 01:37:13,357 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6273f06a - End of configuration.
[testng] [2024-07-06 01:37:13,382] [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] 01:37:13,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:37:13,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:13,383 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-06_01-37-13.log]
[testng] 01:37:13,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@84bc4d2 - End of configuration.
[testng] [2024-07-06 01:37:13,424] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex:
[testng] 01:37:13,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:37:13,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:13,425 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-06_01-37-13.log]
[testng] 01:37:13,426 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b535d62 - End of configuration.
[testng] [2024-07-06 01:37:13,872] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex:
[testng] 01:37:13,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:37:13,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:13,873 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-06_01-37-13.log]
[testng] 01:37:13,874 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5000dd6c - End of configuration.
[testng] [2024-07-06 01:37:14,306] [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] 01:37:14,306 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:37:14,306 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:14,307 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-06_01-37-14.log]
[testng] 01:37:14,307 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e8cafe4 - End of configuration.
[testng] [2024-07-06 01:37:14,333] [pool-1-thread-3] Initializing /data/tony/003008000.flex:
[testng] 01:37:14,334 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:37:14,334 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:14,334 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-06_01-37-14.log]
[testng] 01:37:14,335 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40215639 - End of configuration.
[testng] [2024-07-06 01:37:14,376] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex:
[testng] 01:37:14,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:37:14,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:37:14,377 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-06_01-37-14.log]
[testng] 01:37:14,378 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4aa773fa - End of configuration.
[testng] [2024-07-06 01:37:16,987] [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] [2024-07-06 01:37:17,043] [pool-1-thread-1] Initializing /data/qa-17190/002002011.flex:
[testng] [2024-07-06 01:37:17,087] [pool-1-thread-10] Initializing /data/tony/test.tiff:
[testng] [2024-07-06 01:37:17,166] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex:
[testng] [2024-07-06 01:37:17,676] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex:
[testng] [2024-07-06 01:37:17,722] [pool-1-thread-9] Initializing /data/tony/001014000 - from flex.tif:
[testng] [2024-07-06 01:37:17,772] [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] [2024-07-06 01:37:18,376] [pool-1-thread-1] Initializing /data/tony/015002000.tiff:
[testng] [2024-07-06 01:37:18,707] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex:
[testng] [2024-07-06 01:37:18,744] [pool-1-thread-9] Initializing /data/qa-18096/002002001.flex:
[testng] [2024-07-06 01:37:19,233] [pool-1-thread-1] Initializing /data/stephane/006013000.flex:
[testng] [2024-07-06 01:37:19,311] [pool-1-thread-4] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex:
[testng] [2024-07-06 01:37:19,474] [pool-1-thread-9] Initializing /data/ghislain/test.flex:
[testng] [2024-07-06 01:37:20,016] [pool-1-thread-10] Initializing /data/tamjid/006004000.flex:
[testng] [2024-07-06 01:37:20,314] [pool-1-thread-9] Initializing /data/tamjid/006005000.flex:
[testng] [2024-07-06 01:37:20,338] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex:
[testng] [2024-07-06 01:37:20,708] [pool-1-thread-10] Initializing /data/tony/000101400 - from PE sofwatre.tif:
[testng] [2024-07-06 01:37:20,848] [pool-1-thread-9] Initializing /data/tony/test1.flex:
[testng] [2024-07-06 01:37:21,200] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex:
[testng] [2024-07-06 01:37:21,264] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex:
[testng] [2024-07-06 01:37:21,716] [pool-1-thread-10] Initializing /data/stephane/002007000.flex:
[testng] [2024-07-06 01:37:21,866] [pool-1-thread-7] Initializing /data/anatole/001004000.flex:
[testng] [2024-07-06 01:37:21,937] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex:
[testng] [2024-07-06 01:37:22,472] [pool-1-thread-8] Initializing /data/qa-7469/002002.flex:
[testng] [2024-07-06 01:37:22,863] [pool-1-thread-4] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex:
[testng] [2024-07-06 01:37:23,144] [pool-1-thread-10] Initializing /data/tony/001001000_objects.flex:
[testng] [2024-07-06 01:37:23,305] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex:
[testng] [2024-07-06 01:37:23,941] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex:
[testng] [2024-07-06 01:37:24,271] [pool-1-thread-10] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex:
[testng] [2024-07-06 01:37:24,613] [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: 9 minutes 1 second
Finished: SUCCESS