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Started by upstream project "BIOFORMATS-test-repo" build number 199 originally caused by: Started by upstream project "Trigger" build number 223 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/jenkins8513761462062432268.sh + '[' flex = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_31525_merge_ci -v /test/idr/repos/curated/flex:/data -v /test/idr-scratch/merge-ci/curated/flex:/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] 01:30:49,115 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:30:49,117 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:30:49,117 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:30:49,118 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:30:49,118 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:30:49,118 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:30:49,119 |-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] 01:30:49,119 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:30:49,119 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:30:49,120 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:30:49,120 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:30:49,120 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:30:49,302 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:30:49,302 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:30:49,327 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:30:49,327 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:30:49,333 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:30:49,333 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:30:49,334 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:30:49,334 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:30:49,334 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:30:49,335 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:30:49,335 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 216 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-25 01:30:49,345] [main] java.version = 17.0.2 [testng] 01:30:49,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:30:49,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:30:49,391 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-25_01-30-49.log] [testng] 01:30:49,393 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-09-25 01:30:49,395] [main] testng.directory = /data [testng] [2024-09-25 01:30:49,395] [main] testng.configDirectory = /config [testng] [2024-09-25 01:30:49,405] [main] testng.multiplier = 1.0 [testng] [2024-09-25 01:30:49,406] [main] testng.in-memory = false [testng] [2024-09-25 01:30:49,406] [main] testng.allow-missing = false [testng] [2024-09-25 01:30:49,406] [main] user.language = en [testng] [2024-09-25 01:30:49,406] [main] user.country = ${user.country} [testng] [2024-09-25 01:30:49,406] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-25 01:31:01,418] [main] ---------------------------------------- [testng] [2024-09-25 01:31:01,418] [main] Total files: 791 [testng] [2024-09-25 01:31:01,418] [main] Scan time: 12.012 s (15 ms/file) [testng] [2024-09-25 01:31:01,418] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-25 01:37:06,439] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] 01:37:06,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:37:06,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:06,441 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-25_01-37-06.log] [testng] 01:37:06,442 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f7ff73f - End of configuration. [testng] [2024-09-25 01:37:06,524] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] 01:37:06,524 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:37:06,524 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:06,525 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-25_01-37-06.log] [testng] 01:37:06,525 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6da861eb - End of configuration. [testng] [2024-09-25 01:37:06,554] [pool-1-thread-11] Initializing /data/tony/test.tiff: [testng] 01:37:06,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:37:06,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:06,555 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-25_01-37-06.log] [testng] 01:37:06,555 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b67495b - End of configuration. [testng] [2024-09-25 01:37:06,617] [pool-1-thread-10] Initializing /data/tony/003008000.flex: [testng] 01:37:06,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:37:06,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:06,618 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-25_01-37-06.log] [testng] 01:37:06,619 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d312120 - End of configuration. [testng] [2024-09-25 01:37:06,667] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] 01:37:06,667 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:37:06,667 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:06,669 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-25_01-37-06.log] [testng] 01:37:06,669 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bc152a7 - End of configuration. [testng] [2024-09-25 01:37:06,697] [pool-1-thread-8] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 01:37:06,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:37:06,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:06,698 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-25_01-37-06.log] [testng] 01:37:06,699 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68dfff08 - End of configuration. [testng] [2024-09-25 01:37:06,734] [pool-1-thread-7] Initializing /data/qa-18096/002002001.flex: [testng] 01:37:06,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:37:06,735 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:06,735 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-25_01-37-06.log] [testng] 01:37:06,736 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ef87e45 - End of configuration. [testng] [2024-09-25 01:37:06,789] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 01:37:06,789 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:37:06,789 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:06,790 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-25_01-37-06.log] [testng] 01:37:06,790 |-INFO in ch.qos.logback.core.sift.SiftProcessor@368ec75c - End of configuration. [testng] [2024-09-25 01:37:07,300] [pool-1-thread-5] Initializing /data/stephane/002007000.flex: [testng] 01:37:07,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:37:07,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:07,301 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-25_01-37-07.log] [testng] 01:37:07,302 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ae25506 - End of configuration. [testng] [2024-09-25 01:37:07,337] [pool-1-thread-4] Initializing /data/tony/015002000.tiff: [testng] 01:37:07,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:37:07,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:07,338 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-25_01-37-07.log] [testng] 01:37:07,338 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d632233 - End of configuration. [testng] [2024-09-25 01:37:07,397] [pool-1-thread-3] Initializing /data/qa-17190/002002011.flex: [testng] 01:37:07,397 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:37:07,397 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:07,398 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-25_01-37-07.log] [testng] 01:37:07,398 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f82be93 - End of configuration. [testng] [2024-09-25 01:37:07,429] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] 01:37:07,429 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:37:07,429 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:07,430 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-25_01-37-07.log] [testng] 01:37:07,430 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6477d1f3 - End of configuration. [testng] [2024-09-25 01:37:09,605] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-09-25 01:37:10,077] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex: [testng] [2024-09-25 01:37:10,131] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-09-25 01:37:10,171] [pool-1-thread-11] Initializing /data/tamjid/006003000.flex: [testng] [2024-09-25 01:37:10,193] [pool-1-thread-4] Initializing /data/tamjid/006005000.flex: [testng] [2024-09-25 01:37:10,216] [pool-1-thread-9] Initializing /data/stephane/006013000.flex: [testng] [2024-09-25 01:37:10,262] [pool-1-thread-12] Initializing /data/manuel/003003001.flex: [testng] [2024-09-25 01:37:10,360] [pool-1-thread-5] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-09-25 01:37:10,870] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-09-25 01:37:11,364] [pool-1-thread-4] Initializing /data/tony/003003000.tiff: [testng] [2024-09-25 01:37:11,723] [pool-1-thread-3] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-09-25 01:37:11,833] [pool-1-thread-1] Initializing /data/tony/001001000_objects.flex: [testng] [2024-09-25 01:37:12,358] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2024-09-25 01:37:12,505] [pool-1-thread-1] Initializing /data/qa-7469/002002.flex: [testng] [2024-09-25 01:37:12,540] [pool-1-thread-12] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-09-25 01:37:12,786] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-09-25 01:37:13,075] [pool-1-thread-5] Initializing /data/achim/003003000.flex: [testng] [2024-09-25 01:37:13,366] [pool-1-thread-1] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-09-25 01:37:13,960] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2024-09-25 01:37:14,361] [pool-1-thread-5] Initializing /data/tamjid/006004000.flex: [testng] [2024-09-25 01:37:14,388] [pool-1-thread-4] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-09-25 01:37:14,891] [pool-1-thread-5] Initializing /data/ghislain/test.flex: [testng] [2024-09-25 01:37:15,034] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-09-25 01:37:15,188] [pool-1-thread-7] Initializing /data/anatole/001004000.flex: [testng] [2024-09-25 01:37:15,328] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-09-25 01:37:15,410] [pool-1-thread-9] Initializing /data/tony/test1.flex: [testng] [2024-09-25 01:37:15,693] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [2024-09-25 01:37:15,832] [pool-1-thread-9] Initializing /data/qa-18096/002003001.flex: [testng] [2024-09-25 01:37:16,454] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-09-25 01:37:17,049] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 9 minutes 38 seconds Finished: SUCCESS