Started by upstream project "BIOFORMATS-test-repo" build number 230 originally caused by: Started by upstream project "Trigger" build number 255 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins13002262503803490458.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_36092_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] 01:48:53,052 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:48:53,054 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 01:48:53,054 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:48:53,055 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:48:53,055 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:48:53,055 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:48:53,055 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:48:53,055 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:48:53,056 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:48:53,056 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:48:53,056 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:48:53,056 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:48:53,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:48:53,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:48:53,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:48:53,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:48:53,300 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:48:53,300 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:48:53,300 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:48:53,300 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:48:53,300 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 01:48:53,301 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 01:48:53,301 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 245 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-21 01:48:53,311] [main] java.version = 1.8.0_342 [testng] 01:48:53,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:48:53,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:53,358 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-21_01-48-53.log] [testng] 01:48:53,359 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-21 01:48:53,361] [main] testng.directory = /data [testng] [2024-10-21 01:48:53,362] [main] testng.configDirectory = /config [testng] [2024-10-21 01:48:53,377] [main] testng.multiplier = 1.0 [testng] [2024-10-21 01:48:53,378] [main] testng.in-memory = false [testng] [2024-10-21 01:48:53,378] [main] testng.allow-missing = false [testng] [2024-10-21 01:48:53,378] [main] user.language = fr [testng] [2024-10-21 01:48:53,378] [main] user.country = FR [testng] [2024-10-21 01:48:53,378] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-21 01:49:20,758] [main] ---------------------------------------- [testng] [2024-10-21 01:49:20,759] [main] Total files: 791 [testng] [2024-10-21 01:49:20,759] [main] Scan time: 27.38 s (34 ms/file) [testng] [2024-10-21 01:49:20,759] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-21 01:54:02,390] [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] 01:54:02,391 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:54:02,391 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:02,393 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-21_01-54-02.log] [testng] 01:54:02,393 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44917f64 - End of configuration. [testng] [2024-10-21 01:54:03,048] [pool-1-thread-12] Initializing /data/tamjid/006004000.flex: [testng] 01:54:03,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:54:03,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:03,049 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-21_01-54-03.log] [testng] 01:54:03,049 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18ab729e - End of configuration. [testng] [2024-10-21 01:54:03,681] [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] 01:54:03,681 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:54:03,681 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:03,682 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-21_01-54-03.log] [testng] 01:54:03,683 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f4c40ae - End of configuration. [testng] [2024-10-21 01:54:04,364] [pool-1-thread-10] Initializing /data/manuel/003003001.flex: [testng] 01:54:04,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:54:04,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:04,366 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-21_01-54-04.log] [testng] 01:54:04,367 |-INFO in ch.qos.logback.core.sift.SiftProcessor@349bca3 - End of configuration. [testng] [2024-10-21 01:54:05,034] [pool-1-thread-9] Initializing /data/stephane/006013000.flex: [testng] 01:54:05,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:54:05,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:05,036 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-21_01-54-05.log] [testng] 01:54:05,036 |-INFO in ch.qos.logback.core.sift.SiftProcessor@dd919c1 - End of configuration. [testng] [2024-10-21 01:54:05,665] [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] 01:54:05,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:54:05,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:05,666 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-21_01-54-05.log] [testng] 01:54:05,666 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b3b401e - End of configuration. [testng] [2024-10-21 01:54:06,271] [pool-1-thread-7] Initializing /data/qa-17190/002002011.flex: [testng] 01:54:06,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:54:06,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:06,272 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-21_01-54-06.log] [testng] 01:54:06,273 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7af017db - End of configuration. [testng] [2024-10-21 01:54:06,906] [pool-1-thread-6] Initializing /data/tony/001001000_objects.flex: [testng] 01:54:06,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:54:06,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:06,907 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-21_01-54-06.log] [testng] 01:54:06,907 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bd9c7df - End of configuration. [testng] [2024-10-21 01:54:07,547] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] 01:54:07,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:54:07,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:07,548 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-21_01-54-07.log] [testng] 01:54:07,548 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49ab3002 - End of configuration. [testng] [2024-10-21 01:54:12,093] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 01:54:12,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:54:12,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:12,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-21_01-54-12.log] [testng] 01:54:12,094 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d63f7c5 - End of configuration. [testng] [2024-10-21 01:54:17,545] [pool-1-thread-3] Initializing /data/tony/001014000 - from flex.tif: [testng] 01:54:17,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:54:17,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:17,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-21_01-54-17.log] [testng] 01:54:17,547 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f6557de - End of configuration. [testng] [2024-10-21 01:54:18,963] [pool-1-thread-2] Initializing /data/tony/test.tiff: [testng] 01:54:18,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:54:18,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:18,964 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-21_01-54-18.log] [testng] 01:54:18,964 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c30feb - End of configuration. [testng] [2024-10-21 01:54:29,445] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex: [testng] [2024-10-21 01:54:30,257] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-10-21 01:54:35,408] [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] [2024-10-21 01:54:36,509] [pool-1-thread-12] Initializing /data/ghislain/test.flex: [testng] [2024-10-21 01:54:37,308] [pool-1-thread-6] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-10-21 01:54:42,976] [pool-1-thread-9] Initializing /data/tony/test1.flex: [testng] [2024-10-21 01:54:43,759] [pool-1-thread-8] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-10-21 01:54:45,355] [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] [2024-10-21 01:54:47,134] [pool-1-thread-3] Initializing /data/qa-7469/002002.flex: [testng] [2024-10-21 01:54:49,022] [pool-1-thread-6] Initializing /data/achim/003003000.flex: [testng] [2024-10-21 01:54:49,928] [pool-1-thread-11] Initializing /data/qa-18096/002003001.flex: [testng] [2024-10-21 01:54:51,876] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-10-21 01:54:58,649] [pool-1-thread-12] Initializing /data/tony/015002000.tiff: [testng] [2024-10-21 01:55:04,721] [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] [2024-10-21 01:55:05,703] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-10-21 01:55:07,848] [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] [2024-10-21 01:55:08,994] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-10-21 01:55:12,164] [pool-1-thread-6] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-10-21 01:55:12,958] [pool-1-thread-12] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-10-21 01:55:21,654] [pool-1-thread-9] Initializing /data/anatole/001004000.flex: [testng] [2024-10-21 01:55:24,538] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-10-21 01:55:25,319] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-10-21 01:55:31,415] [pool-1-thread-6] Initializing /data/tamjid/006003000.flex: [testng] [2024-10-21 01:55:34,472] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-10-21 01:55:48,207] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-10-21 01:55:55,757] [pool-1-thread-3] Initializing /data/stephane/002007000.flex: [testng] [2024-10-21 01:55:59,040] [pool-1-thread-1] Initializing /data/qa-18096/002002001.flex: [testng] [2024-10-21 01:56:04,485] [pool-1-thread-9] Initializing /data/tamjid/006005000.flex: [testng] [2024-10-21 01:56:08,200] [pool-1-thread-3] Initializing /data/tony/003003000.tiff: [testng] [2024-10-21 01:56:10,873] [pool-1-thread-1] 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: 12 minutes 35 seconds Finished: SUCCESS