Started by upstream project "BIOFORMATS-test-repo" build number 366
originally caused by:
Started by upstream project "Trigger" build number 392
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3
[BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins8840602027643725168.sh
+ '[' imspector = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_58415_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release
[javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
[javac] 4 warnings
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] 04:12:49,124 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15
[testng] 04:12:49,125 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - No custom configurators were discovered as a service.
[testng] 04:12:49,125 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 04:12:49,126 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 04:12:49,127 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 04:12:49,127 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 04:12:49,127 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 04:12:49,128 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 04:12:49,128 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 04:12:49,129 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 04:12:49,129 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 04:12:49,129 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 04:12:49,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 04:12:49,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 04:12:49,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 04:12:49,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 04:12:49,319 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 04:12:49,319 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 04:12:49,319 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 04:12:49,320 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 04:12:49,320 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@4310d43 - End of configuration.
[testng] 04:12:49,321 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@1b11171f - Registering current configuration as safe fallback point
[testng] 04:12:49,321 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 193 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2025-03-06 04:12:49,330] [main] java.version = 21
[testng] 04:12:49,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 04:12:49,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:12:49,375 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-06_04-12-49.log]
[testng] 04:12:49,376 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69504ae9 - End of configuration.
[testng] [2025-03-06 04:12:49,378] [main] testng.directory = /data
[testng] [2025-03-06 04:12:49,378] [main] testng.configDirectory = /config
[testng] [2025-03-06 04:12:49,387] [main] testng.multiplier = 1.0
[testng] [2025-03-06 04:12:49,387] [main] testng.in-memory = false
[testng] [2025-03-06 04:12:49,387] [main] testng.allow-missing = false
[testng] [2025-03-06 04:12:49,387] [main] user.language = en
[testng] [2025-03-06 04:12:49,387] [main] user.country = ${user.country}
[testng] [2025-03-06 04:12:49,387] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2025-03-06 04:13:15,841] [main] ----------------------------------------
[testng] [2025-03-06 04:13:15,841] [main] Total files: 31
[testng] [2025-03-06 04:13:15,841] [main] Scan time: 26.454 s (853 ms/file)
[testng] [2025-03-06 04:13:15,842] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 29 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2025-03-06 04:13:54,328] [pool-1-thread-1] Initializing /data/qa-7936/z-TC - for LOCI.msr:
[testng] 04:13:54,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 04:13:54,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:13:54,329 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-06_04-13-54.log]
[testng] 04:13:54,330 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12b47397 - End of configuration.
[testng] [2025-03-06 04:13:55,239] [pool-1-thread-12] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr:
[testng] 04:13:55,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 04:13:55,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:13:55,241 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-06_04-13-55.log]
[testng] 04:13:55,241 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67628b32 - End of configuration.
[testng] [2025-03-06 04:13:56,200] [pool-1-thread-11] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr:
[testng] 04:13:56,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 04:13:56,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:13:56,201 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-06_04-13-56.log]
[testng] 04:13:56,202 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34bbcb71 - End of configuration.
[testng] [2025-03-06 04:13:57,099] [pool-1-thread-10] Initializing /data/qa-7658/Document1_13-09-25.msr:
[testng] 04:13:57,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 04:13:57,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:13:57,100 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-06_04-13-57.log]
[testng] 04:13:57,100 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f731d9e - End of configuration.
[testng] [2025-03-06 04:13:58,060] [pool-1-thread-9] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr:
[testng] 04:13:58,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 04:13:58,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:13:58,061 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-06_04-13-58.log]
[testng] 04:13:58,061 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20b3b008 - End of configuration.
[testng] [2025-03-06 04:13:59,030] [pool-1-thread-8] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr:
[testng] 04:13:59,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 04:13:59,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:13:59,032 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-06_04-13-59.log]
[testng] 04:13:59,032 |-INFO in ch.qos.logback.core.sift.SiftProcessor@109f3fbb - End of configuration.
[testng] [2025-03-06 04:13:59,900] [pool-1-thread-7] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr:
[testng] 04:13:59,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 04:13:59,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:13:59,901 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-06_04-13-59.log]
[testng] 04:13:59,902 |-INFO in ch.qos.logback.core.sift.SiftProcessor@529be425 - End of configuration.
[testng] [2025-03-06 04:14:00,836] [pool-1-thread-6] Initializing /data/qa-17102/1 channel binning 8 time series.msr:
[testng] 04:14:00,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 04:14:00,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:14:00,838 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-06_04-14-00.log]
[testng] 04:14:00,838 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f489524 - End of configuration.
[testng] [2025-03-06 04:14:01,807] [pool-1-thread-5] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr:
[testng] 04:14:01,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 04:14:01,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:14:01,808 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-06_04-14-01.log]
[testng] 04:14:01,809 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e00f3cb - End of configuration.
[testng] [2025-03-06 04:14:02,716] [pool-1-thread-4] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr:
[testng] 04:14:02,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 04:14:02,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:14:02,716 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-06_04-14-02.log]
[testng] 04:14:02,717 |-INFO in ch.qos.logback.core.sift.SiftProcessor@640fd262 - End of configuration.
[testng] [2025-03-06 04:14:03,677] [pool-1-thread-3] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif:
[testng] 04:14:03,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 04:14:03,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:14:03,678 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-06_04-14-03.log]
[testng] 04:14:03,678 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d059742 - End of configuration.
[testng] [2025-03-06 04:14:05,303] [pool-1-thread-2] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr:
[testng] 04:14:05,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 04:14:05,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:14:05,304 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-06_04-14-05.log]
[testng] 04:14:05,304 |-INFO in ch.qos.logback.core.sift.SiftProcessor@96d371b - End of configuration.
[testng] [2025-03-06 04:14:14,247] [pool-1-thread-7] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr:
[testng] [2025-03-06 04:14:15,110] [pool-1-thread-4] Initializing /data/qa-17102/1 channel binning 4 time series.msr:
[testng] [2025-03-06 04:14:15,952] [pool-1-thread-6] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif:
[testng] [2025-03-06 04:14:17,509] [pool-1-thread-11] Initializing /data/qa-7992/NegativeArraySizeException_small.msr:
[testng] [2025-03-06 04:14:18,421] [pool-1-thread-1] Initializing /data/qa-17102/2 channels FLIM time series.msr:
[testng] [2025-03-06 04:14:19,259] [pool-1-thread-12] Initializing /data/qa-7992/IllegalArgumentException.msr:
[testng] [2025-03-06 04:14:20,109] [pool-1-thread-10] Initializing /data/qa-7936/02 - not working.msr:
[testng] [2025-03-06 04:14:21,067] [pool-1-thread-5] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr:
[testng] [2025-03-06 04:14:21,888] [pool-1-thread-8] Initializing /data/public/zenodo-10476252/test.msr:
[testng] [2025-03-06 04:14:22,815] [pool-1-thread-9] Initializing /data/qa-17102/2 channels FLIM z stack.msr:
[testng] [2025-03-06 04:14:23,633] [pool-1-thread-2] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr:
[testng] [2025-03-06 04:14:25,711] [pool-1-thread-3] Initializing /data/qa-7936/01 - working.msr:
[testng] [2025-03-06 04:14:31,460] [pool-1-thread-7] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr:
[testng] [2025-03-06 04:14:32,422] [pool-1-thread-4] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr:
[testng] [2025-03-06 04:14:33,322] [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] [2025-03-06 04:14:37,085] [pool-1-thread-2] Initializing /data/qa-27309/181109_e3_cut.msr:
[testng] [2025-03-06 04:14:37,861] [pool-1-thread-8] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1537, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 2 minutes 21 seconds
Finished: SUCCESS