Started by upstream project "BIOFORMATS-test-repo" build number 215
originally caused by:
Started by upstream project "Trigger" build number 242
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4
[BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins3612927212893716061.sh
+ '[' flex = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_34096_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] 01:53:20,857 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:53:20,859 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 01:53:20,859 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:53:20,859 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:53:20,860 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:53:20,860 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:53:20,860 |-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] 01:53:20,860 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:53:20,861 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:53:20,861 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:53:20,862 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:53:20,862 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:53:21,020 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:53:21,020 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:53:21,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:53:21,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:53:21,047 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:53:21,047 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:53:21,047 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:53:21,048 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:53:21,048 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 01:53:21,049 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 01:53:21,049 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 188 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-09 01:53:21,057] [main] java.version = 17.0.2
[testng] 01:53:21,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:53:21,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:53:21,101 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-09_01-53-21.log]
[testng] 01:53:21,102 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-10-09 01:53:21,104] [main] testng.directory = /data
[testng] [2024-10-09 01:53:21,104] [main] testng.configDirectory = /config
[testng] [2024-10-09 01:53:21,113] [main] testng.multiplier = 1.0
[testng] [2024-10-09 01:53:21,114] [main] testng.in-memory = false
[testng] [2024-10-09 01:53:21,114] [main] testng.allow-missing = false
[testng] [2024-10-09 01:53:21,114] [main] user.language = en
[testng] [2024-10-09 01:53:21,114] [main] user.country = ${user.country}
[testng] [2024-10-09 01:53:21,114] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-10-09 01:54:54,240] [main] ----------------------------------------
[testng] [2024-10-09 01:54:54,240] [main] Total files: 791
[testng] [2024-10-09 01:54:54,240] [main] Scan time: 93.126 s (117 ms/file)
[testng] [2024-10-09 01:54:54,240] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 42 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-09 02:01:30,345] [pool-1-thread-1] Initializing /data/ghislain/test.flex:
[testng] 02:01:30,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:01:30,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:01:30,347 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-09_02-01-30.log]
[testng] 02:01:30,347 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63dfa38a - End of configuration.
[testng] [2024-10-09 02:01:31,232] [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] 02:01:31,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:01:31,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:01:31,234 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-09_02-01-31.log]
[testng] 02:01:31,234 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b67495b - End of configuration.
[testng] [2024-10-09 02:01:32,120] [pool-1-thread-11] Initializing /data/tony/003008000.flex:
[testng] 02:01:32,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:01:32,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:01:32,121 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-09_02-01-32.log]
[testng] 02:01:32,121 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d312120 - End of configuration.
[testng] [2024-10-09 02:01:33,022] [pool-1-thread-10] Initializing /data/tony/001014000 - from flex.tif:
[testng] 02:01:33,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:01:33,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:01:33,023 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-09_02-01-33.log]
[testng] 02:01:33,024 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18e890e2 - End of configuration.
[testng] [2024-10-09 02:01:34,845] [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] 02:01:34,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:01:34,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:01:34,846 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-09_02-01-34.log]
[testng] 02:01:34,847 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68dfff08 - End of configuration.
[testng] [2024-10-09 02:01:35,716] [pool-1-thread-8] Initializing /data/tamjid/006004000.flex:
[testng] 02:01:35,717 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:01:35,717 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:01:35,717 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-09_02-01-35.log]
[testng] 02:01:35,718 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ef87e45 - End of configuration.
[testng] [2024-10-09 02:01:36,568] [pool-1-thread-7] Initializing /data/public/idr0007/Plate1/001001000.flex:
[testng] 02:01:36,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:01:36,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:01:36,568 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-09_02-01-36.log]
[testng] 02:01:36,569 |-INFO in ch.qos.logback.core.sift.SiftProcessor@368ec75c - End of configuration.
[testng] [2024-10-09 02:01:43,451] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex:
[testng] 02:01:43,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:01:43,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:01:43,452 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-09_02-01-43.log]
[testng] 02:01:43,453 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ae25506 - End of configuration.
[testng] [2024-10-09 02:01:57,211] [pool-1-thread-5] Initializing /data/qa-2983/004007000.flex:
[testng] 02:01:57,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:01:57,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:01:57,212 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-09_02-01-57.log]
[testng] 02:01:57,212 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d632233 - End of configuration.
[testng] [2024-10-09 02:01:58,143] [pool-1-thread-4] Initializing /data/tony/003003000.tiff:
[testng] 02:01:58,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:01:58,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:01:58,144 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-09_02-01-58.log]
[testng] 02:01:58,144 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f82be93 - End of configuration.
[testng] [2024-10-09 02:02:00,352] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex:
[testng] 02:02:00,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:02:00,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:02:00,353 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-09_02-02-00.log]
[testng] 02:02:00,353 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6477d1f3 - End of configuration.
[testng] [2024-10-09 02:02:08,801] [pool-1-thread-2] Initializing /data/manuel/003003001.flex:
[testng] 02:02:08,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:02:08,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:02:08,803 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-09_02-02-08.log]
[testng] 02:02:08,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@692d5e0b - End of configuration.
[testng] [2024-10-09 02:02:23,298] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex:
[testng] [2024-10-09 02:02:31,393] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex:
[testng] [2024-10-09 02:02:32,457] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex:
[testng] [2024-10-09 02:02:33,447] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex:
[testng] [2024-10-09 02:02:34,393] [pool-1-thread-1] Initializing /data/stephane/002007000.flex:
[testng] [2024-10-09 02:02:37,021] [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] [2024-10-09 02:02:40,689] [pool-1-thread-12] Initializing /data/qa-18096/002002001.flex:
[testng] [2024-10-09 02:02:41,775] [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] [2024-10-09 02:02:47,801] [pool-1-thread-5] Initializing /data/tony/test.tiff:
[testng] [2024-10-09 02:02:49,993] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex:
[testng] [2024-10-09 02:02:57,136] [pool-1-thread-2] Initializing /data/tony/001001000_objects.flex:
[testng] [2024-10-09 02:02:58,087] [pool-1-thread-1] Initializing /data/achim/003003000.flex:
[testng] [2024-10-09 02:03:04,687] [pool-1-thread-4] Initializing /data/tamjid/006005000.flex:
[testng] [2024-10-09 02:03:05,887] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex:
[testng] [2024-10-09 02:03:06,984] [pool-1-thread-12] Initializing /data/qa-18096/002003001.flex:
[testng] [2024-10-09 02:03:10,753] [pool-1-thread-5] Initializing /data/anatole/001004000.flex:
[testng] [2024-10-09 02:03:13,793] [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] [2024-10-09 02:03:15,086] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex:
[testng] [2024-10-09 02:03:29,856] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex:
[testng] [2024-10-09 02:03:31,120] [pool-1-thread-12] Initializing /data/stephane/006013000.flex:
[testng] [2024-10-09 02:03:32,672] [pool-1-thread-1] Initializing /data/tony/000101400 - from PE sofwatre.tif:
[testng] [2024-10-09 02:03:38,020] [pool-1-thread-11] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex:
[testng] [2024-10-09 02:03:48,904] [pool-1-thread-1] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex:
[testng] [2024-10-09 02:03:52,221] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex:
[testng] [2024-10-09 02:04:01,018] [pool-1-thread-12] Initializing /data/tony/015002000.tiff:
[testng] [2024-10-09 02:04:06,022] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex:
[testng] [2024-10-09 02:04:14,840] [pool-1-thread-5] Initializing /data/qa-17190/002002011.flex:
[testng] [2024-10-09 02:04:18,100] [pool-1-thread-12] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex:
[testng] [2024-10-09 02:04:31,021] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex:
[testng] [2024-10-09 02:04:46,943] [pool-1-thread-12] 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: 19 minutes 40 seconds
Finished: SUCCESS