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Started by upstream project "BIOFORMATS-test-repo" build number 214 originally caused by: Started by upstream project "Trigger" build number 241 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins14602961262260189955.sh + '[' flex = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_33985_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] 09:18:52,573 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 09:18:52,574 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 09:18:52,574 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:18:52,575 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:18:52,576 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 09:18:52,576 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 09:18:52,576 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 09:18:52,576 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:18:52,577 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:18:52,578 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 09:18:52,578 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 09:18:52,578 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 09:18:52,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 09:18:52,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 09:18:52,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 09:18:52,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 09:18:52,777 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 09:18:52,777 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 09:18:52,777 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 09:18:52,777 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 09:18:52,777 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 09:18:52,778 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 09:18:52,778 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 201 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-08 09:18:52,787] [main] java.version = 11.0.16 [testng] 09:18:52,790 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:18:52,790 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:18:52,838 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-08_09-18-52.log] [testng] 09:18:52,839 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-08 09:18:52,841] [main] testng.directory = /data [testng] [2024-10-08 09:18:52,841] [main] testng.configDirectory = /config [testng] [2024-10-08 09:18:52,852] [main] testng.multiplier = 1.0 [testng] [2024-10-08 09:18:52,853] [main] testng.in-memory = false [testng] [2024-10-08 09:18:52,853] [main] testng.allow-missing = false [testng] [2024-10-08 09:18:52,853] [main] user.language = en [testng] [2024-10-08 09:18:52,853] [main] user.country = ${user.country} [testng] [2024-10-08 09:18:52,853] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-08 09:20:53,222] [main] ---------------------------------------- [testng] [2024-10-08 09:20:53,222] [main] Total files: 791 [testng] [2024-10-08 09:20:53,222] [main] Scan time: 120.369 s (152 ms/file) [testng] [2024-10-08 09:20:53,222] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-08 09:27:12,817] [pool-1-thread-1] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] 09:27:12,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 09:27:12,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:27:12,819 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-08_09-27-12.log] [testng] 09:27:12,820 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d1512a4 - End of configuration. [testng] [2024-10-08 09:27:13,876] [pool-1-thread-12] Initializing /data/qa-18096/002003001.flex: [testng] 09:27:13,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 09:27:13,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:27:13,877 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-08_09-27-13.log] [testng] 09:27:13,877 |-INFO in ch.qos.logback.core.sift.SiftProcessor@aa0111e - End of configuration. [testng] [2024-10-08 09:27:14,926] [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] 09:27:14,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 09:27:14,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:27:14,928 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-08_09-27-14.log] [testng] 09:27:14,928 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77c0599d - End of configuration. [testng] [2024-10-08 09:27:16,815] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] 09:27:16,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 09:27:16,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:27:16,816 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-08_09-27-16.log] [testng] 09:27:16,816 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d8c6b - End of configuration. [testng] [2024-10-08 09:27:17,915] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 09:27:17,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 09:27:17,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:27:17,917 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-08_09-27-17.log] [testng] 09:27:17,917 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ca105f - End of configuration. [testng] [2024-10-08 09:27:26,301] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] 09:27:26,302 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 09:27:26,302 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:27:26,302 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-08_09-27-26.log] [testng] 09:27:26,303 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f600f56 - End of configuration. [testng] [2024-10-08 09:27:27,556] [pool-1-thread-7] Initializing /data/tony/003008000.flex: [testng] 09:27:27,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 09:27:27,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:27:27,556 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-08_09-27-27.log] [testng] 09:27:27,557 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e436faa - End of configuration. [testng] [2024-10-08 09:27:28,801] [pool-1-thread-6] Initializing /data/tony/003003000.tiff: [testng] 09:27:28,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 09:27:28,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:27:28,801 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-08_09-27-28.log] [testng] 09:27:28,802 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c481d0e - End of configuration. [testng] [2024-10-08 09:27:31,305] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] 09:27:31,305 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 09:27:31,305 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:27:31,306 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-08_09-27-31.log] [testng] 09:27:31,306 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d834852 - End of configuration. [testng] [2024-10-08 09:27:32,464] [pool-1-thread-4] Initializing /data/qa-2983/004007000.flex: [testng] 09:27:32,464 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 09:27:32,464 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:27:32,465 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-08_09-27-32.log] [testng] 09:27:32,465 |-INFO in ch.qos.logback.core.sift.SiftProcessor@630fd9d0 - End of configuration. [testng] [2024-10-08 09:27:33,635] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] 09:27:33,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 09:27:33,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:27:33,636 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-08_09-27-33.log] [testng] 09:27:33,636 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d629d5b - End of configuration. [testng] [2024-10-08 09:27:35,494] [pool-1-thread-2] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 09:27:35,494 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 09:27:35,494 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:27:35,495 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-08_09-27-35.log] [testng] 09:27:35,495 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78e44e99 - End of configuration. [testng] [2024-10-08 09:27:51,861] [pool-1-thread-2] Initializing /data/anatole/001004000.flex: [testng] [2024-10-08 09:27:54,088] [pool-1-thread-6] Initializing /data/qa-18096/002002001.flex: [testng] [2024-10-08 09:27:55,327] [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] [2024-10-08 09:27:56,458] [pool-1-thread-4] Initializing /data/tony/test1.flex: [testng] [2024-10-08 09:27:57,515] [pool-1-thread-1] Initializing /data/stephane/002007000.flex: [testng] [2024-10-08 09:28:00,589] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-10-08 09:28:04,994] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex: [testng] [2024-10-08 09:28:06,274] [pool-1-thread-11] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-10-08 09:28:14,684] [pool-1-thread-6] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-10-08 09:28:17,111] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-10-08 09:28:18,254] [pool-1-thread-1] Initializing /data/ghislain/test.flex: [testng] [2024-10-08 09:28:19,372] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-10-08 09:28:32,641] [pool-1-thread-10] Initializing /data/tamjid/006005000.flex: [testng] [2024-10-08 09:28:35,442] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-10-08 09:28:45,035] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-10-08 09:28:54,781] [pool-1-thread-5] Initializing /data/manuel/003003001.flex: [testng] [2024-10-08 09:28:59,116] [pool-1-thread-6] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-10-08 09:29:12,372] [pool-1-thread-1] Initializing /data/stephane/006013000.flex: [testng] [2024-10-08 09:29:15,291] [pool-1-thread-10] Initializing /data/tony/015002000.tiff: [testng] [2024-10-08 09:29:18,106] [pool-1-thread-4] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-10-08 09:29:19,910] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-10-08 09:29:21,166] [pool-1-thread-2] Initializing /data/tony/test.tiff: [testng] [2024-10-08 09:29:31,691] [pool-1-thread-5] Initializing /data/tamjid/006003000.flex: [testng] [2024-10-08 09:29:37,827] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-10-08 09:29:49,443] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-10-08 09:30:05,299] [pool-1-thread-1] Initializing /data/qa-17190/002002011.flex: [testng] [2024-10-08 09:30:08,433] [pool-1-thread-3] Initializing /data/tony/001001000_objects.flex: [testng] [2024-10-08 09:30:11,581] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2024-10-08 09:30:21,161] [pool-1-thread-11] Initializing /data/achim/003003000.flex: [testng] [2024-10-08 09:30:24,658] [pool-1-thread-1] Initializing /data/tamjid/006004000.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 20 minutes 49 seconds Finished: SUCCESS