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Started by upstream project "BIOFORMATS-test-repo" build number 291 originally caused by: Started by upstream project "Trigger" build number 310 originally caused by: Started by timer 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/jenkins6701127748882385051.sh + '[' flex = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_45970_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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 02:03:38,935 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:03:38,936 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 02:03:38,936 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:03:38,937 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:03:38,938 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:03:38,938 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:03:38,938 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:03:38,938 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:03:38,939 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:03:38,939 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:03:38,939 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:03:38,940 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:03:39,096 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:03:39,096 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:03:39,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:03:39,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:03:39,123 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:03:39,123 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:03:39,123 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:03:39,123 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:03:39,123 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 02:03:39,124 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 02:03:39,124 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 185 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-15 02:03:39,133] [main] java.version = 17.0.2 [testng] 02:03:39,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:03:39,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:03:39,175 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-15_02-03-39.log] [testng] 02:03:39,176 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-15 02:03:39,178] [main] testng.directory = /data [testng] [2024-12-15 02:03:39,178] [main] testng.configDirectory = /config [testng] [2024-12-15 02:03:39,186] [main] testng.multiplier = 1.0 [testng] [2024-12-15 02:03:39,186] [main] testng.in-memory = false [testng] [2024-12-15 02:03:39,187] [main] testng.allow-missing = false [testng] [2024-12-15 02:03:39,187] [main] user.language = en [testng] [2024-12-15 02:03:39,187] [main] user.country = ${user.country} [testng] [2024-12-15 02:03:39,187] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-15 02:07:44,705] [main] ---------------------------------------- [testng] [2024-12-15 02:07:44,705] [main] Total files: 791 [testng] [2024-12-15 02:07:44,705] [main] Scan time: 245.518 s (310 ms/file) [testng] [2024-12-15 02:07:44,705] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-15 02:17:12,706] [pool-1-thread-1] Initializing /data/ghislain/test.flex: [testng] 02:17:12,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:17:12,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:12,708 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-15_02-17-12.log] [testng] 02:17:12,708 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59721b70 - End of configuration. [testng] [2024-12-15 02:17:14,034] [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] 02:17:14,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:17:14,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:14,036 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-15_02-17-14.log] [testng] 02:17:14,036 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b69b5d - End of configuration. [testng] [2024-12-15 02:17:16,012] [pool-1-thread-11] Initializing /data/tony/003008000.flex: [testng] 02:17:16,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:17:16,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:16,013 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-15_02-17-16.log] [testng] 02:17:16,013 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51f47228 - End of configuration. [testng] [2024-12-15 02:17:17,594] [pool-1-thread-10] Initializing /data/tony/001014000 - from flex.tif: [testng] 02:17:17,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:17:17,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:17,595 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-15_02-17-17.log] [testng] 02:17:17,595 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5476e175 - End of configuration. [testng] [2024-12-15 02:17:21,160] [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] 02:17:21,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:17:21,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:21,161 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-15_02-17-21.log] [testng] 02:17:21,161 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19bd51bf - End of configuration. [testng] [2024-12-15 02:17:22,514] [pool-1-thread-8] Initializing /data/tamjid/006004000.flex: [testng] 02:17:22,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:17:22,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:22,515 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-15_02-17-22.log] [testng] 02:17:22,515 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46a2e9b8 - End of configuration. [testng] [2024-12-15 02:17:24,196] [pool-1-thread-7] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] 02:17:24,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:17:24,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:24,197 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-15_02-17-24.log] [testng] 02:17:24,198 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8660002 - End of configuration. [testng] [2024-12-15 02:17:39,269] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 02:17:39,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:17:39,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:39,270 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-15_02-17-39.log] [testng] 02:17:39,271 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7aaf9984 - End of configuration. [testng] [2024-12-15 02:17:55,984] [pool-1-thread-5] Initializing /data/qa-2983/004007000.flex: [testng] 02:17:55,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:17:55,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:55,984 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-15_02-17-55.log] [testng] 02:17:55,985 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f397a48 - End of configuration. [testng] [2024-12-15 02:17:58,832] [pool-1-thread-4] Initializing /data/tony/003003000.tiff: [testng] 02:17:58,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:17:58,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:58,833 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-15_02-17-58.log] [testng] 02:17:58,833 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52670bb6 - End of configuration. [testng] [2024-12-15 02:18:03,481] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 02:18:03,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:18:03,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:03,482 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-15_02-18-03.log] [testng] 02:18:03,482 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41a79943 - End of configuration. [testng] [2024-12-15 02:18:24,243] [pool-1-thread-2] Initializing /data/manuel/003003001.flex: [testng] 02:18:24,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:18:24,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:24,244 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-15_02-18-24.log] [testng] 02:18:24,244 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26ca95a5 - End of configuration. [testng] [2024-12-15 02:18:58,487] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-12-15 02:19:20,098] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-12-15 02:19:22,848] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex: [testng] [2024-12-15 02:19:25,173] [pool-1-thread-4] Initializing /data/qa-7469/002002.flex: [testng] [2024-12-15 02:19:27,505] [pool-1-thread-1] Initializing /data/stephane/002007000.flex: [testng] [2024-12-15 02:19:34,754] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-12-15 02:19:43,588] [pool-1-thread-12] Initializing /data/qa-18096/002002001.flex: [testng] [2024-12-15 02:19:46,162] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-12-15 02:20:03,227] [pool-1-thread-2] Initializing /data/tony/test.tiff: [testng] [2024-12-15 02:20:08,353] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-12-15 02:20:26,899] [pool-1-thread-4] Initializing /data/achim/003003000.flex: [testng] [2024-12-15 02:20:29,319] [pool-1-thread-1] Initializing /data/tony/001001000_objects.flex: [testng] [2024-12-15 02:20:34,942] [pool-1-thread-5] Initializing /data/tamjid/006005000.flex: [testng] [2024-12-15 02:20:45,379] [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] [2024-12-15 02:20:48,059] [pool-1-thread-11] Initializing /data/qa-18096/002003001.flex: [testng] [2024-12-15 02:20:57,574] [pool-1-thread-9] Initializing /data/anatole/001004000.flex: [testng] [2024-12-15 02:21:07,749] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-12-15 02:21:13,294] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-12-15 02:21:31,968] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-12-15 02:21:45,414] [pool-1-thread-11] Initializing /data/stephane/006013000.flex: [testng] [2024-12-15 02:21:47,793] [pool-1-thread-4] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-12-15 02:21:58,922] [pool-1-thread-12] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-12-15 02:22:20,505] [pool-1-thread-4] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-12-15 02:22:25,154] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-12-15 02:22:34,434] [pool-1-thread-1] Initializing /data/tony/015002000.tiff: [testng] [2024-12-15 02:22:43,062] [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] [2024-12-15 02:22:45,909] [pool-1-thread-11] Initializing /data/qa-17190/002002011.flex: [testng] [2024-12-15 02:23:07,823] [pool-1-thread-1] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-12-15 02:23:18,209] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-12-15 02:24:02,310] [pool-1-thread-1] Initializing /data/tony/test1.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 37 minutes 18 seconds Finished: SUCCESS