Started by upstream project "BIOFORMATS-test-repo" build number 294
originally caused by:
Started by upstream project "Trigger" build number 313
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/jenkins388012448680062340.sh
+ '[' imspector = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_46529_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] 11:34:33,076 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 11:34:33,077 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 11:34:33,077 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 11:34:33,078 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 11:34:33,078 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 11:34:33,079 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 11:34:33,079 |-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] 11:34:33,079 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 11:34:33,079 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 11:34:33,080 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 11:34:33,080 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 11:34:33,080 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 11:34:33,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 11:34:33,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 11:34:33,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 11:34:33,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 11:34:33,270 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 11:34:33,270 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 11:34:33,270 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 11:34:33,271 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 11:34:33,271 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 11:34:33,271 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 11:34:33,272 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 193 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-12-18 11:34:33,280] [main] java.version = 17.0.2
[testng] 11:34:33,283 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 11:34:33,283 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:34:33,323 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-18_11-34-33.log]
[testng] 11:34:33,325 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-12-18 11:34:33,327] [main] testng.directory = /data
[testng] [2024-12-18 11:34:33,327] [main] testng.configDirectory = /config
[testng] [2024-12-18 11:34:33,336] [main] testng.multiplier = 1.0
[testng] [2024-12-18 11:34:33,336] [main] testng.in-memory = false
[testng] [2024-12-18 11:34:33,336] [main] testng.allow-missing = false
[testng] [2024-12-18 11:34:33,336] [main] user.language = en
[testng] [2024-12-18 11:34:33,337] [main] user.country = ${user.country}
[testng] [2024-12-18 11:34:33,337] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-12-18 11:34:51,254] [main] ----------------------------------------
[testng] [2024-12-18 11:34:51,255] [main] Total files: 29
[testng] [2024-12-18 11:34:51,255] [main] Scan time: 17.917 s (617 ms/file)
[testng] [2024-12-18 11:34:51,255] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 28 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-12-18 11:35:18,052] [pool-1-thread-1] Initializing /data/qa-7658/Document1_13-09-25.msr:
[testng] 11:35:18,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 11:35:18,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:35:18,054 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-18_11-35-18.log]
[testng] 11:35:18,054 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42fbcb62 - End of configuration.
[testng] [2024-12-18 11:35:18,814] [pool-1-thread-12] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr:
[testng] 11:35:18,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 11:35:18,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:35:18,815 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-18_11-35-18.log]
[testng] 11:35:18,816 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7687c68c - End of configuration.
[testng] [2024-12-18 11:35:19,462] [pool-1-thread-11] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif:
[testng] 11:35:19,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 11:35:19,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:35:19,463 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-18_11-35-19.log]
[testng] 11:35:19,464 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fbc1981 - End of configuration.
[testng] [2024-12-18 11:35:20,832] [pool-1-thread-10] Initializing /data/qa-7936/02 - not working.msr:
[testng] 11:35:20,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 11:35:20,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:35:20,833 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-18_11-35-20.log]
[testng] 11:35:20,833 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d912429 - End of configuration.
[testng] [2024-12-18 11:35:21,512] [pool-1-thread-9] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr:
[testng] 11:35:21,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 11:35:21,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:35:21,513 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-18_11-35-21.log]
[testng] 11:35:21,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4df93ee6 - End of configuration.
[testng] [2024-12-18 11:35:22,203] [pool-1-thread-8] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr:
[testng] 11:35:22,203 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 11:35:22,203 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:35:22,205 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-18_11-35-22.log]
[testng] 11:35:22,205 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a1d3393 - End of configuration.
[testng] [2024-12-18 11:35:22,859] [pool-1-thread-7] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr:
[testng] 11:35:22,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 11:35:22,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:35:22,861 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-18_11-35-22.log]
[testng] 11:35:22,861 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e0c401 - End of configuration.
[testng] [2024-12-18 11:35:23,520] [pool-1-thread-6] Initializing /data/qa-7992/NegativeArraySizeException_small.msr:
[testng] 11:35:23,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 11:35:23,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:35:23,521 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-18_11-35-23.log]
[testng] 11:35:23,521 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25d8368d - End of configuration.
[testng] [2024-12-18 11:35:24,167] [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] 11:35:24,167 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 11:35:24,167 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:35:24,168 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-18_11-35-24.log]
[testng] 11:35:24,168 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5086552f - End of configuration.
[testng] [2024-12-18 11:35:27,062] [pool-1-thread-4] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr:
[testng] 11:35:27,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 11:35:27,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:35:27,063 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-18_11-35-27.log]
[testng] 11:35:27,063 |-INFO in ch.qos.logback.core.sift.SiftProcessor@465b9f37 - End of configuration.
[testng] [2024-12-18 11:35:27,727] [pool-1-thread-3] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr:
[testng] 11:35:27,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 11:35:27,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:35:27,728 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-18_11-35-27.log]
[testng] 11:35:27,728 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35e3860f - End of configuration.
[testng] [2024-12-18 11:35:28,401] [pool-1-thread-2] Initializing /data/qa-27309/181109_e3_cut.msr:
[testng] 11:35:28,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 11:35:28,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:35:28,401 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-18_11-35-28.log]
[testng] 11:35:28,402 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71f57d19 - End of configuration.
[testng] [2024-12-18 11:35:36,391] [pool-1-thread-2] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr:
[testng] [2024-12-18 11:35:37,047] [pool-1-thread-8] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr:
[testng] [2024-12-18 11:35:37,835] [pool-1-thread-4] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif:
[testng] [2024-12-18 11:35:39,108] [pool-1-thread-12] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr:
[testng] [2024-12-18 11:35:39,822] [pool-1-thread-7] Initializing /data/qa-17102/2 channels FLIM time series.msr:
[testng] [2024-12-18 11:35:40,481] [pool-1-thread-10] Initializing /data/qa-7936/z-TC - for LOCI.msr:
[testng] [2024-12-18 11:35:41,156] [pool-1-thread-3] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr:
[testng] [2024-12-18 11:35:41,828] [pool-1-thread-9] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr:
[testng] [2024-12-18 11:35:42,425] [pool-1-thread-6] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr:
[testng] [2024-12-18 11:35:42,944] [pool-1-thread-1] Initializing /data/qa-17102/1 channel binning 8 time series.msr:
[testng] [2024-12-18 11:35:44,665] [pool-1-thread-11] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr:
[testng] [2024-12-18 11:35:49,977] [pool-1-thread-1] Initializing /data/qa-17102/1 channel binning 4 time series.msr:
[testng] [2024-12-18 11:35:50,821] [pool-1-thread-9] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr:
[testng] [2024-12-18 11:35:51,640] [pool-1-thread-3] Initializing /data/qa-17102/2 channels FLIM z stack.msr:
[testng] [2024-12-18 11:35:52,379] [pool-1-thread-7] Initializing /data/qa-7936/01 - working.msr:
[testng] [2024-12-18 11:35:53,103] [pool-1-thread-12] Initializing /data/qa-7992/IllegalArgumentException.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 32 seconds
Finished: SUCCESS