Started by upstream project "BIOFORMATS-test-repo" build number 105
originally caused by:
Started by upstream project "Trigger" build number 117
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/jenkins7532319186385937988.sh
+ '[' imspector = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_16331_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
test-automated:
[testng] File leak detector installed
[testng] 02:27:16,499 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:27:16,501 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service.
[testng] 02:27:16,501 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:27:16,502 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:27:16,502 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:27:16,502 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:27:16,502 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 02:27:16,502 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:27:16,503 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:27:16,503 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:27:16,503 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:27:16,504 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:27:16,747 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:27:16,747 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:27:16,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:27:16,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:27:16,783 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:27:16,784 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:27:16,784 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:27:16,784 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:27:16,784 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration.
[testng] 02:27:16,785 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point
[testng] 02:27:16,785 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 282 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-28 02:27:16,795] [main] java.version = 1.8.0_342
[testng] 02:27:16,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:27:16,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:16,844 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-28_02-27-16.log]
[testng] 02:27:16,846 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration.
[testng] [2024-06-28 02:27:16,848] [main] testng.directory = /data
[testng] [2024-06-28 02:27:16,848] [main] testng.configDirectory = /config
[testng] [2024-06-28 02:27:16,861] [main] testng.multiplier = 1.0
[testng] [2024-06-28 02:27:16,861] [main] testng.in-memory = false
[testng] [2024-06-28 02:27:16,861] [main] testng.allow-missing = false
[testng] [2024-06-28 02:27:16,861] [main] user.language = en
[testng] [2024-06-28 02:27:16,861] [main] user.country = ${user.country}
[testng] [2024-06-28 02:27:16,861] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-06-28 02:27:19,817] [main] ----------------------------------------
[testng] [2024-06-28 02:27:19,818] [main] Total files: 29
[testng] [2024-06-28 02:27:19,818] [main] Scan time: 2.956 s (101 ms/file)
[testng] [2024-06-28 02:27:19,818] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 28 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-28 02:27:25,382] [pool-1-thread-1] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr:
[testng] 02:27:25,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:27:25,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:25,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-28_02-27-25.log]
[testng] 02:27:25,386 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b48ad25 - End of configuration.
[testng] [2024-06-28 02:27:25,445] [pool-1-thread-11] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr:
[testng] 02:27:25,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:27:25,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:25,448 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-28_02-27-25.log]
[testng] 02:27:25,449 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e57bccb - End of configuration.
[testng] [2024-06-28 02:27:25,498] [pool-1-thread-12] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr:
[testng] 02:27:25,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:27:25,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:25,500 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-28_02-27-25.log]
[testng] 02:27:25,500 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56f58fb8 - End of configuration.
[testng] [2024-06-28 02:27:25,523] [pool-1-thread-10] Initializing /data/qa-7992/IllegalArgumentException.msr:
[testng] 02:27:25,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:27:25,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:25,524 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-28_02-27-25.log]
[testng] 02:27:25,524 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4230e23b - End of configuration.
[testng] [2024-06-28 02:27:25,566] [pool-1-thread-9] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif:
[testng] 02:27:25,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:27:25,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:25,568 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-28_02-27-25.log]
[testng] 02:27:25,569 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66f1d2bc - End of configuration.
[testng] [2024-06-28 02:27:25,816] [pool-1-thread-8] Initializing /data/qa-17102/2 channels FLIM time series.msr:
[testng] 02:27:25,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:27:25,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:25,818 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-28_02-27-25.log]
[testng] 02:27:25,818 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1af55b40 - End of configuration.
[testng] [2024-06-28 02:27:25,853] [pool-1-thread-5] Initializing /data/qa-7658/Document1_13-09-25.msr:
[testng] 02:27:25,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:27:25,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:25,854 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-28_02-27-25.log]
[testng] 02:27:25,854 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ea77aea - End of configuration.
[testng] [2024-06-28 02:27:25,889] [pool-1-thread-6] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr:
[testng] 02:27:25,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:27:25,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:25,889 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-28_02-27-25.log]
[testng] 02:27:25,890 |-INFO in ch.qos.logback.core.sift.SiftProcessor@758588b2 - End of configuration.
[testng] [2024-06-28 02:27:25,916] [pool-1-thread-7] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr:
[testng] 02:27:25,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:27:25,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:25,917 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-28_02-27-25.log]
[testng] 02:27:25,917 |-INFO in ch.qos.logback.core.sift.SiftProcessor@477b72bf - End of configuration.
[testng] [2024-06-28 02:27:25,944] [pool-1-thread-4] Initializing /data/qa-7936/01 - working.msr:
[testng] 02:27:25,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:27:25,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:25,945 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-28_02-27-25.log]
[testng] 02:27:25,945 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50ef404 - End of configuration.
[testng] [2024-06-28 02:27:25,981] [pool-1-thread-3] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr:
[testng] 02:27:25,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:27:25,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:25,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-28_02-27-25.log]
[testng] 02:27:25,983 |-INFO in ch.qos.logback.core.sift.SiftProcessor@649bd1df - End of configuration.
[testng] [2024-06-28 02:27:26,025] [pool-1-thread-2] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr:
[testng] 02:27:26,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:27:26,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:26,026 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-28_02-27-26.log]
[testng] 02:27:26,026 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74a7a534 - End of configuration.
[testng] [2024-06-28 02:27:28,058] [pool-1-thread-8] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr:
[testng] [2024-06-28 02:27:28,093] [pool-1-thread-4] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr:
[testng] [2024-06-28 02:27:28,112] [pool-1-thread-3] Initializing /data/qa-27309/181109_e3_cut.msr:
[testng] [2024-06-28 02:27:28,130] [pool-1-thread-6] Initializing /data/qa-7936/02 - not working.msr:
[testng] [2024-06-28 02:27:28,160] [pool-1-thread-10] Initializing /data/qa-17102/2 channels FLIM z stack.msr:
[testng] [2024-06-28 02:27:28,188] [pool-1-thread-5] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif:
[testng] [2024-06-28 02:27:28,472] [pool-1-thread-11] Initializing /data/qa-17102/1 channel binning 8 time series.msr:
[testng] [2024-06-28 02:27:28,495] [pool-1-thread-1] Initializing /data/qa-17102/1 channel binning 4 time series.msr:
[testng] [2024-06-28 02:27:28,518] [pool-1-thread-12] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr:
[testng] [2024-06-28 02:27:28,538] [pool-1-thread-2] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr:
[testng] [2024-06-28 02:27:28,559] [pool-1-thread-7] Initializing /data/qa-7936/z-TC - for LOCI.msr:
[testng] [2024-06-28 02:27:28,896] [pool-1-thread-9] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr:
[testng] [2024-06-28 02:27:28,919] [pool-1-thread-3] Initializing /data/qa-7992/NegativeArraySizeException_small.msr:
[testng] [2024-06-28 02:27:28,944] [pool-1-thread-2] 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] [2024-06-28 02:27:29,263] [pool-1-thread-10] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr:
[testng] [2024-06-28 02:27:29,309] [pool-1-thread-4] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1484, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 18 seconds
Finished: SUCCESS