Started by upstream project "BIOFORMATS-test-repo" build number 365
originally caused by:
Started by upstream project "Trigger" build number 391
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/jenkins7486083961871268805.sh
+ '[' li-flim = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_58169_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] 00:44:10,608 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15
[testng] 00:44:10,609 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service.
[testng] 00:44:10,609 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:44:10,610 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:44:10,610 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:44:10,611 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:44:10,611 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 00:44:10,611 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:44:10,611 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:44:10,612 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:44:10,612 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:44:10,612 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:44:10,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:44:10,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:44:10,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:44:10,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:44:10,796 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:44:10,796 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:44:10,797 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:44:10,797 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:44:10,797 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration.
[testng] 00:44:10,798 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point
[testng] 00:44:10,798 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 187 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2025-03-05 00:44:10,807] [main] java.version = 17.0.2
[testng] 00:44:10,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:44:10,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:44:10,849 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-05_00-44-10.log]
[testng] 00:44:10,851 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration.
[testng] [2025-03-05 00:44:10,853] [main] testng.directory = /data
[testng] [2025-03-05 00:44:10,853] [main] testng.configDirectory = /config
[testng] [2025-03-05 00:44:10,861] [main] testng.multiplier = 1.0
[testng] [2025-03-05 00:44:10,862] [main] testng.in-memory = false
[testng] [2025-03-05 00:44:10,862] [main] testng.allow-missing = false
[testng] [2025-03-05 00:44:10,862] [main] user.language = en
[testng] [2025-03-05 00:44:10,862] [main] user.country = ${user.country}
[testng] [2025-03-05 00:44:10,862] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2025-03-05 00:44:13,429] [main] ----------------------------------------
[testng] [2025-03-05 00:44:13,429] [main] Total files: 28
[testng] [2025-03-05 00:44:13,429] [main] Scan time: 2.567 s (91 ms/file)
[testng] [2025-03-05 00:44:13,429] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 26 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2025-03-05 00:44:21,992] [pool-1-thread-1] Initializing /data/samples/sample-extended.fli:
[testng] 00:44:21,993 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:44:21,993 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:44:21,994 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-05_00-44-21.log]
[testng] 00:44:21,994 |-INFO in ch.qos.logback.core.sift.SiftProcessor@612c3340 - End of configuration.
[testng] [2025-03-05 00:44:22,268] [pool-1-thread-12] Initializing /data/LambertInstruments/cp70-siso_Lambert HS1000_1875-ST-250(lsb).fli:
[testng] 00:44:22,268 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:44:22,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:44:22,270 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-05_00-44-22.log]
[testng] 00:44:22,270 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f8495e8 - End of configuration.
[testng] [2025-03-05 00:44:22,459] [pool-1-thread-11] Initializing /data/jean-marie/IMG_4936.JPG:
[testng] 00:44:22,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:44:22,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:44:22,460 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-05_00-44-22.log]
[testng] 00:44:22,460 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53d1cecf - End of configuration.
[testng] [2025-03-05 00:44:22,805] [pool-1-thread-10] Initializing /data/jean-marie/Flimdata/lif_A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli:
[testng] 00:44:22,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:44:22,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:44:22,806 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-05_00-44-22.log]
[testng] 00:44:22,806 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42eecbf5 - End of configuration.
[testng] [2025-03-05 00:44:23,003] [pool-1-thread-9] Initializing /data/samples/sample-simple.fli:
[testng] 00:44:23,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:44:23,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:44:23,004 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-05_00-44-23.log]
[testng] 00:44:23,005 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6714276d - End of configuration.
[testng] [2025-03-05 00:44:23,133] [pool-1-thread-8] Initializing /data/LambertInstruments/LambertInstruments-fli-2/15-8bit_CameraSimulator_LI-Camera-Simulator.fli:
[testng] 00:44:23,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:44:23,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:44:23,134 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-05_00-44-23.log]
[testng] 00:44:23,134 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5059cab0 - End of configuration.
[testng] [2025-03-05 00:44:23,265] [pool-1-thread-7] Initializing /data/jean-marie/Flimdata/A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli:
[testng] 00:44:23,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:44:23,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:44:23,267 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-05_00-44-23.log]
[testng] 00:44:23,267 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76e7b656 - End of configuration.
[testng] [2025-03-05 00:44:23,412] [pool-1-thread-6] Initializing /data/samples/reference-extended.fli:
[testng] 00:44:23,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:44:23,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:44:23,413 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-05_00-44-23.log]
[testng] 00:44:23,413 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66fde7f2 - End of configuration.
[testng] [2025-03-05 00:44:23,605] [pool-1-thread-5] Initializing /data/jean-marie/Flimdata/lif_C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli:
[testng] 00:44:23,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:44:23,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:44:23,606 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-05_00-44-23.log]
[testng] 00:44:23,606 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52d0199d - End of configuration.
[testng] [2025-03-05 00:44:23,811] [pool-1-thread-4] Initializing /data/rharkes/2018-11-28_10.04.10_sample_Rhodamine6G.fli:
[testng] 00:44:23,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:44:23,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:44:23,812 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-05_00-44-23.log]
[testng] 00:44:23,813 |-INFO in ch.qos.logback.core.sift.SiftProcessor@439ac465 - End of configuration.
[testng] [2025-03-05 00:44:24,029] [pool-1-thread-3] Initializing /data/jean-marie/Flimdata/C Reference fluorescein4ns-CFPbpFILTER.fli:
[testng] 00:44:24,029 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:44:24,029 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:44:24,030 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-05_00-44-24.log]
[testng] 00:44:24,030 |-INFO in ch.qos.logback.core.sift.SiftProcessor@217aa209 - End of configuration.
[testng] [2025-03-05 00:44:24,248] [pool-1-thread-2] Initializing /data/jean-marie/IMG_4935.JPG:
[testng] 00:44:24,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:44:24,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:44:24,249 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-05_00-44-24.log]
[testng] 00:44:24,249 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f312b63 - End of configuration.
[testng] [2025-03-05 00:44:26,510] [pool-1-thread-9] Initializing /data/samples/lifetime-extended.fli:
[testng] [2025-03-05 00:44:26,655] [pool-1-thread-6] Initializing /data/jean-marie/Flimdata/E Sample Typical-Dicot-Root-Zserie-CSU22.fli:
[testng] [2025-03-05 00:44:26,777] [pool-1-thread-1] Initializing /data/jean-marie/Flimdata/E Reference fluorescein4ns-CSU22.fli:
[testng] [2025-03-05 00:44:26,999] [pool-1-thread-5] Initializing /data/jean-marie/Flimdata/C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli:
[testng] [2025-03-05 00:44:27,154] [pool-1-thread-10] Initializing /data/LambertInstruments/LambertInstruments-fli-2/16-8bit_CameraSimulator_LI-Camera-Simulator.fli:
[testng] [2025-03-05 00:44:27,436] [pool-1-thread-12] Initializing /data/jean-marie/Flimdata/lif_D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli:
[testng] [2025-03-05 00:44:27,748] [pool-1-thread-4] Initializing /data/samples/reference-simple.fli:
[testng] [2025-03-05 00:44:27,891] [pool-1-thread-8] Initializing /data/LambertInstruments/cp70-euresys_Lambert HS1000_1875-ST-250(msb).fli:
[testng] [2025-03-05 00:44:28,048] [pool-1-thread-7] Initializing /data/jean-marie/Flimdata/lif_E Sample Typical-Dicot-Root-Zserie-CSU22.fli:
[testng] [2025-03-05 00:44:28,246] [pool-1-thread-3] Initializing /data/qian/vxl-mbad-737-1um-01687.fli:
[testng] [2025-03-05 00:44:28,719] [pool-1-thread-9] Initializing /data/qa-17164/ExampleFile - LiFlimReader fix ExposureTime .fli:
[testng] [2025-03-05 00:44:29,454] [pool-1-thread-10] Initializing /data/jean-marie/Flimdata/D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli:
[testng] [2025-03-05 00:44:29,693] [pool-1-thread-12] Initializing /data/samples/lifetime-simple.fli:
[testng] [2025-03-05 00:44:29,955] [pool-1-thread-4] Initializing /data/jean-marie/Flimdata/A Reference fluorescein4ns-CFPbpFILTER.fli:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1378, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 34 seconds
Finished: SUCCESS