Started by upstream project "BIOFORMATS-test-repo" build number 97 originally caused by: Started by upstream project "Trigger" build number 108 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins9294750667605176048.sh + '[' ome-tiff = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_14958_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] 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] 01:36:46,878 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:36:46,880 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:36:46,880 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:36:46,880 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:36:46,881 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:36:46,881 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:36:46,881 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:36:46,881 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:36:46,882 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:36:46,882 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:36:46,883 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:36:46,883 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:36:47,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:36:47,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:36:47,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:36:47,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:36:47,062 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:36:47,062 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:36:47,062 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:36:47,063 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:36:47,063 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:36:47,063 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:36:47,063 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 181 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-19 01:36:47,072] [main] java.version = 17.0.2 [testng] 01:36:47,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:36:47,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:47,114 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-19_01-36-47.log] [testng] 01:36:47,116 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-19 01:36:47,118] [main] testng.directory = /data [testng] [2024-06-19 01:36:47,118] [main] testng.configDirectory = /config [testng] [2024-06-19 01:36:47,126] [main] testng.multiplier = 1.0 [testng] [2024-06-19 01:36:47,127] [main] testng.in-memory = false [testng] [2024-06-19 01:36:47,127] [main] testng.allow-missing = false [testng] [2024-06-19 01:36:47,127] [main] user.language = en [testng] [2024-06-19 01:36:47,127] [main] user.country = ${user.country} [testng] [2024-06-19 01:36:47,127] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-19 01:39:39,310] [main] ---------------------------------------- [testng] [2024-06-19 01:39:39,310] [main] Total files: 4771 [testng] [2024-06-19 01:39:39,310] [main] Scan time: 172.183 s (36 ms/file) [testng] [2024-06-19 01:39:39,310] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 1455 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-19 01:45:42,207] [pool-1-thread-1] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y01/image--L02--S00--U00--V00--J00--X00--Y01--T02--Z00--C00.ome.tif: [testng] 01:45:42,207 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:45:42,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:42,209 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-19_01-45-42.log] [testng] 01:45:42,209 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77aeae2e - End of configuration. [testng] [2024-06-19 01:45:42,260] [pool-1-thread-6] Initializing /data/oliver/LA_ProtocolCombination_12.10.2009_21_40_58_Marker_5__7.tif: [testng] 01:45:42,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:45:42,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:42,261 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-19_01-45-42.log] [testng] 01:45:42,261 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ab2d04f - End of configuration. [testng] [2024-06-19 01:45:46,470] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y03/image--L07--S00--U00--V00--J00--X01--Y03--T07--Z00--C00.ome.tif: [testng] 01:45:46,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:45:46,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:46,471 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-19_01-45-46.log] [testng] 01:45:46,472 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58a1051f - End of configuration. [testng] [2024-06-19 01:45:46,528] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y00/image--L14--S00--U00--V00--J00--X05--Y00--T14--Z00--C00.ome.tif: [testng] 01:45:46,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:45:46,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:46,529 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-19_01-45-46.log] [testng] 01:45:46,529 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1954ff0e - End of configuration. [testng] [2024-06-19 01:45:46,567] [pool-1-thread-3] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y00/image--L05--S00--U00--V00--J00--X03--Y00--T05--Z00--C00.ome.tif: [testng] 01:45:46,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:45:46,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:46,568 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-19_01-45-46.log] [testng] 01:45:46,568 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5997696e - End of configuration. [testng] [2024-06-19 01:45:46,598] [pool-1-thread-2] 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] 01:45:46,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:45:46,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:46,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-19_01-45-46.log] [testng] 01:45:46,600 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5aba6719 - End of configuration. [testng] [2024-06-19 01:45:46,648] [pool-1-thread-12] Initializing /data/public/2007-06/Iron-Plate.ome.tiff: [testng] 01:45:46,649 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:45:46,649 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:46,650 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-19_01-45-46.log] [testng] 01:45:46,650 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65ccf838 - End of configuration. [testng] [2024-06-19 01:45:46,693] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME184_WAVELENGTH1_0.ome.tif: [testng] 01:45:46,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:45:46,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:46,694 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-19_01-45-46.log] [testng] 01:45:46,694 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fa2a37c - End of configuration. [testng] [2024-06-19 01:45:46,719] [pool-1-thread-10] Initializing /data/andor/iQMM_FURA_TIME109_WAVELENGTH1_0.ome.tif: [testng] 01:45:46,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:45:46,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:46,721 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-19_01-45-46.log] [testng] 01:45:46,721 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bb339d5 - End of configuration. [testng] [2024-06-19 01:45:46,762] [pool-1-thread-9] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y02/image--L06--S00--U00--V00--J00--X04--Y02--T06--Z00--C00.ome.tif: [testng] 01:45:46,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:45:46,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:46,762 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-19_01-45-46.log] [testng] 01:45:46,763 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41c60d3a - End of configuration. [testng] [2024-06-19 01:45:46,793] [pool-1-thread-8] Initializing /data/curtis/mc4d-i5d.ome.tif: [testng] 01:45:46,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:45:46,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:46,794 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-19_01-45-46.log] [testng] 01:45:46,794 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ea7708a - End of configuration. [testng] [2024-06-19 01:45:46,823] [pool-1-thread-7] Initializing /data/public/2008-09/multi-channel.ome.tiff: [testng] 01:45:46,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:45:46,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:46,824 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-19_01-45-46.log] [testng] 01:45:46,825 |-INFO in ch.qos.logback.core.sift.SiftProcessor@589494a4 - End of configuration. [testng] [2024-06-19 01:45:54,960] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME75_WAVELENGTH0_0.ome.tif: [testng] [2024-06-19 01:45:54,991] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_43_34/slide--S00/chamber--U00--V00/field--X05--Y00/image--L00--S00--U00--V00--J00--X05--Y00--T00--Z00--C00.ome.tif: [testng] [2024-06-19 01:45:55,026] [pool-1-thread-9] Initializing /data/andor/iQMM_FURA_TIME156_WAVELENGTH0_0.ome.tif: [testng] [2024-06-19 01:45:55,054] [pool-1-thread-3] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y05/image--L07--S00--U00--V00--J00--X06--Y05--T07--Z00--C00.ome.tif: [testng] [2024-06-19 01:45:55,092] [pool-1-thread-1] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y04/image--L12--S00--U00--V00--J00--X06--Y04--T12--Z00--C00.ome.tif: [testng] [2024-06-19 01:45:55,125] [pool-1-thread-5] Initializing /data/andor/iQMM_FURA_TIME162_WAVELENGTH0_0.ome.tif: [testng] [2024-06-19 01:45:55,152] [pool-1-thread-4] Initializing /data/public/2012-06/tubhiswt-4D/tubhiswt_C0_TP0.ome.tif: [testng] [2024-06-19 01:45:55,470] [pool-1-thread-8] Initializing /data/andor/iQMM_FURA_TIME196_WAVELENGTH1_0.ome.tif: [testng] [2024-06-19 01:45:55,506] [pool-1-thread-7] Initializing /data/andor/iQMM_FURA_TIME189_WAVELENGTH0_0.ome.tif: [testng] [2024-06-19 01:45:55,539] [pool-1-thread-10] Initializing /data/andor/iQMM_FURA_TIME18_WAVELENGTH0_0.ome.tif: [testng] [2024-06-19 01:45:55,569] [pool-1-thread-2] Initializing /data/andor/iQMM_FURA_TIME111_WAVELENGTH0_0.ome.tif: [testng] [2024-06-19 01:45:56,772] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y03/image--L12--S00--U00--V00--J00--X03--Y03--T12--Z00--C00.ome.tif: [testng] [2024-06-19 01:45:56,851] [pool-1-thread-9] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y02/image--L11--S00--U00--V00--J00--X00--Y02--T11--Z00--C00.ome.tif: [testng] [2024-06-19 01:45:57,015] [pool-1-thread-8] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y05/image--L05--S00--U00--V00--J00--X05--Y05--T05--Z00--C00.ome.tif: [testng] [2024-06-19 01:45:57,048] [pool-1-thread-7] Initializing /data/public/2008-09/single-image.ome.tiff: [testng] [2024-06-19 01:45:57,068] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME191_WAVELENGTH0_0.ome.tif: [testng] [2024-06-19 01:45:57,096] [pool-1-thread-10] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y00/image--L09--S00--U00--V00--J00--X03--Y00--T09--Z00--C00.ome.tif: [testng] [2024-06-19 01:45:57,132] [pool-1-thread-1] Initializing /data/andor/iQMM_FURA_TIME27_WAVELENGTH1_0.ome.tif: [testng] [2024-06-19 01:45:57,164] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y00/image--L04--S00--U00--V00--J00--X03--Y00--T04--Z00--C00.ome.tif: [testng] [2024-06-19 01:45:57,200] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y03/image--L09--S00--U00--V00--J00--X03--Y03--T09--Z00--C00.ome.tif: [testng] [2024-06-19 01:45:57,262] [pool-1-thread-3] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y00/image--L13--S00--U00--V00--J00--X02--Y00--T13--Z00--C00.ome.tif: [testng] [2024-06-19 01:45:58,162] [pool-1-thread-5] Initializing /data/andor/iQMM_FURA_TIME188_WAVELENGTH0_0.ome.tif: [testng] [2024-06-19 01:45:58,287] [pool-1-thread-9] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y01/image--L05--S00--U00--V00--J00--X00--Y01--T05--Z00--C00.ome.tif: [testng] [2024-06-19 01:45:58,599] [pool-1-thread-7] 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01:52:37,794] [pool-1-thread-4] Initializing /data/public/2010-04/multi-channel-z-series-time-series.ome.tiff: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 77115, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 28 minutes 31 seconds Finished: SUCCESS