Started by upstream project "BIOFORMATS-test-repo" build number 1
originally caused by:
Started by upstream project "Trigger" build number 1
originally caused by:
Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6
[BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins7953350671103755041.sh
+ '[' li-flim = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_43_merge_ci -v /uod/idr/repos/curated/li-flim:/data -v /uod/idr-scratch/devspace/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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release
[javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
[javac] 4 warnings
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] 16:09:02,185 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 16:09:02,187 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service.
[testng] 16:09:02,187 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 16:09:02,188 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 16:09:02,188 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 16:09:02,188 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 16:09:02,189 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 16:09:02,189 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 16:09:02,189 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 16:09:02,190 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 16:09:02,190 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 16:09:02,190 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 16:09:02,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 16:09:02,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 16:09:02,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 16:09:02,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 16:09:02,382 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 16:09:02,382 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 16:09:02,382 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 16:09:02,383 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 16:09:02,383 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration.
[testng] 16:09:02,383 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point
[testng] 16:09:02,384 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 194 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-03-14 16:09:02,393] [main] java.version = 21
[testng] 16:09:02,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 16:09:02,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:09:02,439 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-14_16-09-02.log]
[testng] 16:09:02,440 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration.
[testng] [2024-03-14 16:09:02,442] [main] testng.directory = /data
[testng] [2024-03-14 16:09:02,442] [main] testng.configDirectory = /config
[testng] [2024-03-14 16:09:02,451] [main] testng.multiplier = 1.0
[testng] [2024-03-14 16:09:02,451] [main] testng.in-memory = false
[testng] [2024-03-14 16:09:02,451] [main] testng.allow-missing = false
[testng] [2024-03-14 16:09:02,451] [main] user.language = en
[testng] [2024-03-14 16:09:02,451] [main] user.country = ${user.country}
[testng] [2024-03-14 16:09:02,451] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-03-14 16:09:03,492] [main] ----------------------------------------
[testng] [2024-03-14 16:09:03,492] [main] Total files: 28
[testng] [2024-03-14 16:09:03,492] [main] Scan time: 1.04 s (37 ms/file)
[testng] [2024-03-14 16:09:03,493] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 26 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-03-14 16:09:06,940] [pool-1-thread-1] Initializing /data/jean-marie/Flimdata/lif_D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli:
[testng] 16:09:06,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 16:09:06,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:09:06,942 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-14_16-09-06.log]
[testng] 16:09:06,942 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49992987 - End of configuration.
[testng] [2024-03-14 16:09:06,994] [pool-1-thread-12] Initializing /data/jean-marie/Flimdata/E Sample Typical-Dicot-Root-Zserie-CSU22.fli:
[testng] 16:09:06,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 16:09:06,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:09:06,996 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-14_16-09-06.log]
[testng] 16:09:06,996 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4516e0a0 - End of configuration.
[testng] [2024-03-14 16:09:07,087] [pool-1-thread-11] Initializing /data/jean-marie/Flimdata/D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli:
[testng] 16:09:07,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 16:09:07,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:09:07,088 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-14_16-09-07.log]
[testng] 16:09:07,088 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1aa92df7 - End of configuration.
[testng] [2024-03-14 16:09:07,153] [pool-1-thread-10] Initializing /data/jean-marie/Flimdata/C Reference fluorescein4ns-CFPbpFILTER.fli:
[testng] 16:09:07,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 16:09:07,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:09:07,154 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-14_16-09-07.log]
[testng] 16:09:07,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6be46894 - End of configuration.
[testng] [2024-03-14 16:09:07,192] [pool-1-thread-9] Initializing /data/rharkes/2018-11-28_10.04.10_sample_Rhodamine6G.fli:
[testng] 16:09:07,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 16:09:07,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:09:07,193 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-14_16-09-07.log]
[testng] 16:09:07,194 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fb6303 - End of configuration.
[testng] [2024-03-14 16:09:07,244] [pool-1-thread-8] Initializing /data/jean-marie/Flimdata/A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli:
[testng] 16:09:07,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 16:09:07,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:09:07,245 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-14_16-09-07.log]
[testng] 16:09:07,245 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fd184a - End of configuration.
[testng] [2024-03-14 16:09:07,275] [pool-1-thread-7] Initializing /data/qa-17164/ExampleFile - LiFlimReader fix ExposureTime .fli:
[testng] 16:09:07,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 16:09:07,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:09:07,276 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-14_16-09-07.log]
[testng] 16:09:07,277 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71c0d3fa - End of configuration.
[testng] [2024-03-14 16:09:07,307] [pool-1-thread-6] Initializing /data/samples/sample-simple.fli:
[testng] 16:09:07,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 16:09:07,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:09:07,308 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-14_16-09-07.log]
[testng] 16:09:07,308 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40dac40d - End of configuration.
[testng] [2024-03-14 16:09:07,334] [pool-1-thread-5] Initializing /data/LambertInstruments/LambertInstruments-fli-2/16-8bit_CameraSimulator_LI-Camera-Simulator.fli:
[testng] 16:09:07,334 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 16:09:07,334 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:09:07,335 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-14_16-09-07.log]
[testng] 16:09:07,335 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b9a3531 - End of configuration.
[testng] [2024-03-14 16:09:07,371] [pool-1-thread-4] Initializing /data/LambertInstruments/cp70-euresys_Lambert HS1000_1875-ST-250(msb).fli:
[testng] 16:09:07,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 16:09:07,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:09:07,372 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-14_16-09-07.log]
[testng] 16:09:07,372 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10b56cf9 - End of configuration.
[testng] [2024-03-14 16:09:07,403] [pool-1-thread-3] Initializing /data/jean-marie/Flimdata/lif_C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli:
[testng] 16:09:07,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 16:09:07,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:09:07,404 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-14_16-09-07.log]
[testng] 16:09:07,405 |-INFO in ch.qos.logback.core.sift.SiftProcessor@472f748f - End of configuration.
[testng] [2024-03-14 16:09:07,442] [pool-1-thread-2] Initializing /data/samples/lifetime-simple.fli:
[testng] 16:09:07,443 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 16:09:07,443 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:09:07,443 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-14_16-09-07.log]
[testng] 16:09:07,444 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b429b3e - End of configuration.
[testng] [2024-03-14 16:09:08,659] [pool-1-thread-2] Initializing /data/LambertInstruments/LambertInstruments-fli-2/15-8bit_CameraSimulator_LI-Camera-Simulator.fli:
[testng] [2024-03-14 16:09:08,693] [pool-1-thread-6] Initializing /data/jean-marie/Flimdata/lif_E Sample Typical-Dicot-Root-Zserie-CSU22.fli:
[testng] [2024-03-14 16:09:08,863] [pool-1-thread-1] Initializing /data/samples/reference-simple.fli:
[testng] [2024-03-14 16:09:08,887] [pool-1-thread-3] Initializing /data/LambertInstruments/cp70-siso_Lambert HS1000_1875-ST-250(lsb).fli:
[testng] [2024-03-14 16:09:09,007] [pool-1-thread-7] Initializing /data/jean-marie/Flimdata/E Reference fluorescein4ns-CSU22.fli:
[testng] [2024-03-14 16:09:09,170] [pool-1-thread-4] Initializing /data/jean-marie/Flimdata/lif_A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli:
[testng] [2024-03-14 16:09:09,347] [pool-1-thread-5] Initializing /data/samples/sample-extended.fli:
[testng] [2024-03-14 16:09:09,665] [pool-1-thread-1] Initializing /data/jean-marie/IMG_4936.JPG:
[testng] [2024-03-14 16:09:10,020] [pool-1-thread-9] Initializing /data/jean-marie/Flimdata/C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli:
[testng] [2024-03-14 16:09:10,116] [pool-1-thread-8] Initializing /data/jean-marie/IMG_4935.JPG:
[testng] [2024-03-14 16:09:10,558] [pool-1-thread-2] Initializing /data/jean-marie/Flimdata/A Reference fluorescein4ns-CFPbpFILTER.fli:
[testng] [2024-03-14 16:09:10,748] [pool-1-thread-6] Initializing /data/samples/lifetime-extended.fli:
[testng] [2024-03-14 16:09:10,868] [pool-1-thread-10] Initializing /data/qian/vxl-mbad-737-1um-01687.fli:
[testng] [2024-03-14 16:09:10,905] [pool-1-thread-5] Initializing /data/samples/reference-extended.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