Started by upstream project "BIOFORMATS-test-repo" build number 84
originally caused by:
Started by upstream project "Trigger" build number 95
originally caused by:
Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7
[BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins436734264110073167.sh
+ '[' flex = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_12822_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 09:06:21,409 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 09:06:21,411 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service.
[testng] 09:06:21,411 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 09:06:21,412 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 09:06:21,412 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 09:06:21,413 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 09:06:21,413 |-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] 09:06:21,413 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 09:06:21,413 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 09:06:21,414 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 09:06:21,414 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 09:06:21,415 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 09:06:21,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 09:06:21,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 09:06:21,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 09:06:21,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 09:06:21,626 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 09:06:21,626 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 09:06:21,627 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 09:06:21,627 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 09:06:21,627 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration.
[testng] 09:06:21,628 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point
[testng] 09:06:21,628 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 215 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-06 09:06:21,638] [main] java.version = 21
[testng] 09:06:21,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 09:06:21,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:06:21,685 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-06_09-06-21.log]
[testng] 09:06:21,687 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration.
[testng] [2024-06-06 09:06:21,689] [main] testng.directory = /data
[testng] [2024-06-06 09:06:21,689] [main] testng.configDirectory = /config
[testng] [2024-06-06 09:06:21,698] [main] testng.multiplier = 1.0
[testng] [2024-06-06 09:06:21,699] [main] testng.in-memory = false
[testng] [2024-06-06 09:06:21,699] [main] testng.allow-missing = false
[testng] [2024-06-06 09:06:21,699] [main] user.language = en
[testng] [2024-06-06 09:06:21,700] [main] user.country = ${user.country}
[testng] [2024-06-06 09:06:21,700] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-06-06 09:06:36,082] [main] ----------------------------------------
[testng] [2024-06-06 09:06:36,082] [main] Total files: 791
[testng] [2024-06-06 09:06:36,083] [main] Scan time: 14.382 s (18 ms/file)
[testng] [2024-06-06 09:06:36,083] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 42 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-06 09:12:24,722] [pool-1-thread-1] Initializing /data/tony/000101400 - from PE sofwatre.tif:
[testng] 09:12:24,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 09:12:24,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:12:24,725 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-06_09-12-24.log]
[testng] 09:12:24,725 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3828a3b6 - End of configuration.
[testng] [2024-06-06 09:12:24,785] [pool-1-thread-12] Initializing /data/tamjid/006003000.flex:
[testng] 09:12:24,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 09:12:24,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:12:24,786 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-06_09-12-24.log]
[testng] 09:12:24,787 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56db8742 - End of configuration.
[testng] [2024-06-06 09:12:24,829] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex:
[testng] 09:12:24,829 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 09:12:24,829 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:12:24,830 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-06_09-12-24.log]
[testng] 09:12:24,830 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7055fa48 - End of configuration.
[testng] [2024-06-06 09:12:24,880] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex:
[testng] 09:12:24,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 09:12:24,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:12:24,881 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-06_09-12-24.log]
[testng] 09:12:24,882 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e9d855 - End of configuration.
[testng] [2024-06-06 09:12:24,952] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex:
[testng] 09:12:24,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 09:12:24,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:12:24,953 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-06_09-12-24.log]
[testng] 09:12:24,953 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7084f9b8 - End of configuration.
[testng] [2024-06-06 09:12:24,999] [pool-1-thread-8] Initializing /data/tony/test1.flex:
[testng] 09:12:25,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 09:12:25,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:12:25,001 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-06_09-12-25.log]
[testng] 09:12:25,001 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7676f92a - End of configuration.
[testng] [2024-06-06 09:12:25,031] [pool-1-thread-7] Initializing /data/tony/001014000 - from flex.tif:
[testng] 09:12:25,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 09:12:25,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:12:25,032 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-06_09-12-25.log]
[testng] 09:12:25,032 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b334369 - End of configuration.
[testng] [2024-06-06 09:12:25,128] [pool-1-thread-6] Initializing /data/tamjid/006005000.flex:
[testng] 09:12:25,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 09:12:25,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:12:25,129 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-06_09-12-25.log]
[testng] 09:12:25,129 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f5eb0ce - End of configuration.
[testng] [2024-06-06 09:12:25,153] [pool-1-thread-5] Initializing /data/stephane/006013000.flex:
[testng] 09:12:25,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 09:12:25,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:12:25,155 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-06_09-12-25.log]
[testng] 09:12:25,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@742da30 - End of configuration.
[testng] [2024-06-06 09:12:25,210] [pool-1-thread-4] Initializing /data/achim/003003000.flex:
[testng] 09:12:25,210 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 09:12:25,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:12:25,211 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-06_09-12-25.log]
[testng] 09:12:25,212 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a5a2ede - End of configuration.
[testng] [2024-06-06 09:12:25,339] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex:
[testng] 09:12:25,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 09:12:25,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:12:25,340 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-06_09-12-25.log]
[testng] 09:12:25,341 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5afacdd7 - End of configuration.
[testng] [2024-06-06 09:12:25,395] [pool-1-thread-2] Initializing /data/ghislain/test.flex:
[testng] 09:12:25,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 09:12:25,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:12:25,395 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-06_09-12-25.log]
[testng] 09:12:25,396 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f035dac - End of configuration.
[testng] [2024-06-06 09:12:27,501] [pool-1-thread-6] Initializing /data/tony/003003000.tiff:
[testng] [2024-06-06 09:12:27,597] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex:
[testng] [2024-06-06 09:12:27,625] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex:
[testng] [2024-06-06 09:12:27,682] [pool-1-thread-12] Initializing /data/tony/001001000_objects.flex:
[testng] [2024-06-06 09:12:27,721] [pool-1-thread-1] Initializing /data/tamjid/006004000.flex:
[testng] [2024-06-06 09:12:27,754] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex:
[testng] [2024-06-06 09:12:27,799] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex:
[testng] [2024-06-06 09:12:28,255] [pool-1-thread-3] Initializing /data/manuel/003003001.flex:
[testng] [2024-06-06 09:12:28,380] [pool-1-thread-9] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex:
[testng] [2024-06-06 09:12:28,686] [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] [2024-06-06 09:12:29,139] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex:
[testng] [2024-06-06 09:12:29,779] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex:
[testng] [2024-06-06 09:12:29,938] [pool-1-thread-6] Initializing /data/qa-18096/002003001.flex:
[testng] [2024-06-06 09:12:29,984] [pool-1-thread-7] Initializing /data/qa-17190/002002011.flex:
[testng] [2024-06-06 09:12:30,018] [pool-1-thread-4] Initializing /data/qa-7469/002002.flex:
[testng] [2024-06-06 09:12:30,390] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex:
[testng] [2024-06-06 09:12:30,429] [pool-1-thread-7] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex:
[testng] [2024-06-06 09:12:30,554] [pool-1-thread-11] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex:
[testng] [2024-06-06 09:12:30,597] [pool-1-thread-6] Initializing /data/anatole/001004000.flex:
[testng] [2024-06-06 09:12:30,663] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex:
[testng] [2024-06-06 09:12:31,545] [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] [2024-06-06 09:12:31,782] [pool-1-thread-5] Initializing /data/tony/015002000.tiff:
[testng] [2024-06-06 09:12:32,059] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex:
[testng] [2024-06-06 09:12:32,939] [pool-1-thread-5] Initializing /data/tony/003008000.flex:
[testng] [2024-06-06 09:12:33,002] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex:
[testng] [2024-06-06 09:12:33,576] [pool-1-thread-8] Initializing /data/public/idr0007/Plate1/001001000.flex:
[testng] [2024-06-06 09:12:33,868] [pool-1-thread-10] Initializing /data/qa-18096/002002001.flex:
[testng] [2024-06-06 09:12:34,422] [pool-1-thread-10] Initializing /data/stephane/002007000.flex:
[testng] [2024-06-06 09:12:35,217] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex:
[testng] [2024-06-06 09:12:35,947] [pool-1-thread-10] Initializing /data/tony/test.tiff:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2226, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 9 minutes 18 seconds
Finished: SUCCESS