Started by upstream project "BIOFORMATS-test-repo" build number 259
originally caused by:
Started by upstream project "Trigger" build number 283
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5
[BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins6420257923243281060.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_40849_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] 00:49:33,523 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 00:49:33,525 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service.
[testng] 00:49:33,525 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:49:33,526 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:49:33,527 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:49:33,527 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:49:33,527 |-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] 00:49:33,527 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:49:33,527 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:49:33,528 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:49:33,528 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:49:33,528 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:49:33,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:49:33,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:49:33,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:49:33,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:49:33,796 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:49:33,796 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:49:33,796 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:49:33,797 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:49:33,797 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration.
[testng] 00:49:33,798 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point
[testng] 00:49:33,798 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 271 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-18 00:49:33,808] [main] java.version = 1.8.0_342
[testng] 00:49:33,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:49:33,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:49:33,860 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-18_00-49-33.log]
[testng] 00:49:33,862 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration.
[testng] [2024-11-18 00:49:33,864] [main] testng.directory = /data
[testng] [2024-11-18 00:49:33,864] [main] testng.configDirectory = /config
[testng] [2024-11-18 00:49:33,877] [main] testng.multiplier = 1.0
[testng] [2024-11-18 00:49:33,877] [main] testng.in-memory = false
[testng] [2024-11-18 00:49:33,877] [main] testng.allow-missing = false
[testng] [2024-11-18 00:49:33,878] [main] user.language = fr
[testng] [2024-11-18 00:49:33,878] [main] user.country = FR
[testng] [2024-11-18 00:49:33,878] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-11-18 00:50:02,049] [main] ----------------------------------------
[testng] [2024-11-18 00:50:02,049] [main] Total files: 791
[testng] [2024-11-18 00:50:02,049] [main] Scan time: 28.171 s (35 ms/file)
[testng] [2024-11-18 00:50:02,049] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 42 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-18 00:54:30,257] [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] 00:54:30,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:54:30,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:54:30,258 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-18_00-54-30.log]
[testng] 00:54:30,259 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73ae13b0 - End of configuration.
[testng] [2024-11-18 00:54:30,866] [pool-1-thread-12] Initializing /data/tamjid/006004000.flex:
[testng] 00:54:30,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:54:30,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:54:30,868 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-18_00-54-30.log]
[testng] 00:54:30,868 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21c4f224 - End of configuration.
[testng] [2024-11-18 00:54:31,404] [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] 00:54:31,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:54:31,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:54:31,406 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-18_00-54-31.log]
[testng] 00:54:31,406 |-INFO in ch.qos.logback.core.sift.SiftProcessor@524827bd - End of configuration.
[testng] [2024-11-18 00:54:31,994] [pool-1-thread-10] Initializing /data/manuel/003003001.flex:
[testng] 00:54:31,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:54:31,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:54:31,995 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-18_00-54-31.log]
[testng] 00:54:31,995 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3273d65 - End of configuration.
[testng] [2024-11-18 00:54:32,581] [pool-1-thread-9] Initializing /data/stephane/006013000.flex:
[testng] 00:54:32,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:54:32,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:54:32,583 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-18_00-54-32.log]
[testng] 00:54:32,583 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22b399a7 - End of configuration.
[testng] [2024-11-18 00:54:33,135] [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] 00:54:33,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:54:33,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:54:33,136 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-18_00-54-33.log]
[testng] 00:54:33,136 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32c2c412 - End of configuration.
[testng] [2024-11-18 00:54:33,688] [pool-1-thread-7] Initializing /data/qa-17190/002002011.flex:
[testng] 00:54:33,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:54:33,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:54:33,689 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-18_00-54-33.log]
[testng] 00:54:33,689 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a9ba184 - End of configuration.
[testng] [2024-11-18 00:54:34,247] [pool-1-thread-6] Initializing /data/tony/001001000_objects.flex:
[testng] 00:54:34,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:54:34,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:54:34,248 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-18_00-54-34.log]
[testng] 00:54:34,249 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d2a0409 - End of configuration.
[testng] [2024-11-18 00:54:34,833] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex:
[testng] 00:54:34,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:54:34,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:54:34,835 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-18_00-54-34.log]
[testng] 00:54:34,836 |-INFO in ch.qos.logback.core.sift.SiftProcessor@653b4893 - End of configuration.
[testng] [2024-11-18 00:54:39,185] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex:
[testng] 00:54:39,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:54:39,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:54:39,186 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-18_00-54-39.log]
[testng] 00:54:39,186 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c548639 - End of configuration.
[testng] [2024-11-18 00:54:43,674] [pool-1-thread-3] Initializing /data/tony/001014000 - from flex.tif:
[testng] 00:54:43,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:54:43,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:54:43,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-18_00-54-43.log]
[testng] 00:54:43,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@510eb298 - End of configuration.
[testng] [2024-11-18 00:54:45,076] [pool-1-thread-2] Initializing /data/tony/test.tiff:
[testng] 00:54:45,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:54:45,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:54:45,077 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-18_00-54-45.log]
[testng] 00:54:45,077 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ebcd880 - End of configuration.
[testng] [2024-11-18 00:54:56,308] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex:
[testng] [2024-11-18 00:54:57,066] [pool-1-thread-7] Initializing /data/ghislain/test.flex:
[testng] [2024-11-18 00:54:57,696] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex:
[testng] [2024-11-18 00:55:02,433] [pool-1-thread-12] Initializing /data/tony/000101400 - from PE sofwatre.tif:
[testng] [2024-11-18 00:55:03,673] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex:
[testng] [2024-11-18 00:55:08,536] [pool-1-thread-1] Initializing /data/tony/test1.flex:
[testng] [2024-11-18 00:55:09,234] [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] [2024-11-18 00:55:09,971] [pool-1-thread-9] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex:
[testng] [2024-11-18 00:55:14,919] [pool-1-thread-11] Initializing /data/qa-7469/002002.flex:
[testng] [2024-11-18 00:55:15,715] [pool-1-thread-12] Initializing /data/achim/003003000.flex:
[testng] [2024-11-18 00:55:16,637] [pool-1-thread-10] Initializing /data/qa-18096/002003001.flex:
[testng] [2024-11-18 00:55:17,395] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex:
[testng] [2024-11-18 00:55:23,706] [pool-1-thread-7] Initializing /data/tony/015002000.tiff:
[testng] [2024-11-18 00:55:29,466] [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] [2024-11-18 00:55:35,311] [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] [2024-11-18 00:55:36,463] [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] [2024-11-18 00:55:38,854] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex:
[testng] [2024-11-18 00:55:39,780] [pool-1-thread-7] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex:
[testng] [2024-11-18 00:55:45,167] [pool-1-thread-12] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex:
[testng] [2024-11-18 00:55:50,001] [pool-1-thread-1] Initializing /data/anatole/001004000.flex:
[testng] [2024-11-18 00:55:54,152] [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] [2024-11-18 00:55:55,102] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex:
[testng] [2024-11-18 00:56:03,044] [pool-1-thread-10] Initializing /data/tamjid/006003000.flex:
[testng] [2024-11-18 00:56:03,912] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex:
[testng] [2024-11-18 00:56:17,956] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex:
[testng] [2024-11-18 00:56:29,267] [pool-1-thread-10] Initializing /data/stephane/002007000.flex:
[testng] [2024-11-18 00:56:30,489] [pool-1-thread-8] Initializing /data/qa-18096/002002001.flex:
[testng] [2024-11-18 00:56:34,279] [pool-1-thread-1] Initializing /data/tamjid/006005000.flex:
[testng] [2024-11-18 00:56:42,413] [pool-1-thread-8] Initializing /data/tony/003003000.tiff:
[testng] [2024-11-18 00:56:44,341] [pool-1-thread-10] 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 42 seconds
Finished: SUCCESS