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Started by upstream project "BIOFORMATS-test-repo" build number 62 originally caused by: Started by upstream project "Trigger" build number 69 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins3221855218973516311.sh + '[' ome-tiff = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_9218_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 -Duser.language=fr -Duser.country=FR 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 test-automated: [testng] File leak detector installed [testng] 01:38:37,859 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:38:37,861 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:38:37,861 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:38:37,862 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:38:37,862 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:38:37,862 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:38:37,862 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:38:37,862 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:38:37,863 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:38:37,863 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:38:37,863 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:38:37,863 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:38:38,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:38:38,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:38:38,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:38:38,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:38:38,144 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:38:38,144 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:38:38,144 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:38:38,145 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:38:38,145 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:38:38,146 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:38:38,146 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 283 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-13 01:38:38,156] [main] java.version = 1.8.0_342 [testng] 01:38:38,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:38:38,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:38,203 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-13_01-38-38.log] [testng] 01:38:38,205 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-05-13 01:38:38,207] [main] testng.directory = /data [testng] [2024-05-13 01:38:38,207] [main] testng.configDirectory = /config [testng] [2024-05-13 01:38:38,219] [main] testng.multiplier = 1.0 [testng] [2024-05-13 01:38:38,220] [main] testng.in-memory = false [testng] [2024-05-13 01:38:38,220] [main] testng.allow-missing = false [testng] [2024-05-13 01:38:38,220] [main] user.language = fr [testng] [2024-05-13 01:38:38,220] [main] user.country = FR [testng] [2024-05-13 01:38:38,220] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-05-13 01:41:16,043] [main] ---------------------------------------- [testng] [2024-05-13 01:41:16,043] [main] Total files: 4771 [testng] [2024-05-13 01:41:16,043] [main] Scan time: 157.823 s (33 ms/file) [testng] [2024-05-13 01:41:16,043] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 1455 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-13 01:48:34,281] [pool-1-thread-1] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y05/image--L09--S00--U00--V00--J00--X00--Y05--T09--Z00--C00.ome.tif: [testng] 01:48:34,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:48:34,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:34,283 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-13_01-48-34.log] [testng] 01:48:34,284 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18f4d8c - End of configuration. [testng] [2024-05-13 01:48:34,327] [pool-1-thread-9] Initializing /data/oliver/LA_ProtocolCombination_12.10.2009_21_40_58_Marker_1__3 3.tif: [testng] 01:48:34,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:48:34,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:34,329 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-13_01-48-34.log] [testng] 01:48:34,329 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f468430 - End of configuration. [testng] [2024-05-13 01:48:37,763] [pool-1-thread-8] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y00/image--L08--S00--U00--V00--J00--X05--Y00--T08--Z00--C00.ome.tif: [testng] 01:48:37,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:48:37,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:37,764 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-13_01-48-37.log] [testng] 01:48:37,765 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45da4684 - End of configuration. [testng] [2024-05-13 01:48:37,792] [pool-1-thread-7] Initializing /data/pam/try2-09242010-1031-049/try2-09242010-1031-049.xml: [testng] 01:48:37,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:48:37,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:37,793 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-13_01-48-37.log] [testng] 01:48:37,794 |-INFO in ch.qos.logback.core.sift.SiftProcessor@290ea946 - End of configuration. [testng] [2024-05-13 01:48:37,820] [pool-1-thread-6] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y03/image--L01--S00--U00--V00--J00--X01--Y03--T01--Z00--C00.ome.tif: [testng] 01:48:37,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:48:37,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:37,821 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-13_01-48-37.log] [testng] 01:48:37,821 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a1c341f - End of configuration. [testng] [2024-05-13 01:48:37,857] [pool-1-thread-5] Initializing /data/andor/iQMM_FURA_TIME119_WAVELENGTH1_0.ome.tif: [testng] 01:48:37,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:48:37,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:37,858 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-13_01-48-37.log] [testng] 01:48:37,858 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4044f8c4 - End of configuration. [testng] [2024-05-13 01:48:37,922] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y05/image--L01--S00--U00--V00--J00--X00--Y05--T01--Z00--C00.ome.tif: [testng] 01:48:37,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:48:37,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:37,922 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-13_01-48-37.log] [testng] 01:48:37,923 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1102d473 - End of configuration. [testng] [2024-05-13 01:48:37,953] [pool-1-thread-3] Initializing /data/andor/iQMM_FURA_TIME21_WAVELENGTH1_0.ome.tif: [testng] 01:48:37,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:48:37,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:37,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-13_01-48-37.log] [testng] 01:48:37,954 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17c763fc - End of configuration. [testng] [2024-05-13 01:48:37,997] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y03/image--L13--S00--U00--V00--J00--X03--Y03--T13--Z00--C00.ome.tif: [testng] 01:48:37,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:48:37,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:37,998 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-13_01-48-37.log] [testng] 01:48:37,998 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a0075fb - End of configuration. [testng] [2024-05-13 01:48:38,054] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y00/image--L15--S00--U00--V00--J00--X00--Y00--T15--Z00--C00.ome.tif: [testng] 01:48:38,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:48:38,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:38,060 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-13_01-48-38.log] [testng] 01:48:38,060 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38dc4bc6 - End of configuration. [testng] [2024-05-13 01:48:38,090] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME22_WAVELENGTH0_0.ome.tif: [testng] 01:48:38,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:48:38,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:38,091 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-13_01-48-38.log] [testng] 01:48:38,091 |-INFO in ch.qos.logback.core.sift.SiftProcessor@562df39c - End of configuration. [testng] [2024-05-13 01:48:38,698] [pool-1-thread-10] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y00/image--L05--S00--U00--V00--J00--X01--Y00--T05--Z00--C00.ome.tif: [testng] 01:48:38,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:48:38,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:38,699 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-13_01-48-38.log] [testng] 01:48:38,700 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a7dc8dd - End of configuration. [testng] [2024-05-13 01:48:44,949] [pool-1-thread-5] Initializing /data/public/2010-06/multi-channel-z-series.ome.tiff: [testng] [2024-05-13 01:48:44,973] [pool-1-thread-6] Initializing /data/andor/iQMM_FURA_TIME91_WAVELENGTH1_0.ome.tif: [testng] [2024-05-13 01:48:45,133] [pool-1-thread-1] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y04/image--L00--S00--U00--V00--J00--X02--Y04--T00--Z00--C00.ome.tif: [testng] [2024-05-13 01:48:45,169] [pool-1-thread-10] Initializing /data/public/2010-04/one-screen-one-plate-four-wells.ome.tiff: [testng] [2024-05-13 01:48:45,212] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y06/image--L11--S00--U00--V00--J00--X03--Y06--T11--Z00--C00.ome.tif: [testng] [2024-05-13 01:48:45,246] [pool-1-thread-3] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y06/image--L07--S00--U00--V00--J00--X03--Y06--T07--Z00--C00.ome.tif: [testng] [2024-05-13 01:48:45,278] [pool-1-thread-11] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y05/image--L11--S00--U00--V00--J00--X05--Y05--T11--Z00--C00.ome.tif: [testng] [2024-05-13 01:48:45,309] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y02/image--L13--S00--U00--V00--J00--X03--Y02--T13--Z00--C00.ome.tif: [testng] [2024-05-13 01:48:45,340] [pool-1-thread-7] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y02/image--L10--S00--U00--V00--J00--X04--Y02--T10--Z00--C00.ome.tif: [testng] [2024-05-13 01:48:45,372] [pool-1-thread-8] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y01/image--L01--S00--U00--V00--J00--X01--Y01--T01--Z00--C00.ome.tif: [testng] [2024-05-13 01:48:45,412] [pool-1-thread-2] Initializing /data/public/2015-01/modulo/FLIM-ModuloAlongT-TSCPC.ome.tiff: [testng] [2024-05-13 01:48:46,555] [pool-1-thread-6] Initializing /data/andor/iQMM_FURA_TIME190_WAVELENGTH0_0.ome.tif: [testng] [2024-05-13 01:48:46,640] [pool-1-thread-2] Initializing /data/andor/iQMM_FURA_TIME87_WAVELENGTH0_0.ome.tif: [testng] [2024-05-13 01:48:46,706] [pool-1-thread-7] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y06/image--L04--S00--U00--V00--J00--X03--Y06--T04--Z00--C00.ome.tif: [testng] [2024-05-13 01:48:46,735] [pool-1-thread-5] Initializing /data/sebastian/5x5_T=1_Z=1_CH=3_200pix #1.tif: [testng] [2024-05-13 01:48:46,865] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y06/image--L01--S00--U00--V00--J00--X05--Y06--T01--Z00--C00.ome.tif: [testng] [2024-05-13 01:48:46,896] [pool-1-thread-8] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y03/image--L02--S00--U00--V00--J00--X03--Y03--T02--Z00--C00.ome.tif: [testng] [2024-05-13 01:48:46,932] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y03/image--L08--S00--U00--V00--J00--X02--Y03--T08--Z00--C00.ome.tif: [testng] [2024-05-13 01:48:47,005] [pool-1-thread-1] Initializing /data/chris/Fig6/Fig 6A.ome.tiff: [testng] [2024-05-13 01:48:47,135] [pool-1-thread-10] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y01/image--L12--S00--U00--V00--J00--X06--Y01--T12--Z00--C00.ome.tif: [testng] [2024-05-13 01:48:47,192] [pool-1-thread-11] Initializing 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Finished: SUCCESS