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Started by upstream project "BIOFORMATS-test-repo" build number 209 originally caused by: Started by upstream project "Trigger" build number 235 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins13781832935433591760.sh + '[' flex = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_33165_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 test-automated: [testng] File leak detector installed [testng] 01:43:11,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:43:11,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:43:11,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:43:11,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:43:11,514 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:43:11,514 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:43:11,514 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:43:11,515 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:43:11,515 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5c30a9b0 - End of configuration. [testng] 01:43:11,515 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@7a69b07 - Registering current configuration as safe fallback point [testng] 01:43:11,515 |-INFO in ch.qos.logback.classic.util.ContextInitializer@5e82df6a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 389 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-04 01:43:11,525] [main] java.version = 1.8.0_342 [testng] 01:43:11,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:43:11,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:11,574 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-04_01-43-11.log] [testng] 01:43:11,576 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-10-04 01:43:11,578] [main] testng.directory = /data [testng] [2024-10-04 01:43:11,579] [main] testng.configDirectory = /config [testng] [2024-10-04 01:43:11,596] [main] testng.multiplier = 1.0 [testng] [2024-10-04 01:43:11,596] [main] testng.in-memory = false [testng] [2024-10-04 01:43:11,597] [main] testng.allow-missing = false [testng] [2024-10-04 01:43:11,597] [main] user.language = en [testng] [2024-10-04 01:43:11,597] [main] user.country = ${user.country} [testng] [2024-10-04 01:43:11,597] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-04 01:43:55,701] [main] ---------------------------------------- [testng] [2024-10-04 01:43:55,701] [main] Total files: 791 [testng] [2024-10-04 01:43:55,702] [main] Scan time: 44.104 s (55 ms/file) [testng] [2024-10-04 01:43:55,702] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-04 01:48:06,166] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] 01:48:06,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:48:06,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:06,167 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-04_01-48-06.log] [testng] 01:48:06,168 |-INFO in ch.qos.logback.core.sift.SiftProcessor@604fb588 - End of configuration. [testng] [2024-10-04 01:48:06,544] [pool-1-thread-12] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 01:48:06,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:48:06,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:06,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-04_01-48-06.log] [testng] 01:48:06,546 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65935ee9 - End of configuration. [testng] [2024-10-04 01:48:07,276] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] 01:48:07,277 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:48:07,277 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:07,277 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-04_01-48-07.log] [testng] 01:48:07,278 |-INFO in ch.qos.logback.core.sift.SiftProcessor@716a12d3 - End of configuration. [testng] [2024-10-04 01:48:07,640] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] 01:48:07,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:48:07,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:07,642 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-04_01-48-07.log] [testng] 01:48:07,642 |-INFO in ch.qos.logback.core.sift.SiftProcessor@658851d3 - End of configuration. [testng] [2024-10-04 01:48:10,683] [pool-1-thread-9] Initializing /data/tamjid/006004000.flex: [testng] 01:48:10,683 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:48:10,683 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:10,684 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-04_01-48-10.log] [testng] 01:48:10,684 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ab73a86 - End of configuration. [testng] [2024-10-04 01:48:11,060] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] 01:48:11,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:48:11,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:11,061 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-04_01-48-11.log] [testng] 01:48:11,061 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7755d7b5 - End of configuration. [testng] [2024-10-04 01:48:11,474] [pool-1-thread-7] Initializing /data/qa-18096/002003001.flex: [testng] 01:48:11,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:48:11,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:11,475 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-04_01-48-11.log] [testng] 01:48:11,475 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50f931b4 - End of configuration. [testng] [2024-10-04 01:48:11,917] [pool-1-thread-6] Initializing /data/tony/003003000.tiff: [testng] 01:48:11,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:48:11,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:11,917 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-04_01-48-11.log] [testng] 01:48:11,918 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34f00d67 - End of configuration. [testng] [2024-10-04 01:48:12,770] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] 01:48:12,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:48:12,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:12,771 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-04_01-48-12.log] [testng] 01:48:12,771 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c64b44f - End of configuration. [testng] [2024-10-04 01:48:16,088] [pool-1-thread-4] Initializing /data/anatole/001004000.flex: [testng] 01:48:16,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:48:16,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:16,089 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-04_01-48-16.log] [testng] 01:48:16,090 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51a40142 - End of configuration. [testng] [2024-10-04 01:48:16,724] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 01:48:16,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:48:16,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:16,725 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-04_01-48-16.log] [testng] 01:48:16,725 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f67181a - End of configuration. [testng] [2024-10-04 01:48:21,295] [pool-1-thread-2] Initializing /data/tony/003008000.flex: [testng] 01:48:21,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:48:21,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:21,296 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-04_01-48-21.log] [testng] 01:48:21,296 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25cb3c02 - End of configuration. [testng] [2024-10-04 01:48:28,774] [pool-1-thread-12] Initializing /data/stephane/002007000.flex: [testng] [2024-10-04 01:48:29,320] [pool-1-thread-9] Initializing /data/qa-18096/002002001.flex: [testng] [2024-10-04 01:48:29,953] [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] [2024-10-04 01:48:30,485] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-10-04 01:48:34,501] [pool-1-thread-1] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-10-04 01:48:35,453] [pool-1-thread-11] Initializing /data/achim/003003000.flex: [testng] [2024-10-04 01:48:36,052] [pool-1-thread-8] Initializing /data/manuel/003003001.flex: [testng] [2024-10-04 01:48:36,908] [pool-1-thread-2] Initializing /data/ghislain/test.flex: [testng] [2024-10-04 01:48:39,087] [pool-1-thread-9] Initializing /data/stephane/006013000.flex: [testng] [2024-10-04 01:48:39,584] [pool-1-thread-12] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-10-04 01:48:42,307] [pool-1-thread-1] Initializing /data/qa-7469/002002.flex: [testng] [2024-10-04 01:48:43,572] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2024-10-04 01:48:49,453] [pool-1-thread-4] Initializing /data/tony/test1.flex: [testng] [2024-10-04 01:48:50,609] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-10-04 01:48:51,424] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [2024-10-04 01:48:55,559] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-10-04 01:48:56,734] [pool-1-thread-11] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-10-04 01:48:59,448] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-10-04 01:49:06,983] [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] [2024-10-04 01:49:08,373] [pool-1-thread-9] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-10-04 01:49:12,200] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-10-04 01:49:12,865] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-10-04 01:49:21,859] [pool-1-thread-11] Initializing /data/tamjid/006005000.flex: [testng] [2024-10-04 01:49:29,932] [pool-1-thread-11] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-10-04 01:49:37,176] [pool-1-thread-6] Initializing /data/qa-17190/002002011.flex: [testng] [2024-10-04 01:49:44,379] [pool-1-thread-1] Initializing /data/tamjid/006003000.flex: [testng] [2024-10-04 01:49:45,254] [pool-1-thread-6] Initializing /data/qa-2983/004007000.flex: [testng] [2024-10-04 01:49:45,904] [pool-1-thread-4] Initializing /data/tony/001001000_objects.flex: [testng] [2024-10-04 01:49:54,273] [pool-1-thread-1] Initializing /data/tony/015002000.tiff: [testng] [2024-10-04 01:49:56,126] [pool-1-thread-6] Initializing /data/tony/test.tiff: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 12 minutes 46 seconds Finished: SUCCESS