Started by upstream project "BIOFORMATS-test-repo" build number 200
originally caused by:
Started by upstream project "Trigger" build number 225
originally caused by:
Started by user devspace
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/jenkins8972692919191470070.sh
+ '[' flex = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_31689_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release
[javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
[javac] 4 warnings
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] 06:49:38,506 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 06:49:38,507 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service.
[testng] 06:49:38,507 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 06:49:38,508 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 06:49:38,509 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 06:49:38,509 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 06:49:38,509 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 06:49:38,509 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 06:49:38,510 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 06:49:38,510 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 06:49:38,511 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 06:49:38,511 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 06:49:38,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 06:49:38,669 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 06:49:38,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 06:49:38,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 06:49:38,699 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 06:49:38,700 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 06:49:38,700 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 06:49:38,700 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 06:49:38,700 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration.
[testng] 06:49:38,701 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point
[testng] 06:49:38,701 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 191 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-09-26 06:49:38,710] [main] java.version = 21
[testng] 06:49:38,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 06:49:38,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:49:38,754 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-26_06-49-38.log]
[testng] 06:49:38,756 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration.
[testng] [2024-09-26 06:49:38,757] [main] testng.directory = /data
[testng] [2024-09-26 06:49:38,757] [main] testng.configDirectory = /config
[testng] [2024-09-26 06:49:38,766] [main] testng.multiplier = 1.0
[testng] [2024-09-26 06:49:38,767] [main] testng.in-memory = false
[testng] [2024-09-26 06:49:38,767] [main] testng.allow-missing = false
[testng] [2024-09-26 06:49:38,767] [main] user.language = en
[testng] [2024-09-26 06:49:38,767] [main] user.country = ${user.country}
[testng] [2024-09-26 06:49:38,767] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-09-26 06:49:59,940] [main] ----------------------------------------
[testng] [2024-09-26 06:49:59,940] [main] Total files: 791
[testng] [2024-09-26 06:49:59,940] [main] Scan time: 21.173 s (26 ms/file)
[testng] [2024-09-26 06:49:59,941] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 42 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-09-26 06:54:31,394] [pool-1-thread-1] Initializing /data/qa-18096/002003001.flex:
[testng] 06:54:31,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 06:54:31,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:54:31,396 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-26_06-54-31.log]
[testng] 06:54:31,396 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7685b6a - End of configuration.
[testng] [2024-09-26 06:54:31,901] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex:
[testng] 06:54:31,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 06:54:31,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:54:31,902 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-26_06-54-31.log]
[testng] 06:54:31,902 |-INFO in ch.qos.logback.core.sift.SiftProcessor@164d047f - End of configuration.
[testng] [2024-09-26 06:54:32,432] [pool-1-thread-11] Initializing /data/stephane/002007000.flex:
[testng] 06:54:32,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 06:54:32,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:54:32,433 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-26_06-54-32.log]
[testng] 06:54:32,433 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b0ca4ce - End of configuration.
[testng] [2024-09-26 06:54:32,943] [pool-1-thread-10] Initializing /data/public/idr0007/Plate1/001001000.flex:
[testng] 06:54:32,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 06:54:32,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:54:32,944 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-26_06-54-32.log]
[testng] 06:54:32,945 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2473ee6e - End of configuration.
[testng] [2024-09-26 06:54:37,179] [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] 06:54:37,180 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 06:54:37,180 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:54:37,181 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-26_06-54-37.log]
[testng] 06:54:37,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b0843e7 - End of configuration.
[testng] [2024-09-26 06:54:37,851] [pool-1-thread-8] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex:
[testng] 06:54:37,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 06:54:37,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:54:37,852 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-26_06-54-37.log]
[testng] 06:54:37,852 |-INFO in ch.qos.logback.core.sift.SiftProcessor@201b561d - End of configuration.
[testng] [2024-09-26 06:54:39,273] [pool-1-thread-7] Initializing /data/tony/test.tiff:
[testng] 06:54:39,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 06:54:39,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:54:39,273 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-26_06-54-39.log]
[testng] 06:54:39,274 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9215979 - End of configuration.
[testng] [2024-09-26 06:54:40,862] [pool-1-thread-6] Initializing /data/tamjid/006005000.flex:
[testng] 06:54:40,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 06:54:40,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:54:40,862 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-26_06-54-40.log]
[testng] 06:54:40,863 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d0e5c37 - End of configuration.
[testng] [2024-09-26 06:54:41,606] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex:
[testng] 06:54:41,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 06:54:41,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:54:41,607 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-26_06-54-41.log]
[testng] 06:54:41,607 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c989f40 - End of configuration.
[testng] [2024-09-26 06:54:42,406] [pool-1-thread-4] Initializing /data/qa-18096/002002001.flex:
[testng] 06:54:42,407 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 06:54:42,407 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:54:42,407 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-26_06-54-42.log]
[testng] 06:54:42,408 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45b26946 - End of configuration.
[testng] [2024-09-26 06:54:43,101] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex:
[testng] 06:54:43,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 06:54:43,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:54:43,102 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-26_06-54-43.log]
[testng] 06:54:43,102 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33d8a3e4 - End of configuration.
[testng] [2024-09-26 06:54:49,729] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex:
[testng] 06:54:49,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 06:54:49,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:54:49,731 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-26_06-54-49.log]
[testng] 06:54:49,731 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20ea61b1 - End of configuration.
[testng] [2024-09-26 06:55:09,457] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex:
[testng] [2024-09-26 06:55:11,118] [pool-1-thread-6] Initializing /data/achim/003003000.flex:
[testng] [2024-09-26 06:55:12,342] [pool-1-thread-11] Initializing /data/tony/000101400 - from PE sofwatre.tif:
[testng] [2024-09-26 06:55:14,780] [pool-1-thread-5] Initializing /data/anatole/001004000.flex:
[testng] [2024-09-26 06:55:16,279] [pool-1-thread-4] Initializing /data/qa-2983/004007000.flex:
[testng] [2024-09-26 06:55:17,399] [pool-1-thread-1] Initializing /data/qa-17190/002002011.flex:
[testng] [2024-09-26 06:55:24,839] [pool-1-thread-12] Initializing /data/tony/001001000_objects.flex:
[testng] [2024-09-26 06:55:29,465] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex:
[testng] [2024-09-26 06:55:30,553] [pool-1-thread-1] Initializing /data/ghislain/test.flex:
[testng] [2024-09-26 06:55:31,586] [pool-1-thread-4] Initializing /data/tony/003003000.tiff:
[testng] [2024-09-26 06:55:37,581] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex:
[testng] [2024-09-26 06:55:46,276] [pool-1-thread-9] Initializing /data/manuel/003003001.flex:
[testng] [2024-09-26 06:55:47,266] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex:
[testng] [2024-09-26 06:55:55,270] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex:
[testng] [2024-09-26 06:56:01,349] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex:
[testng] [2024-09-26 06:56:04,304] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex:
[testng] [2024-09-26 06:56:08,325] [pool-1-thread-5] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex:
[testng] [2024-09-26 06:56:10,032] [pool-1-thread-11] Initializing /data/tamjid/006003000.flex:
[testng] [2024-09-26 06:56:21,731] [pool-1-thread-4] Initializing /data/tony/001014000 - from flex.tif:
[testng] [2024-09-26 06:56:23,641] [pool-1-thread-11] Initializing /data/tony/test1.flex:
[testng] [2024-09-26 06:56:24,548] [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] [2024-09-26 06:56:25,557] [pool-1-thread-1] Initializing /data/stephane/006013000.flex:
[testng] [2024-09-26 06:56:26,612] [pool-1-thread-9] Initializing /data/tony/003008000.flex:
[testng] [2024-09-26 06:56:34,910] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex:
[testng] [2024-09-26 06:56:37,925] [pool-1-thread-11] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex:
[testng] [2024-09-26 06:56:43,993] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex:
[testng] [2024-09-26 06:56:54,957] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex:
[testng] [2024-09-26 06:57:04,744] [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] [2024-09-26 06:57:07,996] [pool-1-thread-9] Initializing /data/tony/015002000.tiff:
[testng] [2024-09-26 06:57:15,368] [pool-1-thread-11] Initializing /data/tamjid/006004000.flex:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2226, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 15 minutes 0 seconds
Finished: SUCCESS