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Started by upstream project "BIOFORMATS-test-repo" build number 303 originally caused by: Started by upstream project "Trigger" build number 325 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins14995540982071628933.sh + '[' flex = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_47950_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 -Duser.language=fr -Duser.country=FR 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] 01:07:17,566 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:07:17,568 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 01:07:17,568 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:07:17,569 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:07:17,569 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:07:17,569 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:07:17,570 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:07:17,570 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:07:17,570 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:07:17,571 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:07:17,571 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:07:17,571 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:07:17,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:07:17,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:07:17,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:07:17,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:07:17,886 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:07:17,886 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:07:17,886 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:07:17,886 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:07:17,887 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 01:07:17,887 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 01:07:17,887 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 317 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-30 01:07:17,898] [main] java.version = 1.8.0_342 [testng] 01:07:17,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:07:17,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:17,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-30_01-07-17.log] [testng] 01:07:17,956 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-30 01:07:17,958] [main] testng.directory = /data [testng] [2024-12-30 01:07:17,958] [main] testng.configDirectory = /config [testng] [2024-12-30 01:07:17,971] [main] testng.multiplier = 1.0 [testng] [2024-12-30 01:07:17,971] [main] testng.in-memory = false [testng] [2024-12-30 01:07:17,972] [main] testng.allow-missing = false [testng] [2024-12-30 01:07:17,972] [main] user.language = fr [testng] [2024-12-30 01:07:17,972] [main] user.country = FR [testng] [2024-12-30 01:07:17,972] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-30 01:09:00,324] [main] ---------------------------------------- [testng] [2024-12-30 01:09:00,325] [main] Total files: 791 [testng] [2024-12-30 01:09:00,325] [main] Scan time: 102.352 s (129 ms/file) [testng] [2024-12-30 01:09:00,325] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-30 01:16:15,815] [pool-1-thread-1] Initializing /data/tony/001014000 - from flex.tif: [testng] 01:16:15,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:16:15,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:16:15,817 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-30_01-16-15.log] [testng] 01:16:15,817 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63932272 - End of configuration. [testng] [2024-12-30 01:16:18,274] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 01:16:18,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:16:18,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:16:18,275 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-30_01-16-18.log] [testng] 01:16:18,275 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d17d25e - End of configuration. [testng] [2024-12-30 01:16:27,671] [pool-1-thread-11] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 01:16:27,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:16:27,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:16:27,672 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-30_01-16-27.log] [testng] 01:16:27,673 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4507870e - End of configuration. [testng] [2024-12-30 01:16:29,815] [pool-1-thread-10] Initializing /data/tamjid/006005000.flex: [testng] 01:16:29,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:16:29,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:16:29,816 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-30_01-16-29.log] [testng] 01:16:29,817 |-INFO in ch.qos.logback.core.sift.SiftProcessor@735679 - End of configuration. [testng] [2024-12-30 01:16:31,266] [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] 01:16:31,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:16:31,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:16:31,267 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-30_01-16-31.log] [testng] 01:16:31,268 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35d9306 - End of configuration. [testng] [2024-12-30 01:16:32,413] [pool-1-thread-8] Initializing /data/tony/015002000.tiff: [testng] 01:16:32,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:16:32,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:16:32,414 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-30_01-16-32.log] [testng] 01:16:32,414 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15982a94 - End of configuration. [testng] [2024-12-30 01:16:34,467] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 01:16:34,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:16:34,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:16:34,468 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-30_01-16-34.log] [testng] 01:16:34,468 |-INFO in ch.qos.logback.core.sift.SiftProcessor@276d28f8 - End of configuration. [testng] [2024-12-30 01:16:43,483] [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] 01:16:43,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:16:43,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:16:43,484 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-30_01-16-43.log] [testng] 01:16:43,484 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3349a005 - End of configuration. [testng] [2024-12-30 01:16:45,300] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] 01:16:45,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:16:45,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:16:45,301 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-30_01-16-45.log] [testng] 01:16:45,301 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d3ee2cf - End of configuration. [testng] [2024-12-30 01:16:46,530] [pool-1-thread-4] Initializing /data/stephane/002007000.flex: [testng] 01:16:46,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:16:46,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:16:46,531 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-30_01-16-46.log] [testng] 01:16:46,531 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32f3a8ea - End of configuration. [testng] [2024-12-30 01:16:47,657] [pool-1-thread-3] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] 01:16:47,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:16:47,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:16:47,658 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-30_01-16-47.log] [testng] 01:16:47,658 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ca14f18 - End of configuration. [testng] [2024-12-30 01:16:56,208] [pool-1-thread-2] Initializing /data/qa-2983/004007000.flex: [testng] 01:16:56,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:16:56,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:16:56,210 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-30_01-16-56.log] [testng] 01:16:56,210 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b333005 - End of configuration. [testng] [2024-12-30 01:17:14,342] [pool-1-thread-1] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-12-30 01:17:16,358] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-12-30 01:17:27,876] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-12-30 01:17:39,493] [pool-1-thread-4] Initializing /data/tamjid/006003000.flex: [testng] [2024-12-30 01:17:40,710] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-12-30 01:17:42,121] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-12-30 01:17:50,494] [pool-1-thread-9] Initializing /data/qa-7469/002002.flex: [testng] [2024-12-30 01:17:52,410] [pool-1-thread-5] Initializing /data/anatole/001004000.flex: [testng] [2024-12-30 01:17:58,608] [pool-1-thread-6] Initializing /data/stephane/006013000.flex: [testng] [2024-12-30 01:18:03,541] [pool-1-thread-4] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-12-30 01:18:12,136] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-12-30 01:18:13,585] [pool-1-thread-2] Initializing /data/tamjid/006004000.flex: [testng] [2024-12-30 01:18:15,652] [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] [2024-12-30 01:18:33,097] [pool-1-thread-4] Initializing /data/qa-18096/002003001.flex: [testng] [2024-12-30 01:18:43,178] [pool-1-thread-6] Initializing /data/tony/001001000_objects.flex: [testng] [2024-12-30 01:18:45,712] [pool-1-thread-2] Initializing /data/tony/003003000.tiff: [testng] [2024-12-30 01:18:55,576] [pool-1-thread-8] Initializing /data/achim/003003000.flex: [testng] [2024-12-30 01:19:06,742] [pool-1-thread-4] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-12-30 01:19:14,812] [pool-1-thread-5] Initializing /data/tony/test1.flex: [testng] [2024-12-30 01:19:21,120] [pool-1-thread-2] Initializing /data/tony/test.tiff: [testng] [2024-12-30 01:19:28,112] [pool-1-thread-6] Initializing /data/ghislain/test.flex: [testng] [2024-12-30 01:19:39,389] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-12-30 01:20:01,495] [pool-1-thread-8] Initializing /data/tony/003008000.flex: [testng] [2024-12-30 01:20:05,607] [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] [2024-12-30 01:20:13,923] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2024-12-30 01:20:16,113] [pool-1-thread-6] Initializing /data/manuel/003003001.flex: [testng] [2024-12-30 01:20:34,094] [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] [2024-12-30 01:20:42,753] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2024-12-30 01:20:59,607] [pool-1-thread-8] Initializing /data/qa-17190/002002011.flex: [testng] [2024-12-30 01:21:11,973] [pool-1-thread-2] Initializing /data/qa-18096/002002001.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 26 minutes 59 seconds Finished: SUCCESS