Started by upstream project "BIOFORMATS-test-repo" build number 211
originally caused by:
Started by upstream project "Trigger" build number 237
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3
[BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins7863698365491595540.sh
+ '[' li-flim = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_33477_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] 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] 01:35:45,805 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:35:45,807 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 01:35:45,807 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:35:45,809 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:35:45,811 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:35:45,811 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:35:45,813 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 4 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:35:45,813 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:35:45,814 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:35:45,816 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:35:45,817 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:35:45,817 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:35:46,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:35:46,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:35:46,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:35:46,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:35:46,055 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:35:46,055 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:35:46,055 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:35:46,056 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:35:46,056 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 01:35:46,057 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 01:35:46,057 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 243 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-06 01:35:46,067] [main] java.version = 17.0.2
[testng] 01:35:46,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:35:46,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:46,112 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-06_01-35-46.log]
[testng] 01:35:46,114 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-10-06 01:35:46,116] [main] testng.directory = /data
[testng] [2024-10-06 01:35:46,116] [main] testng.configDirectory = /config
[testng] [2024-10-06 01:35:46,146] [main] testng.multiplier = 1.0
[testng] [2024-10-06 01:35:46,147] [main] testng.in-memory = false
[testng] [2024-10-06 01:35:46,147] [main] testng.allow-missing = false
[testng] [2024-10-06 01:35:46,147] [main] user.language = en
[testng] [2024-10-06 01:35:46,147] [main] user.country = ${user.country}
[testng] [2024-10-06 01:35:46,147] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-10-06 01:35:48,565] [main] ----------------------------------------
[testng] [2024-10-06 01:35:48,565] [main] Total files: 28
[testng] [2024-10-06 01:35:48,565] [main] Scan time: 2.418 s (86 ms/file)
[testng] [2024-10-06 01:35:48,565] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 26 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-06 01:35:54,051] [pool-1-thread-1] Initializing /data/qian/vxl-mbad-737-1um-01687.fli:
[testng] 01:35:54,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:35:54,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:54,053 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-06_01-35-54.log]
[testng] 01:35:54,053 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76ec59e1 - End of configuration.
[testng] [2024-10-06 01:35:54,291] [pool-1-thread-12] Initializing /data/jean-marie/Flimdata/A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli:
[testng] 01:35:54,291 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:35:54,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:54,293 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-06_01-35-54.log]
[testng] 01:35:54,293 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6714276d - End of configuration.
[testng] [2024-10-06 01:35:54,418] [pool-1-thread-11] Initializing /data/samples/lifetime-extended.fli:
[testng] 01:35:54,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:35:54,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:54,419 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-06_01-35-54.log]
[testng] 01:35:54,420 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53ee17bc - End of configuration.
[testng] [2024-10-06 01:35:54,504] [pool-1-thread-10] Initializing /data/rharkes/2018-11-28_10.04.10_sample_Rhodamine6G.fli:
[testng] 01:35:54,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:35:54,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:54,505 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-06_01-35-54.log]
[testng] 01:35:54,506 |-INFO in ch.qos.logback.core.sift.SiftProcessor@190b907d - End of configuration.
[testng] [2024-10-06 01:35:54,644] [pool-1-thread-9] Initializing /data/samples/sample-simple.fli:
[testng] 01:35:54,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:35:54,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:54,645 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-06_01-35-54.log]
[testng] 01:35:54,646 |-INFO in ch.qos.logback.core.sift.SiftProcessor@636bfb05 - End of configuration.
[testng] [2024-10-06 01:35:54,753] [pool-1-thread-8] Initializing /data/samples/lifetime-simple.fli:
[testng] 01:35:54,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:35:54,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:54,754 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-06_01-35-54.log]
[testng] 01:35:54,755 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fa40cf8 - End of configuration.
[testng] [2024-10-06 01:35:54,818] [pool-1-thread-7] Initializing /data/jean-marie/IMG_4936.JPG:
[testng] 01:35:54,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:35:54,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:54,819 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-06_01-35-54.log]
[testng] 01:35:54,820 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68b92c50 - End of configuration.
[testng] [2024-10-06 01:35:55,147] [pool-1-thread-6] Initializing /data/jean-marie/Flimdata/C Reference fluorescein4ns-CFPbpFILTER.fli:
[testng] 01:35:55,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:35:55,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:55,148 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-06_01-35-55.log]
[testng] 01:35:55,148 |-INFO in ch.qos.logback.core.sift.SiftProcessor@610952ef - End of configuration.
[testng] [2024-10-06 01:35:55,257] [pool-1-thread-5] Initializing /data/samples/reference-simple.fli:
[testng] 01:35:55,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:35:55,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:55,258 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-06_01-35-55.log]
[testng] 01:35:55,258 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6548f089 - End of configuration.
[testng] [2024-10-06 01:35:55,323] [pool-1-thread-4] Initializing /data/jean-marie/Flimdata/lif_D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli:
[testng] 01:35:55,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:35:55,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:55,324 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-06_01-35-55.log]
[testng] 01:35:55,325 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15b9d46d - End of configuration.
[testng] [2024-10-06 01:35:55,414] [pool-1-thread-3] Initializing /data/LambertInstruments/LambertInstruments-fli-2/15-8bit_CameraSimulator_LI-Camera-Simulator.fli:
[testng] 01:35:55,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:35:55,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:55,415 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-06_01-35-55.log]
[testng] 01:35:55,415 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6122faa2 - End of configuration.
[testng] [2024-10-06 01:35:55,494] [pool-1-thread-2] Initializing /data/jean-marie/Flimdata/E Reference fluorescein4ns-CSU22.fli:
[testng] 01:35:55,494 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:35:55,494 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:35:55,495 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-06_01-35-55.log]
[testng] 01:35:55,495 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54f7153b - End of configuration.
[testng] [2024-10-06 01:35:57,313] [pool-1-thread-8] Initializing /data/jean-marie/Flimdata/E Sample Typical-Dicot-Root-Zserie-CSU22.fli:
[testng] [2024-10-06 01:35:57,467] [pool-1-thread-9] Initializing /data/jean-marie/Flimdata/A Reference fluorescein4ns-CFPbpFILTER.fli:
[testng] [2024-10-06 01:35:57,609] [pool-1-thread-5] Initializing /data/samples/sample-extended.fli:
[testng] [2024-10-06 01:35:57,789] [pool-1-thread-11] Initializing /data/LambertInstruments/cp70-siso_Lambert HS1000_1875-ST-250(lsb).fli:
[testng] [2024-10-06 01:35:57,958] [pool-1-thread-4] Initializing /data/jean-marie/Flimdata/lif_E Sample Typical-Dicot-Root-Zserie-CSU22.fli:
[testng] [2024-10-06 01:35:58,921] [pool-1-thread-10] Initializing /data/LambertInstruments/LambertInstruments-fli-2/16-8bit_CameraSimulator_LI-Camera-Simulator.fli:
[testng] [2024-10-06 01:35:59,025] [pool-1-thread-3] Initializing /data/qa-17164/ExampleFile - LiFlimReader fix ExposureTime .fli:
[testng] [2024-10-06 01:35:59,077] [pool-1-thread-12] Initializing /data/jean-marie/Flimdata/C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli:
[testng] [2024-10-06 01:35:59,236] [pool-1-thread-1] Initializing /data/jean-marie/Flimdata/D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli:
[testng] [2024-10-06 01:35:59,323] [pool-1-thread-2] Initializing /data/samples/reference-extended.fli:
[testng] [2024-10-06 01:35:59,704] [pool-1-thread-11] Initializing /data/jean-marie/Flimdata/lif_C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli:
[testng] [2024-10-06 01:35:59,791] [pool-1-thread-6] Initializing /data/jean-marie/Flimdata/lif_A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli:
[testng] [2024-10-06 01:35:59,843] [pool-1-thread-5] Initializing /data/LambertInstruments/cp70-euresys_Lambert HS1000_1875-ST-250(msb).fli:
[testng] [2024-10-06 01:35:59,891] [pool-1-thread-4] Initializing /data/jean-marie/IMG_4935.JPG:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1378, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 27 seconds
Finished: SUCCESS