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Started by upstream project "BIOFORMATS-test-repo" build number 98 originally caused by: Started by upstream project "Trigger" build number 109 originally caused by: Started by timer 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/jenkins10768931065479409960.sh + '[' incell = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_15181_merge_ci -v /uod/idr/repos/curated/incell:/data -v /uod/idr-scratch/merge-ci/curated/incell:/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 02:16:43,781 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:16:43,783 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 02:16:43,783 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:16:43,784 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:16:43,784 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:16:43,785 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:16:43,785 |-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] 02:16:43,785 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:16:43,786 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:16:43,787 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:16:43,788 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:16:43,789 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:16:43,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:16:43,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:16:44,024 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:16:44,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:16:44,034 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:16:44,034 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:16:44,034 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:16:44,035 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:16:44,035 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 02:16:44,036 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 02:16:44,037 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 251 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-20 02:16:44,050] [main] java.version = 21 [testng] 02:16:44,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:16:44,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:44,119 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-20_02-16-44.log] [testng] 02:16:44,122 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-06-20 02:16:44,125] [main] testng.directory = /data [testng] [2024-06-20 02:16:44,125] [main] testng.configDirectory = /config [testng] [2024-06-20 02:16:44,141] [main] testng.multiplier = 1.0 [testng] [2024-06-20 02:16:44,142] [main] testng.in-memory = false [testng] [2024-06-20 02:16:44,142] [main] testng.allow-missing = false [testng] [2024-06-20 02:16:44,143] [main] user.language = en [testng] [2024-06-20 02:16:44,143] [main] user.country = ${user.country} [testng] [2024-06-20 02:16:44,143] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-20 02:23:24,033] [main] ---------------------------------------- [testng] [2024-06-20 02:23:24,033] [main] Total files: 4190 [testng] [2024-06-20 02:23:24,034] [main] Scan time: 399.89 s (95 ms/file) [testng] [2024-06-20 02:23:24,034] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 27 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-20 02:23:42,587] [pool-1-thread-1] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce: [testng] 02:23:42,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:23:42,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:23:42,590 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-20_02-23-42.log] [testng] 02:23:42,591 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f27e5c0 - End of configuration. [testng] [2024-06-20 02:23:42,893] [pool-1-thread-12] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce: [testng] 02:23:42,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:23:42,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:23:42,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-20_02-23-42.log] [testng] 02:23:42,896 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d72b258 - End of configuration. [testng] [2024-06-20 02:23:42,945] [pool-1-thread-11] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce: [testng] 02:23:42,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:23:42,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:23:42,947 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-20_02-23-42.log] [testng] 02:23:42,948 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1eb2b45d - End of configuration. [testng] [2024-06-20 02:23:42,992] [pool-1-thread-10] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce: [testng] 02:23:42,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:23:42,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:23:42,994 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-20_02-23-42.log] [testng] 02:23:42,994 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49ddb402 - End of configuration. [testng] [2024-06-20 02:23:43,128] [pool-1-thread-9] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce: [testng] 02:23:43,129 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:23:43,129 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:23:43,130 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-20_02-23-43.log] [testng] 02:23:43,131 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64b7abc1 - End of configuration. [testng] [2024-06-20 02:23:43,607] [pool-1-thread-8] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_238_IM/2009_97_238_IM.xdce: [testng] 02:23:43,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:23:43,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:23:43,610 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-20_02-23-43.log] [testng] 02:23:43,611 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26100063 - End of configuration. [testng] [2024-06-20 02:23:43,773] [pool-1-thread-7] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/excel output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce: [testng] 02:23:43,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:23:43,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:23:43,775 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-20_02-23-43.log] [testng] 02:23:43,775 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58bafc69 - End of configuration. [testng] [2024-06-20 02:23:43,882] [pool-1-thread-6] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_239_IM/2009_97_239_IM.xdce: [testng] 02:23:43,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:23:43,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:23:43,884 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-20_02-23-43.log] [testng] 02:23:43,885 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24c698c8 - End of configuration. [testng] [2024-06-20 02:23:44,015] [pool-1-thread-5] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce: [testng] 02:23:44,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:23:44,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:23:44,018 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-20_02-23-44.log] [testng] 02:23:44,019 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a6a596b - End of configuration. [testng] [2024-06-20 02:23:44,194] [pool-1-thread-4] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_239_TIFF/PC3_ER2009.97.239.xdce: [testng] 02:23:44,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:23:44,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:23:44,196 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-20_02-23-44.log] [testng] 02:23:44,197 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7532e131 - End of configuration. [testng] [2024-06-20 02:23:44,420] [pool-1-thread-3] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR37/excel output file/HCT116_HR2009.97.037/HCT116_HR2009.97.037.xdce: [testng] 02:23:44,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:23:44,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:23:44,422 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-20_02-23-44.log] [testng] 02:23:44,423 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34b425fd - End of configuration. [testng] [2024-06-20 02:23:44,526] [pool-1-thread-2] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_238_TIFF/PC3_ER2009.97.238.xdce: [testng] 02:23:44,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:23:44,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:23:44,528 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-20_02-23-44.log] [testng] 02:23:44,529 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29708926 - End of configuration. [testng] [2024-06-20 02:24:09,681] [pool-1-thread-12] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce: [testng] [2024-06-20 02:24:12,731] [pool-1-thread-12] Initializing /data/karsten/gabriele_-1_2/gabriele_-1_2.xdce: [testng] [2024-06-20 02:24:29,068] [pool-1-thread-11] Initializing /data/public/idr0017/2011-11-17_X-Man_LOPAC_X01_LP_S01_1/2011-11-17 X-Man LOPAC_X03_LP_S01_1.xdce: [testng] [2024-06-20 02:24:51,882] [pool-1-thread-12] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_240_TIFF/PC3_ER2009.97.240(ok).xdce: [testng] [2024-06-20 02:26:08,174] [pool-1-thread-6] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce: [testng] [2024-06-20 02:26:15,363] [pool-1-thread-8] Initializing /data/brian/H2Blivecell20x/H2Blivecell20x.xdce: [testng] [2024-06-20 02:26:21,078] [pool-1-thread-5] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce: [testng] [2024-06-20 02:26:31,326] [pool-1-thread-10] Initializing /data/brian/livecell/H2b10xtrial.xdce: [testng] [2024-06-20 02:26:46,946] [pool-1-thread-5] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_240_IM/2009_97_240_IM.xdce: [testng] [2024-06-20 02:26:52,042] [pool-1-thread-7] Initializing /data/samples/variable-field-count/test.xdce: [testng] [2024-06-20 02:27:01,563] [pool-1-thread-3] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/txt en XML output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce: [testng] [2024-06-20 02:27:02,679] [pool-1-thread-2] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce: [testng] [2024-06-20 02:27:03,866] [pool-1-thread-4] Initializing /data/samples/images_number_mismatch/test.xdce: [testng] [2024-06-20 02:27:04,034] [pool-1-thread-7] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce: [testng] [2024-06-20 02:27:14,939] [pool-1-thread-4] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1431, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 32 minutes 51 seconds Finished: SUCCESS