Started by upstream project "BIOFORMATS-test-repo" build number 210 originally caused by: Started by upstream project "Trigger" build number 236 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins1225880725982835628.sh + '[' flex = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_33329_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 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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 01:48:55,112 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:48:55,114 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:48:55,114 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:48:55,115 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:48:55,115 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:48:55,116 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:48:55,116 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:48:55,116 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:48:55,116 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:48:55,117 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:48:55,117 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:48:55,118 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:48:55,283 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:48:55,283 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:48:55,305 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:48:55,305 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:48:55,311 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:48:55,311 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:48:55,311 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:48:55,311 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:48:55,311 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:48:55,313 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:48:55,313 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 197 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-05 01:48:55,322] [main] java.version = 11.0.16 [testng] 01:48:55,325 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:48:55,325 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:55,366 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-05_01-48-55.log] [testng] 01:48:55,368 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-10-05 01:48:55,370] [main] testng.directory = /data [testng] [2024-10-05 01:48:55,370] [main] testng.configDirectory = /config [testng] [2024-10-05 01:48:55,380] [main] testng.multiplier = 1.0 [testng] [2024-10-05 01:48:55,381] [main] testng.in-memory = false [testng] [2024-10-05 01:48:55,381] [main] testng.allow-missing = false [testng] [2024-10-05 01:48:55,381] [main] user.language = en [testng] [2024-10-05 01:48:55,381] [main] user.country = ${user.country} [testng] [2024-10-05 01:48:55,382] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-05 01:49:26,941] [main] ---------------------------------------- [testng] [2024-10-05 01:49:26,941] [main] Total files: 791 [testng] [2024-10-05 01:49:26,941] [main] Scan time: 31.559 s (39 ms/file) [testng] [2024-10-05 01:49:26,941] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-05 01:53:38,578] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 01:53:38,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:53:38,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:53:38,580 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-05_01-53-38.log] [testng] 01:53:38,581 |-INFO in ch.qos.logback.core.sift.SiftProcessor@345e5c18 - End of configuration. [testng] [2024-10-05 01:53:41,951] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] 01:53:41,951 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:53:41,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:53:41,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-05_01-53-41.log] [testng] 01:53:41,954 |-INFO in ch.qos.logback.core.sift.SiftProcessor@443e1e1c - End of configuration. [testng] [2024-10-05 01:53:42,340] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] 01:53:42,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:53:42,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:53:42,341 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-05_01-53-42.log] [testng] 01:53:42,341 |-INFO in ch.qos.logback.core.sift.SiftProcessor@324a5c39 - End of configuration. [testng] [2024-10-05 01:53:42,777] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 01:53:42,777 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:53:42,777 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:53:42,778 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-05_01-53-42.log] [testng] 01:53:42,778 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1229ab82 - End of configuration. [testng] [2024-10-05 01:53:46,161] [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] 01:53:46,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:53:46,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:53:46,162 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-05_01-53-46.log] [testng] 01:53:46,162 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24a69c1d - End of configuration. [testng] [2024-10-05 01:53:46,617] [pool-1-thread-8] Initializing /data/tony/test.tiff: [testng] 01:53:46,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:53:46,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:53:46,618 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-05_01-53-46.log] [testng] 01:53:46,619 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5334ebbf - End of configuration. [testng] [2024-10-05 01:53:47,591] [pool-1-thread-7] Initializing /data/tony/015002000.tiff: [testng] 01:53:47,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:53:47,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:53:47,592 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-05_01-53-47.log] [testng] 01:53:47,593 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41eb3d93 - End of configuration. [testng] [2024-10-05 01:53:48,527] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] 01:53:48,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:53:48,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:53:48,528 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-05_01-53-48.log] [testng] 01:53:48,528 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52796683 - End of configuration. [testng] [2024-10-05 01:53:49,026] [pool-1-thread-5] Initializing /data/anatole/001004000.flex: [testng] 01:53:49,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:53:49,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:53:49,027 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-05_01-53-49.log] [testng] 01:53:49,027 |-INFO in ch.qos.logback.core.sift.SiftProcessor@574e1668 - End of configuration. [testng] [2024-10-05 01:53:49,796] [pool-1-thread-4] Initializing /data/stephane/002007000.flex: [testng] 01:53:49,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:53:49,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:53:49,797 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-05_01-53-49.log] [testng] 01:53:49,797 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cd772a3 - End of configuration. [testng] [2024-10-05 01:53:50,308] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] 01:53:50,308 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:53:50,308 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:53:50,308 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-05_01-53-50.log] [testng] 01:53:50,309 |-INFO in ch.qos.logback.core.sift.SiftProcessor@797a1897 - End of configuration. [testng] [2024-10-05 01:53:50,849] [pool-1-thread-2] Initializing /data/tony/001014000 - from flex.tif: [testng] 01:53:50,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:53:50,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:53:50,850 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-05_01-53-50.log] [testng] 01:53:50,851 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13bccedf - End of configuration. [testng] [2024-10-05 01:53:58,779] [pool-1-thread-8] Initializing /data/qa-7469/002002.flex: [testng] [2024-10-05 01:53:59,350] [pool-1-thread-2] Initializing /data/qa-2983/004007000.flex: [testng] [2024-10-05 01:53:59,842] [pool-1-thread-7] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-10-05 01:54:00,516] [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] [2024-10-05 01:54:03,960] [pool-1-thread-9] Initializing /data/tamjid/006003000.flex: [testng] [2024-10-05 01:54:04,388] [pool-1-thread-12] Initializing /data/tony/003008000.flex: [testng] [2024-10-05 01:54:04,829] [pool-1-thread-3] Initializing /data/ghislain/test.flex: [testng] [2024-10-05 01:54:05,252] [pool-1-thread-11] Initializing /data/stephane/006013000.flex: [testng] [2024-10-05 01:54:05,745] [pool-1-thread-6] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-10-05 01:54:08,806] [pool-1-thread-8] Initializing /data/manuel/003003001.flex: [testng] [2024-10-05 01:54:09,363] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-10-05 01:54:17,177] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-10-05 01:54:18,123] [pool-1-thread-9] Initializing /data/tony/001001000_objects.flex: [testng] [2024-10-05 01:54:18,817] [pool-1-thread-5] Initializing /data/qa-17190/002002011.flex: [testng] [2024-10-05 01:54:19,509] [pool-1-thread-3] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-10-05 01:54:24,448] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-10-05 01:54:32,065] [pool-1-thread-12] Initializing /data/qa-18096/002002001.flex: [testng] [2024-10-05 01:54:35,441] [pool-1-thread-11] Initializing /data/tamjid/006004000.flex: [testng] [2024-10-05 01:54:39,540] [pool-1-thread-5] Initializing /data/tony/test1.flex: [testng] [2024-10-05 01:54:40,336] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-10-05 01:54:42,154] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-10-05 01:54:43,631] [pool-1-thread-8] Initializing /data/tamjid/006005000.flex: [testng] [2024-10-05 01:54:44,565] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2024-10-05 01:54:54,626] [pool-1-thread-11] Initializing /data/achim/003003000.flex: [testng] [2024-10-05 01:54:57,517] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-10-05 01:55:07,119] [pool-1-thread-8] Initializing /data/qa-18096/002003001.flex: [testng] [2024-10-05 01:55:15,134] [pool-1-thread-11] Initializing /data/tony/003003000.tiff: [testng] [2024-10-05 01:55:18,636] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-10-05 01:55:22,533] [pool-1-thread-9] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-10-05 01:55:26,337] [pool-1-thread-11] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 11 minutes 55 seconds Finished: SUCCESS