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Started by upstream project "BIOFORMATS-test-repo" build number 129 originally caused by: Started by user devspace 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/jenkins14311922032242359524.sh + '[' flex = 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_20202_merge_ci -v /uod/idr/repos/curated/flex:/data -v /uod/idr-scratch/merge-ci/curated/flex:/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] 14:01:01,665 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 14:01:01,667 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 14:01:01,667 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:01:01,668 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:01:01,668 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 14:01:01,668 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 14:01:01,669 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 14:01:01,669 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:01:01,669 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:01:01,669 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 14:01:01,670 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 14:01:01,670 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 14:01:01,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 14:01:01,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 14:01:01,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 14:01:01,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 14:01:01,957 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 14:01:01,957 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 14:01:01,958 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 14:01:01,958 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 14:01:01,958 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 14:01:01,959 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 14:01:01,959 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 290 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-22 14:01:01,969] [main] java.version = 1.8.0_342 [testng] 14:01:01,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 14:01:01,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:01:02,018 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-22_14-01-01.log] [testng] 14:01:02,019 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-22 14:01:02,021] [main] testng.directory = /data [testng] [2024-07-22 14:01:02,022] [main] testng.configDirectory = /config [testng] [2024-07-22 14:01:02,034] [main] testng.multiplier = 1.0 [testng] [2024-07-22 14:01:02,034] [main] testng.in-memory = false [testng] [2024-07-22 14:01:02,034] [main] testng.allow-missing = false [testng] [2024-07-22 14:01:02,034] [main] user.language = fr [testng] [2024-07-22 14:01:02,034] [main] user.country = FR [testng] [2024-07-22 14:01:02,034] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-22 14:01:13,997] [main] ---------------------------------------- [testng] [2024-07-22 14:01:13,997] [main] Total files: 791 [testng] [2024-07-22 14:01:13,997] [main] Scan time: 11.963 s (15 ms/file) [testng] [2024-07-22 14:01:13,997] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-22 14:07:03,008] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] 14:07:03,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 14:07:03,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:03,010 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-22_14-07-03.log] [testng] 14:07:03,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d4fb138 - End of configuration. [testng] [2024-07-22 14:07:03,061] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] 14:07:03,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 14:07:03,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:03,061 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-22_14-07-03.log] [testng] 14:07:03,062 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1147f9a8 - End of configuration. [testng] [2024-07-22 14:07:03,089] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 14:07:03,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 14:07:03,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:03,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-22_14-07-03.log] [testng] 14:07:03,091 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61fbdb7 - End of configuration. [testng] [2024-07-22 14:07:03,598] [pool-1-thread-10] Initializing /data/tamjid/006003000.flex: [testng] 14:07:03,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 14:07:03,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:03,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-22_14-07-03.log] [testng] 14:07:03,600 |-INFO in ch.qos.logback.core.sift.SiftProcessor@508139fd - End of configuration. [testng] [2024-07-22 14:07:03,623] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] 14:07:03,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 14:07:03,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:03,624 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-22_14-07-03.log] [testng] 14:07:03,625 |-INFO in ch.qos.logback.core.sift.SiftProcessor@262d3262 - End of configuration. [testng] [2024-07-22 14:07:03,654] [pool-1-thread-8] Initializing /data/qa-18096/002002001.flex: [testng] 14:07:03,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 14:07:03,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:03,655 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-22_14-07-03.log] [testng] 14:07:03,655 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d6c16a3 - End of configuration. [testng] [2024-07-22 14:07:03,702] [pool-1-thread-7] Initializing /data/tony/001014000 - from flex.tif: [testng] 14:07:03,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 14:07:03,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:03,703 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-22_14-07-03.log] [testng] 14:07:03,703 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6af5bf2d - End of configuration. [testng] [2024-07-22 14:07:03,746] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 14:07:03,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 14:07:03,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:03,747 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-22_14-07-03.log] [testng] 14:07:03,747 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27fd4c2 - End of configuration. [testng] [2024-07-22 14:07:04,187] [pool-1-thread-5] Initializing /data/achim/003003000.flex: [testng] 14:07:04,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 14:07:04,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:04,187 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-22_14-07-04.log] [testng] 14:07:04,188 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49145fd4 - End of configuration. [testng] [2024-07-22 14:07:04,251] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] 14:07:04,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 14:07:04,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:04,252 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-22_14-07-04.log] [testng] 14:07:04,252 |-INFO in ch.qos.logback.core.sift.SiftProcessor@190a078f - End of configuration. [testng] [2024-07-22 14:07:04,636] [pool-1-thread-3] Initializing /data/tony/003003000.tiff: [testng] 14:07:04,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 14:07:04,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:04,636 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-22_14-07-04.log] [testng] 14:07:04,637 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4487cc96 - End of configuration. [testng] [2024-07-22 14:07:04,727] [pool-1-thread-2] Initializing /data/tony/test1.flex: [testng] 14:07:04,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 14:07:04,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:04,728 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-22_14-07-04.log] [testng] 14:07:04,729 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8e487ea - End of configuration. [testng] [2024-07-22 14:07:06,413] [pool-1-thread-2] Initializing /data/tamjid/006005000.flex: [testng] [2024-07-22 14:07:06,459] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-07-22 14:07:06,507] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-07-22 14:07:06,560] [pool-1-thread-7] Initializing /data/qa-17190/002002011.flex: [testng] [2024-07-22 14:07:06,600] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex: [testng] [2024-07-22 14:07:06,732] [pool-1-thread-3] Initializing /data/tony/001001000_objects.flex: [testng] [2024-07-22 14:07:06,781] [pool-1-thread-1] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-07-22 14:07:06,972] [pool-1-thread-9] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-07-22 14:07:07,260] [pool-1-thread-12] Initializing /data/stephane/002007000.flex: [testng] [2024-07-22 14:07:07,599] [pool-1-thread-2] Initializing /data/anatole/001004000.flex: [testng] [2024-07-22 14:07:07,796] [pool-1-thread-7] Initializing /data/qa-2983/004007000.flex: [testng] [2024-07-22 14:07:07,860] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-07-22 14:07:08,437] [pool-1-thread-3] Initializing /data/tony/test.tiff: [testng] [2024-07-22 14:07:08,681] [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] [2024-07-22 14:07:09,107] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-07-22 14:07:09,332] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-07-22 14:07:09,353] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-07-22 14:07:09,414] [pool-1-thread-1] Initializing /data/manuel/003003001.flex: [testng] [2024-07-22 14:07:10,045] [pool-1-thread-10] Initializing /data/ghislain/test.flex: [testng] [2024-07-22 14:07:10,735] [pool-1-thread-3] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-07-22 14:07:10,835] [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] [2024-07-22 14:07:10,979] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-07-22 14:07:11,504] [pool-1-thread-1] Initializing /data/tamjid/006004000.flex: [testng] [2024-07-22 14:07:11,989] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-07-22 14:07:12,847] [pool-1-thread-12] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-07-22 14:07:14,210] [pool-1-thread-8] Initializing /data/stephane/006013000.flex: [testng] [2024-07-22 14:07:15,913] [pool-1-thread-2] Initializing /data/qa-18096/002003001.flex: [testng] [2024-07-22 14:07:16,578] [pool-1-thread-2] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-07-22 14:07:16,640] [pool-1-thread-7] Initializing /data/tony/003008000.flex: [testng] [2024-07-22 14:07:17,176] [pool-1-thread-2] Initializing /data/tony/015002000.tiff: [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 32 seconds Finished: SUCCESS