Started by upstream project "BIOFORMATS-test-repo" build number 36
originally caused by:
Started by upstream project "Trigger" build number 40
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9
[BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins9202454601155275744.sh
+ '[' li-flim = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_4933_merge_ci -v /uod/idr/repos/curated/li-flim:/data -v /uod/idr-scratch/merge-ci/curated/li-flim:/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] 01:27:07,679 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:27:07,680 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 01:27:07,680 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:27:07,681 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:27:07,682 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:27:07,682 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:27:07,683 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:27:07,683 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:27:07,683 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:27:07,684 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:27:07,684 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:27:07,684 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:27:07,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:27:07,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:27:07,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:27:07,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:27:07,896 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:27:07,897 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:27:07,897 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:27:07,897 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:27:07,897 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 01:27:07,898 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 01:27:07,898 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 215 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-04-16 01:27:07,908] [main] java.version = 11.0.16
[testng] 01:27:07,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:27:07,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:07,957 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-16_01-27-07.log]
[testng] 01:27:07,958 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-04-16 01:27:07,961] [main] testng.directory = /data
[testng] [2024-04-16 01:27:07,961] [main] testng.configDirectory = /config
[testng] [2024-04-16 01:27:07,971] [main] testng.multiplier = 1.0
[testng] [2024-04-16 01:27:07,973] [main] testng.in-memory = false
[testng] [2024-04-16 01:27:07,973] [main] testng.allow-missing = false
[testng] [2024-04-16 01:27:07,973] [main] user.language = en
[testng] [2024-04-16 01:27:07,973] [main] user.country = ${user.country}
[testng] [2024-04-16 01:27:07,974] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-04-16 01:27:08,803] [main] ----------------------------------------
[testng] [2024-04-16 01:27:08,803] [main] Total files: 28
[testng] [2024-04-16 01:27:08,803] [main] Scan time: 0.829 s (29 ms/file)
[testng] [2024-04-16 01:27:08,803] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 26 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-04-16 01:27:11,764] [pool-1-thread-1] Initializing /data/jean-marie/Flimdata/lif_E Sample Typical-Dicot-Root-Zserie-CSU22.fli:
[testng] 01:27:11,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:27:11,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:11,768 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-16_01-27-11.log]
[testng] 01:27:11,768 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7215c718 - End of configuration.
[testng] [2024-04-16 01:27:11,897] [pool-1-thread-12] Initializing /data/LambertInstruments/cp70-euresys_Lambert HS1000_1875-ST-250(msb).fli:
[testng] 01:27:11,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:27:11,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:11,900 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-16_01-27-11.log]
[testng] 01:27:11,900 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61198f63 - End of configuration.
[testng] [2024-04-16 01:27:11,938] [pool-1-thread-11] Initializing /data/qian/vxl-mbad-737-1um-01687.fli:
[testng] 01:27:11,939 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:27:11,939 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:11,940 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-16_01-27-11.log]
[testng] 01:27:11,940 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2505d283 - End of configuration.
[testng] [2024-04-16 01:27:11,975] [pool-1-thread-10] Initializing /data/jean-marie/Flimdata/lif_A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli:
[testng] 01:27:11,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:27:11,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:11,976 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-16_01-27-11.log]
[testng] 01:27:11,977 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e07cbaf - End of configuration.
[testng] [2024-04-16 01:27:12,011] [pool-1-thread-9] Initializing /data/LambertInstruments/LambertInstruments-fli-2/15-8bit_CameraSimulator_LI-Camera-Simulator.fli:
[testng] 01:27:12,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:27:12,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:12,012 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-16_01-27-12.log]
[testng] 01:27:12,012 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1608318c - End of configuration.
[testng] [2024-04-16 01:27:12,041] [pool-1-thread-8] Initializing /data/jean-marie/IMG_4936.JPG:
[testng] 01:27:12,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:27:12,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:12,042 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-16_01-27-12.log]
[testng] 01:27:12,043 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ba8a104 - End of configuration.
[testng] [2024-04-16 01:27:12,411] [pool-1-thread-7] Initializing /data/jean-marie/Flimdata/C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli:
[testng] 01:27:12,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:27:12,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:12,412 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-16_01-27-12.log]
[testng] 01:27:12,412 |-INFO in ch.qos.logback.core.sift.SiftProcessor@766be0b6 - End of configuration.
[testng] [2024-04-16 01:27:12,476] [pool-1-thread-6] Initializing /data/jean-marie/Flimdata/A Reference fluorescein4ns-CFPbpFILTER.fli:
[testng] 01:27:12,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:27:12,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:12,477 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-16_01-27-12.log]
[testng] 01:27:12,477 |-INFO in ch.qos.logback.core.sift.SiftProcessor@350162b7 - End of configuration.
[testng] [2024-04-16 01:27:12,505] [pool-1-thread-5] Initializing /data/samples/sample-simple.fli:
[testng] 01:27:12,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:27:12,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:12,507 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-16_01-27-12.log]
[testng] 01:27:12,507 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3aac21d4 - End of configuration.
[testng] [2024-04-16 01:27:12,525] [pool-1-thread-4] Initializing /data/rharkes/2018-11-28_10.04.10_sample_Rhodamine6G.fli:
[testng] 01:27:12,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:27:12,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:12,527 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-16_01-27-12.log]
[testng] 01:27:12,527 |-INFO in ch.qos.logback.core.sift.SiftProcessor@463bfac - End of configuration.
[testng] [2024-04-16 01:27:12,576] [pool-1-thread-3] Initializing /data/samples/reference-simple.fli:
[testng] 01:27:12,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:27:12,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:12,577 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-16_01-27-12.log]
[testng] 01:27:12,577 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3699ea97 - End of configuration.
[testng] [2024-04-16 01:27:12,592] [pool-1-thread-2] Initializing /data/jean-marie/IMG_4935.JPG:
[testng] 01:27:12,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:27:12,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:12,593 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-16_01-27-12.log]
[testng] 01:27:12,593 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52f55830 - End of configuration.
[testng] [2024-04-16 01:27:14,283] [pool-1-thread-5] Initializing /data/qa-17164/ExampleFile - LiFlimReader fix ExposureTime .fli:
[testng] [2024-04-16 01:27:14,309] [pool-1-thread-3] Initializing /data/LambertInstruments/cp70-siso_Lambert HS1000_1875-ST-250(lsb).fli:
[testng] [2024-04-16 01:27:14,330] [pool-1-thread-10] Initializing /data/jean-marie/Flimdata/lif_C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli:
[testng] [2024-04-16 01:27:14,364] [pool-1-thread-1] Initializing /data/jean-marie/Flimdata/E Reference fluorescein4ns-CSU22.fli:
[testng] [2024-04-16 01:27:14,694] [pool-1-thread-9] Initializing /data/jean-marie/Flimdata/A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli:
[testng] [2024-04-16 01:27:14,757] [pool-1-thread-12] Initializing /data/samples/reference-extended.fli:
[testng] [2024-04-16 01:27:15,452] [pool-1-thread-4] Initializing /data/jean-marie/Flimdata/D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli:
[testng] [2024-04-16 01:27:15,483] [pool-1-thread-5] Initializing /data/jean-marie/Flimdata/E Sample Typical-Dicot-Root-Zserie-CSU22.fli:
[testng] [2024-04-16 01:27:15,507] [pool-1-thread-6] Initializing /data/jean-marie/Flimdata/C Reference fluorescein4ns-CFPbpFILTER.fli:
[testng] [2024-04-16 01:27:15,534] [pool-1-thread-12] Initializing /data/LambertInstruments/LambertInstruments-fli-2/16-8bit_CameraSimulator_LI-Camera-Simulator.fli:
[testng] [2024-04-16 01:27:15,560] [pool-1-thread-11] Initializing /data/samples/sample-extended.fli:
[testng] [2024-04-16 01:27:15,582] [pool-1-thread-10] Initializing /data/samples/lifetime-extended.fli:
[testng] [2024-04-16 01:27:15,726] [pool-1-thread-3] Initializing /data/jean-marie/Flimdata/lif_D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli:
[testng] [2024-04-16 01:27:15,900] [pool-1-thread-10] Initializing /data/samples/lifetime-simple.fli:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1378, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 21 seconds
Finished: SUCCESS