Started by upstream project "BIOFORMATS-test-repo" build number 304 originally caused by: Started by upstream project "Trigger" build number 326 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/jenkins4225392357031844685.sh + '[' ome-tiff = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_48119_merge_ci -v /uod/idr/repos/curated/ome-tiff:/data -v /uod/idr-scratch/merge-ci/curated/ome-tiff:/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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 01:35:53,316 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:35:53,318 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 01:35:53,318 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:35:53,319 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:35:53,319 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:35:53,320 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:35:53,320 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:35:53,320 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:35:53,321 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:35:53,321 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:35:53,322 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:35:53,322 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:35:53,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:35:53,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:35:53,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:35:53,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:35:53,518 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:35:53,518 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:35:53,519 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:35:53,519 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:35:53,519 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 01:35:53,520 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 01:35:53,520 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 199 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-31 01:35:53,529] [main] java.version = 11.0.16 [testng] 01:35:53,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:35:53,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:35:53,577 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-31_01-35-53.log] [testng] 01:35:53,578 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-12-31 01:35:53,580] [main] testng.directory = /data [testng] [2024-12-31 01:35:53,580] [main] testng.configDirectory = /config [testng] [2024-12-31 01:35:53,590] [main] testng.multiplier = 1.0 [testng] [2024-12-31 01:35:53,592] [main] testng.in-memory = false [testng] [2024-12-31 01:35:53,592] [main] testng.allow-missing = false [testng] [2024-12-31 01:35:53,592] [main] user.language = en [testng] [2024-12-31 01:35:53,592] [main] user.country = ${user.country} [testng] [2024-12-31 01:35:53,592] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-31 01:41:35,553] [main] ---------------------------------------- [testng] [2024-12-31 01:41:35,554] [main] Total files: 4771 [testng] [2024-12-31 01:41:35,554] [main] Scan time: 341.961 s (71 ms/file) [testng] [2024-12-31 01:41:35,554] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 1455 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-31 02:32:04,162] [pool-1-thread-1] Initializing /data/public/2016-06/sub-resolutions/Brightfield/Leica-2/Leica-2.ome.tiff: [testng] 02:32:04,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:32:04,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:04,166 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-31_02-32-04.log] [testng] 02:32:04,166 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c7defed - End of configuration. [testng] [2024-12-31 02:32:05,830] [pool-1-thread-12] Initializing /data/andor/iQMM_FURA_TIME163_WAVELENGTH0_0.ome.tif: [testng] 02:32:05,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:32:05,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:05,831 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-31_02-32-05.log] [testng] 02:32:05,832 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6035a5e9 - End of configuration. [testng] [2024-12-31 02:32:06,912] [pool-1-thread-11] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y06/image--L11--S00--U00--V00--J00--X06--Y06--T11--Z00--C00.ome.tif: [testng] 02:32:06,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:32:06,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:06,913 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-31_02-32-06.log] [testng] 02:32:06,914 |-INFO in ch.qos.logback.core.sift.SiftProcessor@245e8f71 - End of configuration. [testng] [2024-12-31 02:32:07,718] [pool-1-thread-10] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y06/image--L05--S00--U00--V00--J00--X03--Y06--T05--Z00--C00.ome.tif: [testng] 02:32:07,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:32:07,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:07,718 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-31_02-32-07.log] [testng] 02:32:07,719 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46661124 - End of configuration. [testng] [2024-12-31 02:32:08,474] [pool-1-thread-9] Initializing /data/andor/iQMM_FURA_TIME93_WAVELENGTH1_0.ome.tif: [testng] 02:32:08,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:32:08,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:08,474 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-31_02-32-08.log] [testng] 02:32:08,475 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5998a371 - End of configuration. [testng] [2024-12-31 02:32:09,234] [pool-1-thread-8] Initializing /data/ian/01 - urea_irf_image_890nm_2,96ns_delay_128x128px_C0.ome.tif: [testng] 02:32:09,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:32:09,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:09,234 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-31_02-32-09.log] [testng] 02:32:09,235 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4973c356 - End of configuration. [testng] [2024-12-31 02:32:10,500] [pool-1-thread-7] Initializing /data/curtis/single-channel.ome.tif: [testng] 02:32:10,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:32:10,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:10,501 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-31_02-32-10.log] [testng] 02:32:10,501 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49a040d5 - End of configuration. [testng] [2024-12-31 02:32:11,334] [pool-1-thread-6] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y00/image--L06--S00--U00--V00--J00--X01--Y00--T06--Z00--C00.ome.tif: [testng] 02:32:11,334 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:32:11,335 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:11,335 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-31_02-32-11.log] [testng] 02:32:11,335 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f40d4b9 - End of configuration. [testng] [2024-12-31 02:32:12,081] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y04/image--L12--S00--U00--V00--J00--X04--Y04--T12--Z00--C00.ome.tif: [testng] 02:32:12,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:32:12,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:12,081 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-31_02-32-12.log] [testng] 02:32:12,082 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c8a5141 - End of configuration. [testng] [2024-12-31 02:32:12,859] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y04/image--L03--S00--U00--V00--J00--X02--Y04--T03--Z00--C00.ome.tif: [testng] 02:32:12,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:32:12,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:12,860 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-31_02-32-12.log] [testng] 02:32:12,860 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e69ded9 - End of configuration. [testng] [2024-12-31 02:32:13,645] [pool-1-thread-3] Initializing /data/tubhiswtTEST/tubhiswt4D.ome.tif: [testng] 02:32:13,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:32:13,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:13,646 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-31_02-32-13.log] [testng] 02:32:13,646 |-INFO in ch.qos.logback.core.sift.SiftProcessor@375064b - End of configuration. [testng] [2024-12-31 02:32:14,488] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y04/image--L10--S00--U00--V00--J00--X02--Y04--T10--Z00--C00.ome.tif: [testng] 02:32:14,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:32:14,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:14,489 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-31_02-32-14.log] [testng] 02:32:14,489 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5cf10c82 - End of configuration. [testng] [2024-12-31 02:32:23,280] [pool-1-thread-8] Initializing /data/glen/OMETiff Slidebook donotopen/Capture 2 - Position 1_XY1306537975_Z00_T002_C1.tiff: [testng] [2024-12-31 02:32:25,680] [pool-1-thread-3] Initializing /data/andor/iQMM_FURA_TIME53_WAVELENGTH1_0.ome.tif: [testng] [2024-12-31 02:32:29,509] [pool-1-thread-6] Initializing /data/andor/iQMM_FURA_TIME175_WAVELENGTH0_0.ome.tif: [testng] [2024-12-31 02:32:30,335] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y02/image--L05--S00--U00--V00--J00--X06--Y02--T05--Z00--C00.ome.tif: [testng] [2024-12-31 02:32:31,252] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y01/image--L11--S00--U00--V00--J00--X06--Y01--T11--Z00--C00.ome.tif: [testng] [2024-12-31 02:32:32,003] [pool-1-thread-2] Initializing /data/andor/iQMM_FURA_TIME140_WAVELENGTH1_0.ome.tif: [testng] [2024-12-31 02:32:32,784] [pool-1-thread-11] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y05/image--L14--S00--U00--V00--J00--X06--Y05--T14--Z00--C00.ome.tif: [testng] [2024-12-31 02:32:33,490] [pool-1-thread-10] Initializing /data/public/2009-09/multi-channel-z-series-time-series.ome.tiff: [testng] [2024-12-31 02:32:34,582] [pool-1-thread-7] Initializing /data/andor/iQMM_FURA_TIME134_WAVELENGTH1_0.ome.tif: [testng] [2024-12-31 02:32:35,419] [pool-1-thread-12] Initializing /data/andor/iQMM_FURA_TIME168_WAVELENGTH1_0.ome.tif: [testng] [2024-12-31 02:32:36,236] [pool-1-thread-9] Initializing /data/public/2016-06/bioformats-artificial/single-channel.ome.btf: [testng] [2024-12-31 02:32:40,649] [pool-1-thread-8] Initializing /data/andor/iQMM_FURA_TIME167_WAVELENGTH1_0.ome.tif: [testng] [2024-12-31 02:32:44,648] [pool-1-thread-10] Initializing 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3.tif: [testng] 05:47:30,250 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:47:30,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:47:30,251 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-31_05-47-30.log] [testng] 05:47:30,252 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5317103b - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 77115, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 251 minutes 40 seconds Finished: SUCCESS