Started by upstream project "BIOFORMATS-test-repo" build number 59
originally caused by:
Started by upstream project "Trigger" build number 66
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4
[BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins9329215233816728904.sh
+ '[' imspector = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_8787_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] 02:20:12,732 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:20:12,734 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service.
[testng] 02:20:12,734 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:20:12,736 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:20:12,736 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:20:12,736 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:20:12,737 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 02:20:12,737 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:20:12,738 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:20:12,738 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:20:12,738 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:20:12,738 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:20:13,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:20:13,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:20:13,119 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:20:13,119 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:20:13,144 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:20:13,144 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:20:13,144 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:20:13,145 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:20:13,145 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration.
[testng] 02:20:13,146 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point
[testng] 02:20:13,146 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 408 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-05-10 02:20:13,156] [main] java.version = 1.8.0_342
[testng] 02:20:13,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:20:13,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:20:13,382 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-10_02-20-13.log]
[testng] 02:20:13,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration.
[testng] [2024-05-10 02:20:13,387] [main] testng.directory = /data
[testng] [2024-05-10 02:20:13,387] [main] testng.configDirectory = /config
[testng] [2024-05-10 02:20:13,438] [main] testng.multiplier = 1.0
[testng] [2024-05-10 02:20:13,439] [main] testng.in-memory = false
[testng] [2024-05-10 02:20:13,439] [main] testng.allow-missing = false
[testng] [2024-05-10 02:20:13,439] [main] user.language = en
[testng] [2024-05-10 02:20:13,439] [main] user.country = ${user.country}
[testng] [2024-05-10 02:20:13,439] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-05-10 02:20:15,888] [main] ----------------------------------------
[testng] [2024-05-10 02:20:15,889] [main] Total files: 29
[testng] [2024-05-10 02:20:15,889] [main] Scan time: 2.449 s (84 ms/file)
[testng] [2024-05-10 02:20:15,889] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 28 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-05-10 02:20:21,740] [pool-1-thread-1] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr:
[testng] 02:20:21,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:20:21,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:20:21,741 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-10_02-20-21.log]
[testng] 02:20:21,742 |-INFO in ch.qos.logback.core.sift.SiftProcessor@dadd385 - End of configuration.
[testng] [2024-05-10 02:20:21,781] [pool-1-thread-12] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr:
[testng] 02:20:21,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:20:21,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:20:21,782 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-10_02-20-21.log]
[testng] 02:20:21,783 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50ef404 - End of configuration.
[testng] [2024-05-10 02:20:21,807] [pool-1-thread-11] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr:
[testng] 02:20:21,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:20:21,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:20:21,808 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-10_02-20-21.log]
[testng] 02:20:21,809 |-INFO in ch.qos.logback.core.sift.SiftProcessor@649bd1df - End of configuration.
[testng] [2024-05-10 02:20:21,839] [pool-1-thread-10] Initializing /data/qa-7992/IllegalArgumentException.msr:
[testng] 02:20:21,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:20:21,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:20:21,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-10_02-20-21.log]
[testng] 02:20:21,841 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74a7a534 - End of configuration.
[testng] [2024-05-10 02:20:21,866] [pool-1-thread-9] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif:
[testng] 02:20:21,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:20:21,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:20:21,868 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-10_02-20-21.log]
[testng] 02:20:21,868 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ef2c750 - End of configuration.
[testng] [2024-05-10 02:20:22,098] [pool-1-thread-8] Initializing /data/qa-17102/2 channels FLIM time series.msr:
[testng] 02:20:22,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:20:22,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:20:22,099 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-10_02-20-22.log]
[testng] 02:20:22,099 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1308ea3c - End of configuration.
[testng] [2024-05-10 02:20:22,135] [pool-1-thread-7] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr:
[testng] 02:20:22,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:20:22,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:20:22,136 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-10_02-20-22.log]
[testng] 02:20:22,136 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b8b5bb2 - End of configuration.
[testng] [2024-05-10 02:20:22,171] [pool-1-thread-6] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr:
[testng] 02:20:22,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:20:22,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:20:22,172 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-10_02-20-22.log]
[testng] 02:20:22,173 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73ecdbe0 - End of configuration.
[testng] [2024-05-10 02:20:22,197] [pool-1-thread-5] Initializing /data/qa-7658/Document1_13-09-25.msr:
[testng] 02:20:22,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:20:22,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:20:22,198 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-10_02-20-22.log]
[testng] 02:20:22,198 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16d9efd0 - End of configuration.
[testng] [2024-05-10 02:20:22,241] [pool-1-thread-4] Initializing /data/qa-7936/01 - working.msr:
[testng] 02:20:22,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:20:22,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:20:22,242 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-10_02-20-22.log]
[testng] 02:20:22,242 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2401f64b - End of configuration.
[testng] [2024-05-10 02:20:22,271] [pool-1-thread-3] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr:
[testng] 02:20:22,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:20:22,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:20:22,272 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-10_02-20-22.log]
[testng] 02:20:22,273 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a8aa19e - End of configuration.
[testng] [2024-05-10 02:20:22,316] [pool-1-thread-2] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr:
[testng] 02:20:22,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:20:22,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:20:22,317 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-10_02-20-22.log]
[testng] 02:20:22,318 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d1b3d6c - End of configuration.
[testng] [2024-05-10 02:20:24,889] [pool-1-thread-10] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr:
[testng] [2024-05-10 02:20:24,909] [pool-1-thread-4] Initializing /data/qa-7936/z-TC - for LOCI.msr:
[testng] [2024-05-10 02:20:24,936] [pool-1-thread-6] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr:
[testng] [2024-05-10 02:20:24,956] [pool-1-thread-8] Initializing /data/qa-27309/181109_e3_cut.msr:
[testng] [2024-05-10 02:20:24,975] [pool-1-thread-3] Initializing /data/qa-7936/02 - not working.msr:
[testng] [2024-05-10 02:20:24,999] [pool-1-thread-11] Initializing /data/qa-17102/2 channels FLIM z stack.msr:
[testng] [2024-05-10 02:20:25,025] [pool-1-thread-1] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif:
[testng] [2024-05-10 02:20:25,223] [pool-1-thread-5] Initializing /data/qa-17102/1 channel binning 8 time series.msr:
[testng] [2024-05-10 02:20:25,242] [pool-1-thread-12] Initializing /data/qa-17102/1 channel binning 4 time series.msr:
[testng] [2024-05-10 02:20:25,267] [pool-1-thread-2] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr:
[testng] [2024-05-10 02:20:25,290] [pool-1-thread-7] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr:
[testng] [2024-05-10 02:20:25,606] [pool-1-thread-8] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr:
[testng] [2024-05-10 02:20:25,693] [pool-1-thread-7] Initializing /data/qa-7992/NegativeArraySizeException_small.msr:
[testng] [2024-05-10 02:20:25,722] [pool-1-thread-12] 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] [2024-05-10 02:20:25,933] [pool-1-thread-9] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr:
[testng] [2024-05-10 02:20:25,961] [pool-1-thread-2] 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: 21 seconds
Finished: SUCCESS