Started by upstream project "BIOFORMATS-test-repo" build number 262
originally caused by:
Started by upstream project "Trigger" build number 286
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5
[BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins1686196080124450592.sh
+ '[' li-flim = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_41325_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 00:47:05,954 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 00:47:05,955 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service.
[testng] 00:47:05,955 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:47:05,956 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:47:05,957 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:47:05,957 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:47:05,957 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 00:47:05,957 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:47:05,958 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:47:05,958 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:47:05,959 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:47:05,959 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:47:06,123 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:47:06,123 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:47:06,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:47:06,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:47:06,156 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:47:06,156 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:47:06,156 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:47:06,156 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:47:06,156 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration.
[testng] 00:47:06,157 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point
[testng] 00:47:06,157 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 199 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-21 00:47:06,167] [main] java.version = 21
[testng] 00:47:06,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:47:06,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:06,212 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-21_00-47-06.log]
[testng] 00:47:06,214 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration.
[testng] [2024-11-21 00:47:06,215] [main] testng.directory = /data
[testng] [2024-11-21 00:47:06,216] [main] testng.configDirectory = /config
[testng] [2024-11-21 00:47:06,225] [main] testng.multiplier = 1.0
[testng] [2024-11-21 00:47:06,225] [main] testng.in-memory = false
[testng] [2024-11-21 00:47:06,225] [main] testng.allow-missing = false
[testng] [2024-11-21 00:47:06,225] [main] user.language = en
[testng] [2024-11-21 00:47:06,225] [main] user.country = ${user.country}
[testng] [2024-11-21 00:47:06,226] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-11-21 00:47:09,213] [main] ----------------------------------------
[testng] [2024-11-21 00:47:09,214] [main] Total files: 28
[testng] [2024-11-21 00:47:09,214] [main] Scan time: 2.987 s (106 ms/file)
[testng] [2024-11-21 00:47:09,214] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 26 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-21 00:47:18,088] [pool-1-thread-1] Initializing /data/samples/lifetime-simple.fli:
[testng] 00:47:18,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:47:18,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:18,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-21_00-47-18.log]
[testng] 00:47:18,090 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d44a23e - End of configuration.
[testng] [2024-11-21 00:47:18,222] [pool-1-thread-12] Initializing /data/qian/vxl-mbad-737-1um-01687.fli:
[testng] 00:47:18,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:47:18,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:18,223 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-21_00-47-18.log]
[testng] 00:47:18,223 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a1ab702 - End of configuration.
[testng] [2024-11-21 00:47:18,403] [pool-1-thread-11] Initializing /data/jean-marie/IMG_4936.JPG:
[testng] 00:47:18,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:47:18,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:18,404 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-21_00-47-18.log]
[testng] 00:47:18,405 |-INFO in ch.qos.logback.core.sift.SiftProcessor@210b5e37 - End of configuration.
[testng] [2024-11-21 00:47:18,731] [pool-1-thread-10] Initializing /data/jean-marie/Flimdata/lif_E Sample Typical-Dicot-Root-Zserie-CSU22.fli:
[testng] 00:47:18,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:47:18,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:18,732 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-21_00-47-18.log]
[testng] 00:47:18,732 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24c7ac69 - End of configuration.
[testng] [2024-11-21 00:47:18,900] [pool-1-thread-9] Initializing /data/jean-marie/Flimdata/lif_D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli:
[testng] 00:47:18,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:47:18,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:18,901 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-21_00-47-18.log]
[testng] 00:47:18,902 |-INFO in ch.qos.logback.core.sift.SiftProcessor@557919f0 - End of configuration.
[testng] [2024-11-21 00:47:19,073] [pool-1-thread-8] Initializing /data/samples/sample-simple.fli:
[testng] 00:47:19,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:47:19,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:19,074 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-21_00-47-19.log]
[testng] 00:47:19,074 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46965be4 - End of configuration.
[testng] [2024-11-21 00:47:19,385] [pool-1-thread-7] Initializing /data/jean-marie/Flimdata/E Reference fluorescein4ns-CSU22.fli:
[testng] 00:47:19,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:47:19,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:19,386 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-21_00-47-19.log]
[testng] 00:47:19,386 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d9e2b44 - End of configuration.
[testng] [2024-11-21 00:47:19,727] [pool-1-thread-6] Initializing /data/LambertInstruments/cp70-euresys_Lambert HS1000_1875-ST-250(msb).fli:
[testng] 00:47:19,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:47:19,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:19,728 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-21_00-47-19.log]
[testng] 00:47:19,729 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fb93dd7 - End of configuration.
[testng] [2024-11-21 00:47:19,919] [pool-1-thread-5] Initializing /data/jean-marie/Flimdata/A Reference fluorescein4ns-CFPbpFILTER.fli:
[testng] 00:47:19,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:47:19,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:19,920 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-21_00-47-19.log]
[testng] 00:47:19,921 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d76610a - End of configuration.
[testng] [2024-11-21 00:47:20,083] [pool-1-thread-4] Initializing /data/LambertInstruments/LambertInstruments-fli-2/16-8bit_CameraSimulator_LI-Camera-Simulator.fli:
[testng] 00:47:20,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:47:20,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:20,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-21_00-47-20.log]
[testng] 00:47:20,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10f5cd68 - End of configuration.
[testng] [2024-11-21 00:47:20,241] [pool-1-thread-3] Initializing /data/jean-marie/Flimdata/E Sample Typical-Dicot-Root-Zserie-CSU22.fli:
[testng] 00:47:20,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:47:20,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:20,242 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-21_00-47-20.log]
[testng] 00:47:20,242 |-INFO in ch.qos.logback.core.sift.SiftProcessor@320e2851 - End of configuration.
[testng] [2024-11-21 00:47:20,500] [pool-1-thread-2] Initializing /data/samples/lifetime-extended.fli:
[testng] 00:47:20,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:47:20,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:20,501 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-21_00-47-20.log]
[testng] 00:47:20,502 |-INFO in ch.qos.logback.core.sift.SiftProcessor@404d73a5 - End of configuration.
[testng] [2024-11-21 00:47:24,409] [pool-1-thread-1] Initializing /data/jean-marie/Flimdata/C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli:
[testng] [2024-11-21 00:47:24,589] [pool-1-thread-8] Initializing /data/samples/reference-extended.fli:
[testng] [2024-11-21 00:47:24,784] [pool-1-thread-2] Initializing /data/jean-marie/Flimdata/D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli:
[testng] [2024-11-21 00:47:24,958] [pool-1-thread-9] Initializing /data/jean-marie/Flimdata/lif_A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli:
[testng] [2024-11-21 00:47:25,157] [pool-1-thread-4] Initializing /data/qa-17164/ExampleFile - LiFlimReader fix ExposureTime .fli:
[testng] [2024-11-21 00:47:25,314] [pool-1-thread-10] Initializing /data/LambertInstruments/cp70-siso_Lambert HS1000_1875-ST-250(lsb).fli:
[testng] [2024-11-21 00:47:25,462] [pool-1-thread-6] Initializing /data/LambertInstruments/LambertInstruments-fli-2/15-8bit_CameraSimulator_LI-Camera-Simulator.fli:
[testng] [2024-11-21 00:47:25,985] [pool-1-thread-5] Initializing /data/jean-marie/Flimdata/C Reference fluorescein4ns-CFPbpFILTER.fli:
[testng] [2024-11-21 00:47:26,320] [pool-1-thread-12] Initializing /data/rharkes/2018-11-28_10.04.10_sample_Rhodamine6G.fli:
[testng] [2024-11-21 00:47:26,509] [pool-1-thread-7] Initializing /data/samples/sample-extended.fli:
[testng] [2024-11-21 00:47:27,918] [pool-1-thread-8] Initializing /data/jean-marie/IMG_4935.JPG:
[testng] [2024-11-21 00:47:28,311] [pool-1-thread-4] Initializing /data/jean-marie/Flimdata/A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli:
[testng] [2024-11-21 00:47:28,481] [pool-1-thread-9] Initializing /data/samples/reference-simple.fli:
[testng] [2024-11-21 00:47:28,632] [pool-1-thread-6] Initializing /data/jean-marie/Flimdata/lif_C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1378, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 36 seconds
Finished: SUCCESS