Started by upstream project "BIOFORMATS-test-repo" build number 276 originally caused by: Started by upstream project "Trigger" build number 297 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/jenkins1858299782188311689.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_43508_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] 00:51:19,153 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:51:19,155 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:51:19,155 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:51:19,156 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:51:19,157 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:51:19,157 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:51:19,157 |-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] 00:51:19,157 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:51:19,158 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:51:19,158 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:51:19,158 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:51:19,158 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:51:19,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:51:19,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:51:19,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:51:19,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:51:19,463 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:51:19,464 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:51:19,464 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:51:19,464 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:51:19,464 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:51:19,465 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:51:19,465 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 308 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-02 00:51:19,476] [main] java.version = 1.8.0_342 [testng] 00:51:19,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:51:19,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:19,534 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-02_00-51-19.log] [testng] 00:51:19,536 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-02 00:51:19,539] [main] testng.directory = /data [testng] [2024-12-02 00:51:19,539] [main] testng.configDirectory = /config [testng] [2024-12-02 00:51:19,553] [main] testng.multiplier = 1.0 [testng] [2024-12-02 00:51:19,554] [main] testng.in-memory = false [testng] [2024-12-02 00:51:19,554] [main] testng.allow-missing = false [testng] [2024-12-02 00:51:19,554] [main] user.language = fr [testng] [2024-12-02 00:51:19,554] [main] user.country = FR [testng] [2024-12-02 00:51:19,554] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-02 00:51:53,625] [main] ---------------------------------------- [testng] [2024-12-02 00:51:53,625] [main] Total files: 791 [testng] [2024-12-02 00:51:53,625] [main] Scan time: 34.071 s (43 ms/file) [testng] [2024-12-02 00:51:53,626] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-02 00:56:29,572] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] 00:56:29,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:56:29,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:29,573 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-02_00-56-29.log] [testng] 00:56:29,574 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bf98fda - End of configuration. [testng] [2024-12-02 00:56:30,280] [pool-1-thread-12] Initializing /data/tamjid/006004000.flex: [testng] 00:56:30,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:56:30,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:30,282 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-02_00-56-30.log] [testng] 00:56:30,283 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34950e94 - End of configuration. [testng] [2024-12-02 00:56:30,961] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] 00:56:30,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:56:30,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:30,963 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-02_00-56-30.log] [testng] 00:56:30,963 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4459a37e - End of configuration. [testng] [2024-12-02 00:56:31,696] [pool-1-thread-10] Initializing /data/manuel/003003001.flex: [testng] 00:56:31,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:56:31,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:31,697 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-02_00-56-31.log] [testng] 00:56:31,697 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f78d59b - End of configuration. [testng] [2024-12-02 00:56:32,450] [pool-1-thread-9] Initializing /data/stephane/006013000.flex: [testng] 00:56:32,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:56:32,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:32,452 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-02_00-56-32.log] [testng] 00:56:32,452 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6146efb7 - End of configuration. [testng] [2024-12-02 00:56:33,144] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] 00:56:33,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:56:33,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:33,145 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-02_00-56-33.log] [testng] 00:56:33,145 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d8773cf - End of configuration. [testng] [2024-12-02 00:56:33,863] [pool-1-thread-7] Initializing /data/qa-17190/002002011.flex: [testng] 00:56:33,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:56:33,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:33,864 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-02_00-56-33.log] [testng] 00:56:33,865 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13135fc7 - End of configuration. [testng] [2024-12-02 00:56:34,544] [pool-1-thread-6] Initializing /data/tony/001001000_objects.flex: [testng] 00:56:34,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:56:34,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:34,545 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-02_00-56-34.log] [testng] 00:56:34,545 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fa2fbb6 - End of configuration. [testng] [2024-12-02 00:56:35,233] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] 00:56:35,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:56:35,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:35,234 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-02_00-56-35.log] [testng] 00:56:35,235 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58b31e17 - End of configuration. [testng] [2024-12-02 00:56:40,795] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 00:56:40,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:56:40,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:40,796 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-02_00-56-40.log] [testng] 00:56:40,797 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32f3a8ea - End of configuration. [testng] [2024-12-02 00:56:46,551] [pool-1-thread-3] Initializing /data/tony/001014000 - from flex.tif: [testng] 00:56:46,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:56:46,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:46,553 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-02_00-56-46.log] [testng] 00:56:46,553 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38e2e727 - End of configuration. [testng] [2024-12-02 00:56:48,147] [pool-1-thread-2] Initializing /data/tony/test.tiff: [testng] 00:56:48,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:56:48,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:48,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-02_00-56-48.log] [testng] 00:56:48,148 |-INFO in ch.qos.logback.core.sift.SiftProcessor@732354e5 - End of configuration. [testng] [2024-12-02 00:57:00,339] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex: [testng] [2024-12-02 00:57:01,096] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-12-02 00:57:06,455] [pool-1-thread-12] Initializing /data/ghislain/test.flex: [testng] [2024-12-02 00:57:07,151] [pool-1-thread-6] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-12-02 00:57:08,692] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-12-02 00:57:14,219] [pool-1-thread-1] Initializing /data/tony/test1.flex: [testng] [2024-12-02 00:57:15,108] [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] [2024-12-02 00:57:16,107] [pool-1-thread-9] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-12-02 00:57:17,982] [pool-1-thread-11] Initializing /data/qa-7469/002002.flex: [testng] [2024-12-02 00:57:22,196] [pool-1-thread-6] Initializing /data/achim/003003000.flex: [testng] [2024-12-02 00:57:24,176] [pool-1-thread-3] Initializing /data/qa-18096/002003001.flex: [testng] [2024-12-02 00:57:25,208] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-12-02 00:57:32,858] [pool-1-thread-12] Initializing /data/tony/015002000.tiff: [testng] [2024-12-02 00:57:36,068] [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] [2024-12-02 00:57:41,243] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-12-02 00:57:43,525] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-12-02 00:57:47,633] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-12-02 00:57:48,557] [pool-1-thread-12] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-12-02 00:57:49,482] [pool-1-thread-6] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-12-02 00:57:55,573] [pool-1-thread-1] Initializing /data/anatole/001004000.flex: [testng] [2024-12-02 00:58:00,654] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-12-02 00:58:02,448] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-12-02 00:58:10,618] [pool-1-thread-7] Initializing /data/tamjid/006003000.flex: [testng] [2024-12-02 00:58:12,658] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-12-02 00:58:22,108] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-12-02 00:58:32,190] [pool-1-thread-8] Initializing /data/stephane/002007000.flex: [testng] [2024-12-02 00:58:36,161] [pool-1-thread-7] Initializing /data/qa-18096/002002001.flex: [testng] [2024-12-02 00:58:38,740] [pool-1-thread-1] Initializing /data/tamjid/006005000.flex: [testng] [2024-12-02 00:58:45,829] [pool-1-thread-8] Initializing /data/tony/003003000.tiff: [testng] [2024-12-02 00:58:47,855] [pool-1-thread-9] Initializing /data/tony/003008000.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 13 minutes 12 seconds Finished: SUCCESS