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Started by upstream project "BIOFORMATS-test-repo" build number 12 originally caused by: Started by upstream project "Trigger" build number 15 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins14434807512822282890.sh + '[' flex = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_1831_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] 00:35:35,824 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:35:35,826 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 00:35:35,826 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:35:35,827 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:35:35,827 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:35:35,828 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:35:35,828 |-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] 00:35:35,828 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:35:35,829 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:35:35,829 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:35:35,830 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:35:35,830 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:35:36,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:35:36,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:35:36,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:35:36,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:35:36,044 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:35:36,044 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:35:36,044 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:35:36,045 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:35:36,045 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 00:35:36,046 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 00:35:36,046 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 217 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-26 00:35:36,057] [main] java.version = 11.0.16 [testng] 00:35:36,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:35:36,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:36,106 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-26_00-35-36.log] [testng] 00:35:36,108 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-03-26 00:35:36,111] [main] testng.directory = /data [testng] [2024-03-26 00:35:36,112] [main] testng.configDirectory = /config [testng] [2024-03-26 00:35:36,124] [main] testng.multiplier = 1.0 [testng] [2024-03-26 00:35:36,125] [main] testng.in-memory = false [testng] [2024-03-26 00:35:36,126] [main] testng.allow-missing = false [testng] [2024-03-26 00:35:36,126] [main] user.language = en [testng] [2024-03-26 00:35:36,126] [main] user.country = ${user.country} [testng] [2024-03-26 00:35:36,126] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-26 00:35:55,751] [main] ---------------------------------------- [testng] [2024-03-26 00:35:55,752] [main] Total files: 791 [testng] [2024-03-26 00:35:55,752] [main] Scan time: 19.625 s (24 ms/file) [testng] [2024-03-26 00:35:55,752] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-26 00:42:07,172] [pool-1-thread-1] Initializing /data/qa-18096/002003001.flex: [testng] 00:42:07,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:42:07,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:07,175 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-26_00-42-07.log] [testng] 00:42:07,175 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17edb31c - End of configuration. [testng] [2024-03-26 00:42:07,382] [pool-1-thread-12] Initializing /data/tony/003003000.tiff: [testng] 00:42:07,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:42:07,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:07,383 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-26_00-42-07.log] [testng] 00:42:07,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@229951d8 - End of configuration. [testng] [2024-03-26 00:42:07,875] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] 00:42:07,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:42:07,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:07,876 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-26_00-42-07.log] [testng] 00:42:07,876 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1383033d - End of configuration. [testng] [2024-03-26 00:42:09,779] [pool-1-thread-10] Initializing /data/achim/003003000.flex: [testng] 00:42:09,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:42:09,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:09,780 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-26_00-42-09.log] [testng] 00:42:09,781 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61296c3b - End of configuration. [testng] [2024-03-26 00:42:10,400] [pool-1-thread-9] Initializing /data/manuel/003003001.flex: [testng] 00:42:10,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:42:10,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:10,401 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-26_00-42-10.log] [testng] 00:42:10,401 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48f126a2 - End of configuration. [testng] [2024-03-26 00:42:10,666] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex: [testng] 00:42:10,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:42:10,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:10,667 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-26_00-42-10.log] [testng] 00:42:10,667 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b6ef93e - End of configuration. [testng] [2024-03-26 00:42:10,943] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] 00:42:10,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:42:10,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:10,944 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-26_00-42-10.log] [testng] 00:42:10,944 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e143d29 - End of configuration. [testng] [2024-03-26 00:42:11,223] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 00:42:11,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:42:11,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:11,224 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-26_00-42-11.log] [testng] 00:42:11,224 |-INFO in ch.qos.logback.core.sift.SiftProcessor@499262b - End of configuration. [testng] [2024-03-26 00:42:13,339] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 00:42:13,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:42:13,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:13,340 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-26_00-42-13.log] [testng] 00:42:13,340 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57728469 - End of configuration. [testng] [2024-03-26 00:42:16,172] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] 00:42:16,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:42:16,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:16,173 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-26_00-42-16.log] [testng] 00:42:16,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51f1a565 - End of configuration. [testng] [2024-03-26 00:42:16,603] [pool-1-thread-3] Initializing /data/tony/003008000.flex: [testng] 00:42:16,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:42:16,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:16,604 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-26_00-42-16.log] [testng] 00:42:16,604 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7da7abb5 - End of configuration. [testng] [2024-03-26 00:42:17,242] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] 00:42:17,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:42:17,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:17,243 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-26_00-42-17.log] [testng] 00:42:17,244 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c5f17a3 - End of configuration. [testng] [2024-03-26 00:42:29,162] [pool-1-thread-10] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 00:42:29,913] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-03-26 00:42:30,732] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2024-03-26 00:42:31,309] [pool-1-thread-12] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-03-26 00:42:32,688] [pool-1-thread-9] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 00:42:33,807] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-03-26 00:42:34,963] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-03-26 00:42:38,939] [pool-1-thread-10] Initializing /data/tony/test.tiff: [testng] [2024-03-26 00:42:40,279] [pool-1-thread-3] Initializing /data/qa-17190/002002011.flex: [testng] [2024-03-26 00:42:40,735] [pool-1-thread-9] Initializing /data/tony/015002000.tiff: [testng] [2024-03-26 00:42:44,284] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-03-26 00:42:45,631] [pool-1-thread-1] Initializing /data/qa-18096/002002001.flex: [testng] [2024-03-26 00:42:46,550] [pool-1-thread-10] Initializing /data/stephane/006013000.flex: [testng] [2024-03-26 00:42:47,009] [pool-1-thread-3] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-03-26 00:42:47,515] [pool-1-thread-9] Initializing /data/ghislain/test.flex: [testng] [2024-03-26 00:42:51,090] [pool-1-thread-7] Initializing /data/tamjid/006004000.flex: [testng] [2024-03-26 00:42:51,520] [pool-1-thread-1] Initializing /data/tamjid/006005000.flex: [testng] [2024-03-26 00:42:52,457] [pool-1-thread-12] Initializing /data/qa-2983/004007000.flex: [testng] [2024-03-26 00:42:54,359] [pool-1-thread-9] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-03-26 00:42:55,623] [pool-1-thread-3] Initializing /data/tony/test1.flex: [testng] [2024-03-26 00:42:57,730] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-03-26 00:42:58,339] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-03-26 00:43:01,831] [pool-1-thread-8] Initializing /data/stephane/002007000.flex: [testng] [2024-03-26 00:43:02,684] [pool-1-thread-10] Initializing /data/anatole/001004000.flex: [testng] [2024-03-26 00:43:05,562] [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] [2024-03-26 00:43:06,203] [pool-1-thread-9] Initializing /data/qa-7469/002002.flex: [testng] [2024-03-26 00:43:07,610] [pool-1-thread-3] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-03-26 00:43:17,876] [pool-1-thread-1] Initializing /data/tony/001001000_objects.flex: [testng] [2024-03-26 00:43:18,490] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-03-26 00:43:43,359] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-03-26 00:43:44,673] [pool-1-thread-12] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-03-26 00:43:53,776] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 2, Skips: 0 [testng] =============================================== [testng] [testng] The tests failed. BUILD FAILED /bio-formats-build/bioformats/components/test-suite/build.xml:270: if=failedTest Total time: 13 minutes 4 seconds Build step 'Execute shell' marked build as failure Finished: FAILURE