Started by upstream project "BIOFORMATS-test-repo" build number 33
originally caused by:
Started by upstream project "Trigger" build number 37
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/jenkins8891072513647339604.sh
+ '[' imspector = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_4522_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] 02:13:39,652 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:13:39,654 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 02:13:39,654 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:13:39,655 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:13:39,655 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:13:39,655 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:13:39,656 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 02:13:39,656 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:13:39,656 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:13:39,657 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:13:39,657 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:13:39,657 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:13:39,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:13:39,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:13:39,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:13:39,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:13:39,855 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:13:39,855 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:13:39,855 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:13:39,856 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:13:39,856 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 02:13:39,857 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 02:13:39,857 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 201 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-04-14 02:13:39,866] [main] java.version = 17.0.2
[testng] 02:13:39,869 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:13:39,869 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:13:39,911 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-14_02-13-39.log]
[testng] 02:13:39,912 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-04-14 02:13:39,915] [main] testng.directory = /data
[testng] [2024-04-14 02:13:39,915] [main] testng.configDirectory = /config
[testng] [2024-04-14 02:13:39,924] [main] testng.multiplier = 1.0
[testng] [2024-04-14 02:13:39,925] [main] testng.in-memory = false
[testng] [2024-04-14 02:13:39,926] [main] testng.allow-missing = false
[testng] [2024-04-14 02:13:39,926] [main] user.language = en
[testng] [2024-04-14 02:13:39,926] [main] user.country = ${user.country}
[testng] [2024-04-14 02:13:39,926] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-04-14 02:13:41,780] [main] ----------------------------------------
[testng] [2024-04-14 02:13:41,780] [main] Total files: 29
[testng] [2024-04-14 02:13:41,780] [main] Scan time: 1.854 s (63 ms/file)
[testng] [2024-04-14 02:13:41,780] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 28 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-04-14 02:13:47,105] [pool-1-thread-1] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr:
[testng] 02:13:47,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:13:47,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:13:47,106 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-14_02-13-47.log]
[testng] 02:13:47,107 |-INFO in ch.qos.logback.core.sift.SiftProcessor@159b6515 - End of configuration.
[testng] [2024-04-14 02:13:47,164] [pool-1-thread-12] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr:
[testng] 02:13:47,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:13:47,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:13:47,166 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-14_02-13-47.log]
[testng] 02:13:47,166 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5894d086 - End of configuration.
[testng] [2024-04-14 02:13:47,213] [pool-1-thread-11] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr:
[testng] 02:13:47,214 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:13:47,214 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:13:47,214 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-14_02-13-47.log]
[testng] 02:13:47,215 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31ebd510 - End of configuration.
[testng] [2024-04-14 02:13:47,292] [pool-1-thread-10] Initializing /data/qa-17102/1 channel binning 8 time series.msr:
[testng] 02:13:47,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:13:47,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:13:47,293 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-14_02-13-47.log]
[testng] 02:13:47,293 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a8f36a0 - End of configuration.
[testng] [2024-04-14 02:13:47,328] [pool-1-thread-9] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr:
[testng] 02:13:47,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:13:47,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:13:47,329 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-14_02-13-47.log]
[testng] 02:13:47,329 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b2ef8e8 - End of configuration.
[testng] [2024-04-14 02:13:47,368] [pool-1-thread-8] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif:
[testng] 02:13:47,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:13:47,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:13:47,369 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-14_02-13-47.log]
[testng] 02:13:47,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76bc8f10 - End of configuration.
[testng] [2024-04-14 02:13:47,653] [pool-1-thread-7] Initializing /data/qa-27309/181109_e3_cut.msr:
[testng] 02:13:47,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:13:47,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:13:47,654 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-14_02-13-47.log]
[testng] 02:13:47,654 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7588ab55 - End of configuration.
[testng] [2024-04-14 02:13:47,686] [pool-1-thread-6] Initializing /data/qa-7936/02 - not working.msr:
[testng] 02:13:47,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:13:47,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:13:47,687 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-14_02-13-47.log]
[testng] 02:13:47,687 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6256769c - End of configuration.
[testng] [2024-04-14 02:13:47,732] [pool-1-thread-5] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr:
[testng] 02:13:47,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:13:47,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:13:47,733 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-14_02-13-47.log]
[testng] 02:13:47,733 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57f94046 - End of configuration.
[testng] [2024-04-14 02:13:47,766] [pool-1-thread-4] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr:
[testng] 02:13:47,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:13:47,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:13:47,767 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-14_02-13-47.log]
[testng] 02:13:47,767 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ee179d5 - End of configuration.
[testng] [2024-04-14 02:13:47,785] [pool-1-thread-3] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr:
[testng] 02:13:47,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:13:47,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:13:47,786 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-14_02-13-47.log]
[testng] 02:13:47,787 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77a9ce3 - End of configuration.
[testng] [2024-04-14 02:13:47,819] [pool-1-thread-2] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif:
[testng] 02:13:47,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:13:47,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:13:47,820 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-14_02-13-47.log]
[testng] 02:13:47,820 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b1ea55d - End of configuration.
[testng] [2024-04-14 02:13:49,578] [pool-1-thread-7] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr:
[testng] [2024-04-14 02:13:49,659] [pool-1-thread-4] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr:
[testng] [2024-04-14 02:13:49,707] [pool-1-thread-10] Initializing /data/qa-17102/1 channel binning 4 time series.msr:
[testng] [2024-04-14 02:13:49,742] [pool-1-thread-5] Initializing /data/qa-7992/IllegalArgumentException.msr:
[testng] [2024-04-14 02:13:49,779] [pool-1-thread-3] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr:
[testng] [2024-04-14 02:13:49,809] [pool-1-thread-6] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr:
[testng] [2024-04-14 02:13:49,844] [pool-1-thread-12] Initializing /data/qa-7936/01 - working.msr:
[testng] [2024-04-14 02:13:50,026] [pool-1-thread-1] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr:
[testng] [2024-04-14 02:13:50,075] [pool-1-thread-11] Initializing /data/qa-17102/2 channels FLIM time series.msr:
[testng] [2024-04-14 02:13:50,512] [pool-1-thread-10] Initializing /data/qa-17102/2 channels FLIM z stack.msr:
[testng] [2024-04-14 02:13:50,583] [pool-1-thread-12] Initializing /data/qa-7658/Document1_13-09-25.msr:
[testng] [2024-04-14 02:13:50,629] [pool-1-thread-4] 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] [2024-04-14 02:13:50,880] [pool-1-thread-3] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr:
[testng] [2024-04-14 02:13:50,924] [pool-1-thread-5] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr:
[testng] [2024-04-14 02:13:50,999] [pool-1-thread-11] Initializing /data/qa-7936/z-TC - for LOCI.msr:
[testng] [2024-04-14 02:13:51,044] [pool-1-thread-1] 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: 19 seconds
Finished: SUCCESS