Started by upstream project "BIOFORMATS-test-repo" build number 214 originally caused by: Started by upstream project "Trigger" build number 241 originally caused by: Started by user devspace 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/jenkins11927660430879643078.sh + '[' ome-tiff = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_33989_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] 09:37:28,918 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 09:37:28,920 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 09:37:28,920 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:37:28,921 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:37:28,921 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 09:37:28,922 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 09:37:28,922 |-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] 09:37:28,922 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:37:28,922 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:37:28,923 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 09:37:28,923 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 09:37:28,924 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 09:37:29,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 09:37:29,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 09:37:29,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 09:37:29,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 09:37:29,127 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 09:37:29,127 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 09:37:29,127 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 09:37:29,128 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 09:37:29,128 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 09:37:29,129 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 09:37:29,129 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 207 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-08 09:37:29,138] [main] java.version = 11.0.16 [testng] 09:37:29,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:37:29,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:37:29,188 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-08_09-37-29.log] [testng] 09:37:29,190 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-08 09:37:29,192] [main] testng.directory = /data [testng] [2024-10-08 09:37:29,192] [main] testng.configDirectory = /config [testng] [2024-10-08 09:37:29,202] [main] testng.multiplier = 1.0 [testng] [2024-10-08 09:37:29,204] [main] testng.in-memory = false [testng] [2024-10-08 09:37:29,204] [main] testng.allow-missing = false [testng] [2024-10-08 09:37:29,204] [main] user.language = en [testng] [2024-10-08 09:37:29,204] [main] user.country = ${user.country} [testng] [2024-10-08 09:37:29,204] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-08 09:47:46,290] [main] ---------------------------------------- [testng] [2024-10-08 09:47:46,291] [main] Total files: 4771 [testng] [2024-10-08 09:47:46,291] [main] Scan time: 617.086 s (129 ms/file) [testng] [2024-10-08 09:47:46,291] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 1455 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-08 13:02:19,072] [pool-1-thread-1] Initializing /data/public/2016-06/tubhiswt-3D/tubhiswt_C0.ome.tif: [testng] 13:02:19,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 13:02:19,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:02:19,075 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-08_13-02-19.log] [testng] 13:02:19,076 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cc3bc25 - End of configuration. [testng] [2024-10-08 13:02:49,516] [pool-1-thread-12] Initializing /data/heinrich/OMEtiff_MetaData_ReadByImageJ.JPG: [testng] 13:02:49,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 13:02:49,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:02:49,517 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-08_13-02-49.log] [testng] 13:02:49,518 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65938fb1 - End of configuration. [testng] [2024-10-08 13:02:59,318] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME165_WAVELENGTH1_0.ome.tif: [testng] 13:02:59,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 13:02:59,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:02:59,319 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-08_13-02-59.log] [testng] 13:02:59,320 |-INFO in ch.qos.logback.core.sift.SiftProcessor@480c3f6b - End of configuration. [testng] [2024-10-08 13:05:24,395] [pool-1-thread-10] Initializing /data/samples/missing-tiffs/test_Z0.ome.tiff: [testng] 13:05:24,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 13:05:24,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:05:24,396 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-08_13-05-24.log] [testng] 13:05:24,396 |-INFO in ch.qos.logback.core.sift.SiftProcessor@462d376 - End of configuration. [testng] [2024-10-08 13:05:41,876] [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] 13:05:41,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 13:05:41,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:05:41,876 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-08_13-05-41.log] [testng] 13:05:41,877 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2db3521c - End of configuration. [testng] [2024-10-08 13:06:31,571] [pool-1-thread-8] Initializing /data/andor/iQMM_FURA_TIME96_WAVELENGTH0_0.ome.tif: [testng] 13:06:31,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 13:06:31,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:06:31,572 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-08_13-06-31.log] [testng] 13:06:31,572 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8efc5ad - End of configuration. [testng] [2024-10-08 13:07:37,367] [pool-1-thread-7] Initializing /data/jason/P-TRE_10_R3D_D3D.ome.tif: [testng] 13:07:37,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 13:07:37,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:07:37,368 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-08_13-07-37.log] [testng] 13:07:37,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39b12694 - End of configuration. [testng] [2024-10-08 13:08:33,795] [pool-1-thread-6] Initializing /data/glen/OMETiff Slidebook/Capture 1 - Position 1_XY1306965890_Z00_T0_C0.tiff: [testng] 13:08:33,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 13:08:33,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:08:33,796 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-08_13-08-33.log] [testng] 13:08:33,796 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56345b7 - End of configuration. [testng] [2024-10-08 13:09:37,864] [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] 13:09:37,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 13:09:37,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:09:37,864 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-08_13-09-37.log] [testng] 13:09:37,865 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ffc9fbc - End of configuration. [testng] [2024-10-08 13:09:50,358] [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] 13:09:50,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 13:09:50,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:09:50,359 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-08_13-09-50.log] [testng] 13:09:50,359 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ee7825f - End of configuration. [testng] [2024-10-08 13:10:00,311] [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] 13:10:00,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 13:10:00,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:10:00,312 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-08_13-10-00.log] [testng] 13:10:00,312 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ef6e841 - End of configuration. [testng] [2024-10-08 13:10:15,917] [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] 13:10:15,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 13:10:15,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:10:15,918 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-08_13-10-15.log] [testng] 13:10:15,918 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69b3f8f4 - End of configuration. [testng] [2024-10-08 13:11:17,573] [pool-1-thread-12] Initializing /data/andor/iQMM_FURA_TIME56_WAVELENGTH0_0.ome.tif: [testng] [2024-10-08 13:11:44,148] [pool-1-thread-7] Initializing /data/andor/iQMM_FURA_TIME177_WAVELENGTH1_0.ome.tif: [testng] [2024-10-08 13:12:01,805] [pool-1-thread-6] Initializing /data/public/2009-09/time-series.ome.tiff: [testng] [2024-10-08 13:12:42,543] [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] [2024-10-08 13:13:01,324] [pool-1-thread-4] Initializing /data/andor/iQMM_FURA_TIME137_WAVELENGTH0_0.ome.tif: [testng] [2024-10-08 13:13:14,065] [pool-1-thread-3] 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] [2024-10-08 13:13:28,582] [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] [2024-10-08 13:13:43,069] [pool-1-thread-9] Initializing /data/andor/iQMM_FURA_TIME143_WAVELENGTH0_0.ome.tif: [testng] [2024-10-08 13:13:59,357] [pool-1-thread-8] Initializing /data/public/2016-06/bioformats-artificial/time-series.ome.btf: [testng] [2024-10-08 13:14:20,756] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME170_WAVELENGTH0_0.ome.tif: [testng] [2024-10-08 13:15:03,617] [pool-1-thread-6] Initializing /data/andor/iQMM_FURA_TIME16_WAVELENGTH0_0.ome.tif: [testng] [2024-10-08 13:15:37,913] [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] [2024-10-08 13:15:47,192] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y00/image--L00--S00--U00--V00--J00--X00--Y00--T00--Z00--C00.ome.tif: [testng] [2024-10-08 13:16:03,690] [pool-1-thread-1] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y02/image--L08--S00--U00--V00--J00--X05--Y02--T08--Z00--C00.ome.tif: [testng] [2024-10-08 13:16:13,352] [pool-1-thread-7] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y04/image--L12--S00--U00--V00--J00--X02--Y04--T12--Z00--C00.ome.tif: [testng] [2024-10-08 13:16:27,188] [pool-1-thread-8] Initializing /data/andor/iQMM_FURA_TIME172_WAVELENGTH0_0.ome.tif: [testng] [2024-10-08 13:17:23,959] [pool-1-thread-3] Initializing /data/mark/20090422bead20x_C1.ome.tif: [testng] [2024-10-08 13:17:39,210] [pool-1-thread-5] Initializing 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