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Started by upstream project "BIOFORMATS-test-repo" build number 7 originally caused by: Started by upstream project "Trigger" build number 10 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins441635170341248040.sh + '[' ome-tiff = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_1015_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 00:42:49,456 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:42:49,457 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 00:42:49,457 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:42:49,458 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:42:49,459 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:42:49,459 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:42:49,459 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:42:49,459 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:42:49,460 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:42:49,460 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:42:49,461 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:42:49,461 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:42:49,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:42:49,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:42:49,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:42:49,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:42:49,671 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:42:49,671 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:42:49,671 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:42:49,671 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:42:49,671 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 00:42:49,672 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 00:42:49,672 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 212 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-21 00:42:49,683] [main] java.version = 21 [testng] 00:42:49,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:42:49,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:49,737 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-21_00-42-49.log] [testng] 00:42:49,738 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-03-21 00:42:49,740] [main] testng.directory = /data [testng] [2024-03-21 00:42:49,740] [main] testng.configDirectory = /config [testng] [2024-03-21 00:42:49,749] [main] testng.multiplier = 1.0 [testng] [2024-03-21 00:42:49,750] [main] testng.in-memory = false [testng] [2024-03-21 00:42:49,750] [main] testng.allow-missing = false [testng] [2024-03-21 00:42:49,750] [main] user.language = en [testng] [2024-03-21 00:42:49,750] [main] user.country = ${user.country} [testng] [2024-03-21 00:42:49,750] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-21 00:46:20,415] [main] ---------------------------------------- [testng] [2024-03-21 00:46:20,416] [main] Total files: 4771 [testng] [2024-03-21 00:46:20,416] [main] Scan time: 210.665 s (44 ms/file) [testng] [2024-03-21 00:46:20,417] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 1455 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-21 00:56:08,679] [pool-1-thread-1] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y03/image--L09--S00--U00--V00--J00--X02--Y03--T09--Z00--C00.ome.tif: [testng] 00:56:08,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:56:08,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:08,681 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-21_00-56-08.log] [testng] 00:56:08,682 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f9cd32d - End of configuration. [testng] [2024-03-21 00:56:08,768] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y04/image--L08--S00--U00--V00--J00--X00--Y04--T08--Z00--C00.ome.tif: [testng] 00:56:08,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:56:08,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:08,769 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-21_00-56-08.log] [testng] 00:56:08,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37013c0 - End of configuration. [testng] [2024-03-21 00:56:08,896] [pool-1-thread-11] Initializing /data/curtis/multi-channel-z-series.ome.tif: [testng] 00:56:08,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:56:08,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:08,897 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-21_00-56-08.log] [testng] 00:56:08,898 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5595e26e - End of configuration. [testng] [2024-03-21 00:56:09,028] [pool-1-thread-10] Initializing /data/andor/iQMM_FURA_TIME41_WAVELENGTH0_0.ome.tif: [testng] 00:56:09,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:56:09,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:09,029 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-21_00-56-09.log] [testng] 00:56:09,029 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3fab3d5c - End of configuration. [testng] [2024-03-21 00:56:09,104] [pool-1-thread-9] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y04/image--L11--S00--U00--V00--J00--X06--Y04--T11--Z00--C00.ome.tif: [testng] 00:56:09,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:56:09,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:09,105 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-21_00-56-09.log] [testng] 00:56:09,105 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fc645f0 - End of configuration. [testng] [2024-03-21 00:56:09,165] [pool-1-thread-8] Initializing /data/ruben/experiment--2009_10_27_15_43_34/slide--S00/chamber--U00--V00/field--X06--Y01/image--L00--S00--U00--V00--J00--X06--Y01--T00--Z00--C00.ome.tif: [testng] 00:56:09,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:56:09,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:09,166 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-21_00-56-09.log] [testng] 00:56:09,167 |-INFO in ch.qos.logback.core.sift.SiftProcessor@633836a7 - End of configuration. [testng] [2024-03-21 00:56:09,257] [pool-1-thread-7] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y05/image--L02--S00--U00--V00--J00--X00--Y05--T02--Z00--C00.ome.tif: [testng] 00:56:09,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:56:09,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:09,258 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-21_00-56-09.log] [testng] 00:56:09,258 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c3cb327 - End of configuration. [testng] [2024-03-21 00:56:09,313] [pool-1-thread-6] Initializing /data/andor/iQMM_FURA_TIME113_WAVELENGTH0_0.ome.tif: [testng] 00:56:09,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:56:09,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:09,314 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-21_00-56-09.log] [testng] 00:56:09,314 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6dc662ae - End of configuration. [testng] [2024-03-21 00:56:09,430] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y03/image--L10--S00--U00--V00--J00--X00--Y03--T10--Z00--C00.ome.tif: [testng] 00:56:09,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:56:09,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:09,431 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-21_00-56-09.log] [testng] 00:56:09,431 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e2a9944 - End of configuration. [testng] [2024-03-21 00:56:09,486] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y05/image--L14--S00--U00--V00--J00--X03--Y05--T14--Z00--C00.ome.tif: [testng] 00:56:09,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:56:09,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:09,487 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-21_00-56-09.log] [testng] 00:56:09,487 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bcd63f - End of configuration. [testng] [2024-03-21 00:56:09,572] [pool-1-thread-3] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y02/image--L10--S00--U00--V00--J00--X05--Y02--T10--Z00--C00.ome.tif: [testng] 00:56:09,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:56:09,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:09,573 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-21_00-56-09.log] [testng] 00:56:09,574 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d5ee60c - End of configuration. [testng] [2024-03-21 00:56:09,646] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y03/image--L02--S00--U00--V00--J00--X05--Y03--T02--Z00--C00.ome.tif: [testng] 00:56:09,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:56:09,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:09,647 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-21_00-56-09.log] [testng] 00:56:09,648 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c36bef5 - End of configuration. [testng] [2024-03-21 00:56:17,540] [pool-1-thread-10] Initializing /data/public/2015-01/bioformats-artificial/z-series.ome.tif: [testng] [2024-03-21 00:56:17,640] [pool-1-thread-11] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y06/image--L03--S00--U00--V00--J00--X05--Y06--T03--Z00--C00.ome.tif: [testng] [2024-03-21 00:56:17,748] [pool-1-thread-3] Initializing /data/dominik/2009_09_11__14_26_33h__channel00.tif: [testng] [2024-03-21 00:56:17,825] [pool-1-thread-1] Initializing /data/glen/OMETiff Slidebook/Capture 1 - Position 1_XY1306965890_Z00_T0_C0.tiff: [testng] [2024-03-21 00:56:18,148] [pool-1-thread-7] Initializing /data/andor/iQMM_FURA_TIME43_WAVELENGTH1_0.ome.tif: [testng] [2024-03-21 00:56:18,328] [pool-1-thread-4] Initializing /data/andor/iQMM_FURA_TIME15_WAVELENGTH0_0.ome.tif: [testng] [2024-03-21 00:56:18,498] [pool-1-thread-6] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y02/image--L02--S00--U00--V00--J00--X02--Y02--T02--Z00--C00.ome.tif: [testng] [2024-03-21 00:56:18,707] [pool-1-thread-8] Initializing /data/andor/iQMM_FURA_TIME88_WAVELENGTH1_0.ome.tif: [testng] [2024-03-21 00:56:18,891] [pool-1-thread-2] Initializing /data/andor/iQMM_FURA_TIME160_WAVELENGTH0_0.ome.tif: [testng] [2024-03-21 00:56:19,079] [pool-1-thread-9] Initializing /data/andor/iQMM_FURA_TIME94_WAVELENGTH1_0.ome.tif: [testng] [2024-03-21 00:56:19,244] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y01/image--L13--S00--U00--V00--J00--X01--Y01--T13--Z00--C00.ome.tif: [testng] [2024-03-21 00:56:19,474] [pool-1-thread-5] Initializing /data/heinrich/part2/test.ome.tiff: [testng] [2024-03-21 00:56:21,999] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y05/image--L03--S00--U00--V00--J00--X02--Y05--T03--Z00--C00.ome.tif: [testng] [2024-03-21 00:56:22,173] [pool-1-thread-10] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y02/image--L14--S00--U00--V00--J00--X05--Y02--T14--Z00--C00.ome.tif: [testng] [2024-03-21 00:56:22,763] [pool-1-thread-1] Initializing /data/glen/OMETiff Slidebook donotopen/Capture 2 - Position 1_XY1306537975_Z00_T000_C1.tiff: [testng] [2024-03-21 00:56:23,431] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y05/image--L05--S00--U00--V00--J00--X00--Y05--T05--Z00--C00.ome.tif: [testng] [2024-03-21 00:56:24,075] [pool-1-thread-6] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y06/image--L00--S00--U00--V00--J00--X05--Y06--T00--Z00--C00.ome.tif: [testng] [2024-03-21 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