Started by upstream project "BIOFORMATS-test-repo" build number 232
originally caused by:
Started by upstream project "Trigger" build number 257
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder
[BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins9074713594345111940.sh
+ '[' imspector = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_36486_merge_ci -v /uod/idr/repos/curated/imspector:/data -v /uod/idr-scratch/merge-ci/curated/imspector:/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] 04:07:40,291 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 04:07:40,293 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 04:07:40,293 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 04:07:40,294 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 04:07:40,295 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 04:07:40,295 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 04:07:40,295 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 04:07:40,295 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 04:07:40,296 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 04:07:40,297 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 04:07:40,297 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 04:07:40,297 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 04:07:40,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 04:07:40,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 04:07:40,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 04:07:40,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 04:07:40,505 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 04:07:40,505 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 04:07:40,505 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 04:07:40,506 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 04:07:40,506 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 04:07:40,507 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 04:07:40,507 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 211 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-23 04:07:40,521] [main] java.version = 17.0.2
[testng] 04:07:40,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 04:07:40,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:07:40,576 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-23_04-07-40.log]
[testng] 04:07:40,578 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-10-23 04:07:40,580] [main] testng.directory = /data
[testng] [2024-10-23 04:07:40,580] [main] testng.configDirectory = /config
[testng] [2024-10-23 04:07:40,588] [main] testng.multiplier = 1.0
[testng] [2024-10-23 04:07:40,589] [main] testng.in-memory = false
[testng] [2024-10-23 04:07:40,589] [main] testng.allow-missing = false
[testng] [2024-10-23 04:07:40,590] [main] user.language = en
[testng] [2024-10-23 04:07:40,590] [main] user.country = ${user.country}
[testng] [2024-10-23 04:07:40,590] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-10-23 04:07:55,464] [main] ----------------------------------------
[testng] [2024-10-23 04:07:55,464] [main] Total files: 29
[testng] [2024-10-23 04:07:55,464] [main] Scan time: 14.874 s (512 ms/file)
[testng] [2024-10-23 04:07:55,464] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 28 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-23 04:08:20,771] [pool-1-thread-1] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr:
[testng] 04:08:20,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 04:08:20,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:08:20,773 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-23_04-08-20.log]
[testng] 04:08:20,773 |-INFO in ch.qos.logback.core.sift.SiftProcessor@210da2fe - End of configuration.
[testng] [2024-10-23 04:08:21,390] [pool-1-thread-12] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr:
[testng] 04:08:21,391 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 04:08:21,391 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:08:21,392 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-23_04-08-21.log]
[testng] 04:08:21,392 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b429b3e - End of configuration.
[testng] [2024-10-23 04:08:22,159] [pool-1-thread-11] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr:
[testng] 04:08:22,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 04:08:22,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:08:22,160 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-23_04-08-22.log]
[testng] 04:08:22,160 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32e0fa2c - End of configuration.
[testng] [2024-10-23 04:08:23,181] [pool-1-thread-10] Initializing /data/qa-7936/01 - working.msr:
[testng] 04:08:23,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 04:08:23,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:08:23,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-23_04-08-23.log]
[testng] 04:08:23,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@98b88cd - End of configuration.
[testng] [2024-10-23 04:08:23,841] [pool-1-thread-9] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr:
[testng] 04:08:23,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 04:08:23,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:08:23,842 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-23_04-08-23.log]
[testng] 04:08:23,842 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3978a8b8 - End of configuration.
[testng] [2024-10-23 04:08:24,418] [pool-1-thread-8] Initializing /data/qa-27309/181109_e3_cut.msr:
[testng] 04:08:24,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 04:08:24,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:08:24,419 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-23_04-08-24.log]
[testng] 04:08:24,420 |-INFO in ch.qos.logback.core.sift.SiftProcessor@493a83c9 - End of configuration.
[testng] [2024-10-23 04:08:25,088] [pool-1-thread-7] Initializing /data/qa-17102/1 channel binning 8 time series.msr:
[testng] 04:08:25,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 04:08:25,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:08:25,089 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-23_04-08-25.log]
[testng] 04:08:25,089 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a12d5eb - End of configuration.
[testng] [2024-10-23 04:08:25,897] [pool-1-thread-6] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr:
[testng] 04:08:25,898 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 04:08:25,898 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:08:25,898 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-23_04-08-25.log]
[testng] 04:08:25,899 |-INFO in ch.qos.logback.core.sift.SiftProcessor@233528cd - End of configuration.
[testng] [2024-10-23 04:08:26,560] [pool-1-thread-5] Initializing /data/qa-7936/02 - not working.msr:
[testng] 04:08:26,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 04:08:26,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:08:26,561 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-23_04-08-26.log]
[testng] 04:08:26,561 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c54b669 - End of configuration.
[testng] [2024-10-23 04:08:27,168] [pool-1-thread-4] Initializing /data/qa-17102/2 channels FLIM time series.msr:
[testng] 04:08:27,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 04:08:27,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:08:27,169 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-23_04-08-27.log]
[testng] 04:08:27,170 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52a2d684 - End of configuration.
[testng] [2024-10-23 04:08:27,799] [pool-1-thread-3] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr:
[testng] 04:08:27,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 04:08:27,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:08:27,799 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-23_04-08-27.log]
[testng] 04:08:27,800 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d04df70 - End of configuration.
[testng] [2024-10-23 04:08:28,266] [pool-1-thread-2] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif:
[testng] 04:08:28,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 04:08:28,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:08:28,267 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-23_04-08-28.log]
[testng] 04:08:28,267 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5894d086 - End of configuration.
[testng] [2024-10-23 04:08:34,323] [pool-1-thread-8] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr:
[testng] [2024-10-23 04:08:34,990] [pool-1-thread-11] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr:
[testng] [2024-10-23 04:08:35,471] [pool-1-thread-1] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr:
[testng] [2024-10-23 04:08:35,998] [pool-1-thread-7] Initializing /data/qa-7992/IllegalArgumentException.msr:
[testng] [2024-10-23 04:08:36,715] [pool-1-thread-4] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif:
[testng] [2024-10-23 04:08:37,979] [pool-1-thread-10] Initializing /data/qa-7658/Document1_13-09-25.msr:
[testng] [2024-10-23 04:08:38,442] [pool-1-thread-6] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr:
[testng] [2024-10-23 04:08:39,014] [pool-1-thread-12] Initializing /data/qa-17102/2 channels FLIM z stack.msr:
[testng] [2024-10-23 04:08:39,690] [pool-1-thread-5] Initializing /data/qa-7936/z-TC - for LOCI.msr:
[testng] [2024-10-23 04:08:40,407] [pool-1-thread-3] Initializing /data/qa-17102/1 channel binning 4 time series.msr:
[testng] [2024-10-23 04:08:41,461] [pool-1-thread-9] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr:
[testng] [2024-10-23 04:08:43,598] [pool-1-thread-2] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr:
[testng] [2024-10-23 04:08:47,034] [pool-1-thread-8] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr:
[testng] [2024-10-23 04:08:47,567] [pool-1-thread-5] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps/02 - 500x500x105_1046x1046x57_1_875um_steps_11-34-02_PMT - PMT [PMT1] _C0.ome.tif:
[testng] [2024-10-23 04:08:50,098] [pool-1-thread-9] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr:
[testng] [2024-10-23 04:08:50,915] [pool-1-thread-12] Initializing /data/qa-7992/NegativeArraySizeException_small.msr:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1484, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 1 minute 35 seconds
Finished: SUCCESS