Started by upstream project "BIOFORMATS-test-repo" build number 242 originally caused by: Started by upstream project "Trigger" build number 267 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins13153314187884639254.sh + '[' ome-tiff = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_38065_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] 00:50:22,932 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:50:22,933 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 00:50:22,933 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:50:22,934 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:50:22,935 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:50:22,935 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:50:22,935 |-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] 00:50:22,935 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:50:22,936 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:50:22,937 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:50:22,937 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:50:22,938 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:50:23,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:50:23,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:50:23,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:50:23,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:50:23,257 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:50:23,257 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:50:23,257 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:50:23,258 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:50:23,258 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 00:50:23,258 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 00:50:23,258 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 322 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-02 00:50:23,269] [main] java.version = 11.0.16 [testng] 00:50:23,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:50:23,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:23,318 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-02_00-50-23.log] [testng] 00:50:23,320 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-02 00:50:23,322] [main] testng.directory = /data [testng] [2024-11-02 00:50:23,322] [main] testng.configDirectory = /config [testng] [2024-11-02 00:50:23,333] [main] testng.multiplier = 1.0 [testng] [2024-11-02 00:50:23,334] [main] testng.in-memory = false [testng] [2024-11-02 00:50:23,334] [main] testng.allow-missing = false [testng] [2024-11-02 00:50:23,335] [main] user.language = en [testng] [2024-11-02 00:50:23,335] [main] user.country = ${user.country} [testng] [2024-11-02 00:50:23,335] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-02 00:54:05,551] [main] ---------------------------------------- [testng] [2024-11-02 00:54:05,551] [main] Total files: 4771 [testng] [2024-11-02 00:54:05,551] [main] Scan time: 222.216 s (46 ms/file) [testng] [2024-11-02 00:54:05,551] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 1455 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-02 01:36:44,247] [pool-1-thread-1] Initializing /data/public/2016-06/tubhiswt-3D/tubhiswt_C0.ome.tif: [testng] 01:36:44,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:36:44,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:44,250 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-02_01-36-44.log] [testng] 01:36:44,251 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70609698 - End of configuration. [testng] [2024-11-02 01:36:45,567] [pool-1-thread-12] Initializing /data/heinrich/OMEtiff_MetaData_ReadByImageJ.JPG: [testng] 01:36:45,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:36:45,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:45,568 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-02_01-36-45.log] [testng] 01:36:45,568 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f43a1df - End of configuration. [testng] [2024-11-02 01:36:45,821] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME165_WAVELENGTH1_0.ome.tif: [testng] 01:36:45,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:36:45,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:45,822 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-02_01-36-45.log] [testng] 01:36:45,822 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8d7e58c - End of configuration. [testng] [2024-11-02 01:36:46,706] [pool-1-thread-10] Initializing /data/samples/missing-tiffs/test_Z0.ome.tiff: [testng] 01:36:46,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:36:46,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:46,707 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-02_01-36-46.log] [testng] 01:36:46,707 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46851a23 - End of configuration. [testng] [2024-11-02 01:36:47,576] [pool-1-thread-9] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y06/image--L10--S00--U00--V00--J00--X03--Y06--T10--Z00--C00.ome.tif: [testng] 01:36:47,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:36:47,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:47,577 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-02_01-36-47.log] [testng] 01:36:47,577 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e6d47e6 - End of configuration. [testng] [2024-11-02 01:36:48,374] [pool-1-thread-8] Initializing /data/andor/iQMM_FURA_TIME96_WAVELENGTH0_0.ome.tif: [testng] 01:36:48,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:36:48,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:48,375 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-02_01-36-48.log] [testng] 01:36:48,375 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41c617c3 - End of configuration. [testng] [2024-11-02 01:36:49,378] [pool-1-thread-7] Initializing /data/jason/P-TRE_10_R3D_D3D.ome.tif: [testng] 01:36:49,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:36:49,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:49,379 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-02_01-36-49.log] [testng] 01:36:49,379 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ef535e0 - End of configuration. [testng] [2024-11-02 01:36:50,348] [pool-1-thread-6] Initializing /data/glen/OMETiff Slidebook/Capture 1 - Position 1_XY1306965890_Z00_T0_C0.tiff: [testng] 01:36:50,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:36:50,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:50,350 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-02_01-36-50.log] [testng] 01:36:50,351 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a9df1c8 - End of configuration. [testng] [2024-11-02 01:36:51,200] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y00/image--L11--S00--U00--V00--J00--X01--Y00--T11--Z00--C00.ome.tif: [testng] 01:36:51,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:36:51,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:51,201 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-02_01-36-51.log] [testng] 01:36:51,202 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55fe3e9b - End of configuration. [testng] [2024-11-02 01:36:52,133] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y05/image--L02--S00--U00--V00--J00--X04--Y05--T02--Z00--C00.ome.tif: [testng] 01:36:52,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:36:52,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:52,134 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-02_01-36-52.log] [testng] 01:36:52,135 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f449814 - End of configuration. [testng] [2024-11-02 01:36:52,902] [pool-1-thread-3] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y04/image--L08--S00--U00--V00--J00--X02--Y04--T08--Z00--C00.ome.tif: [testng] 01:36:52,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:36:52,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:52,902 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-02_01-36-52.log] [testng] 01:36:52,903 |-INFO in ch.qos.logback.core.sift.SiftProcessor@349d3fc0 - End of configuration. [testng] [2024-11-02 01:36:53,762] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y05/image--L00--S00--U00--V00--J00--X02--Y05--T00--Z00--C00.ome.tif: [testng] 01:36:53,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:36:53,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:53,763 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-02_01-36-53.log] [testng] 01:36:53,764 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b775076 - End of configuration. [testng] [2024-11-02 01:37:00,831] [pool-1-thread-12] Initializing /data/andor/iQMM_FURA_TIME56_WAVELENGTH0_0.ome.tif: [testng] [2024-11-02 01:37:02,093] [pool-1-thread-7] Initializing /data/andor/iQMM_FURA_TIME177_WAVELENGTH1_0.ome.tif: [testng] [2024-11-02 01:37:03,038] [pool-1-thread-6] Initializing /data/public/2009-09/time-series.ome.tiff: [testng] [2024-11-02 01:37:07,276] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y06/image--L04--S00--U00--V00--J00--X06--Y06--T04--Z00--C00.ome.tif: [testng] [2024-11-02 01:37:08,306] [pool-1-thread-4] Initializing /data/andor/iQMM_FURA_TIME143_WAVELENGTH0_0.ome.tif: [testng] [2024-11-02 01:37:09,562] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y02/image--L00--S00--U00--V00--J00--X06--Y02--T00--Z00--C00.ome.tif: [testng] [2024-11-02 01:37:10,425] [pool-1-thread-3] Initializing /data/andor/iQMM_FURA_TIME137_WAVELENGTH0_0.ome.tif: [testng] [2024-11-02 01:37:11,555] [pool-1-thread-9] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y02/image--L10--S00--U00--V00--J00--X06--Y02--T10--Z00--C00.ome.tif: [testng] [2024-11-02 01:37:12,493] [pool-1-thread-8] Initializing /data/public/2016-06/bioformats-artificial/time-series.ome.btf: [testng] [2024-11-02 01:37:13,433] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME170_WAVELENGTH0_0.ome.tif: [testng] [2024-11-02 01:37:14,498] [pool-1-thread-1] Initializing /data/andor/iQMM_FURA_TIME16_WAVELENGTH0_0.ome.tif: [testng] [2024-11-02 01:37:15,388] [pool-1-thread-10] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y01/image--L00--S00--U00--V00--J00--X03--Y01--T00--Z00--C00.ome.tif: [testng] [2024-11-02 01:37:18,364] [pool-1-thread-6] Initializing 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/data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y03/image--L03--S00--U00--V00--J00--X06--Y03--T03--Z00--C00.ome.tif: [testng] [2024-11-02 02:31:07,857] [pool-1-thread-10] Initializing /data/andor/iQMM_FURA_TIME114_WAVELENGTH0_0.ome.tif: [testng] [2024-11-02 02:31:08,791] [pool-1-thread-3] Initializing /data/andor/iQMM_FURA_TIME163_WAVELENGTH0_0.ome.tif: [testng] [2024-11-02 02:31:09,587] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y00/image--L12--S00--U00--V00--J00--X03--Y00--T12--Z00--C00.ome.tif: [testng] [2024-11-02 02:31:13,003] [pool-1-thread-4] Initializing /data/chris/Fig4/Fig 4C.ome.tiff: [testng] [2024-11-02 02:31:13,677] [pool-1-thread-1] Initializing /data/andor/iQMM_FURA_TIME92_WAVELENGTH0_0.ome.tif: [testng] [2024-11-02 02:31:15,191] [pool-1-thread-8] Initializing /data/public/2016-06/bioformats-artificial/single-channel.ome.btf: [testng] [2024-11-02 02:31:17,675] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME83_WAVELENGTH0_0.ome.tif: [testng] [2024-11-02 02:31:18,341] [pool-1-thread-5] Initializing /data/olivier/OE2.ome.tif: [testng] 03:19:04,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:19:04,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:19:04,256 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-02_03-19-04.log] [testng] 03:19:04,257 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cf2b4f5 - 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: 148 minutes 44 seconds Finished: SUCCESS