Started by upstream project "BIOFORMATS-test-repo" build number 236
originally caused by:
Started by upstream project "Trigger" build number 261
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8
[BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins16750661188278721103.sh
+ '[' flex = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_37077_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] 01:50:07,601 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:50:07,602 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 01:50:07,602 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:50:07,603 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:50:07,604 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:50:07,604 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:50:07,605 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:50:07,605 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:50:07,605 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:50:07,606 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:50:07,606 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:50:07,606 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:50:07,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:50:07,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:50:07,835 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:50:07,835 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:50:07,841 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:50:07,841 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:50:07,841 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:50:07,842 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:50:07,842 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 01:50:07,843 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 01:50:07,843 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 238 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-27 01:50:07,852] [main] java.version = 17.0.2
[testng] 01:50:07,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:50:07,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:50:07,900 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-27_01-50-07.log]
[testng] 01:50:07,901 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-10-27 01:50:07,904] [main] testng.directory = /data
[testng] [2024-10-27 01:50:07,904] [main] testng.configDirectory = /config
[testng] [2024-10-27 01:50:07,913] [main] testng.multiplier = 1.0
[testng] [2024-10-27 01:50:07,914] [main] testng.in-memory = false
[testng] [2024-10-27 01:50:07,914] [main] testng.allow-missing = false
[testng] [2024-10-27 01:50:07,914] [main] user.language = en
[testng] [2024-10-27 01:50:07,914] [main] user.country = ${user.country}
[testng] [2024-10-27 01:50:07,914] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-10-27 01:50:51,720] [main] ----------------------------------------
[testng] [2024-10-27 01:50:51,720] [main] Total files: 791
[testng] [2024-10-27 01:50:51,720] [main] Scan time: 43.805 s (55 ms/file)
[testng] [2024-10-27 01:50:51,721] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 42 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-27 01:55:12,273] [pool-1-thread-1] Initializing /data/ghislain/test.flex:
[testng] 01:55:12,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:55:12,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:12,275 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-27_01-55-12.log]
[testng] 01:55:12,275 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7fddcb09 - End of configuration.
[testng] [2024-10-27 01:55:12,708] [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] 01:55:12,708 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:55:12,708 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:12,709 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-27_01-55-12.log]
[testng] 01:55:12,709 |-INFO in ch.qos.logback.core.sift.SiftProcessor@780a43ec - End of configuration.
[testng] [2024-10-27 01:55:13,149] [pool-1-thread-11] Initializing /data/tony/003008000.flex:
[testng] 01:55:13,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:55:13,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:13,151 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-27_01-55-13.log]
[testng] 01:55:13,151 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52bc526f - End of configuration.
[testng] [2024-10-27 01:55:13,614] [pool-1-thread-10] Initializing /data/tony/001014000 - from flex.tif:
[testng] 01:55:13,615 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:55:13,615 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:13,615 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-27_01-55-13.log]
[testng] 01:55:13,616 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a51f77e - End of configuration.
[testng] [2024-10-27 01:55:14,501] [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] 01:55:14,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:55:14,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:14,502 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-27_01-55-14.log]
[testng] 01:55:14,502 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fedb565 - End of configuration.
[testng] [2024-10-27 01:55:15,026] [pool-1-thread-8] Initializing /data/tamjid/006004000.flex:
[testng] 01:55:15,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:55:15,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:15,027 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-27_01-55-15.log]
[testng] 01:55:15,027 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f82be93 - End of configuration.
[testng] [2024-10-27 01:55:15,473] [pool-1-thread-7] Initializing /data/public/idr0007/Plate1/001001000.flex:
[testng] 01:55:15,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:55:15,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:15,474 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-27_01-55-15.log]
[testng] 01:55:15,474 |-INFO in ch.qos.logback.core.sift.SiftProcessor@692d5e0b - End of configuration.
[testng] [2024-10-27 01:55:19,171] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex:
[testng] 01:55:19,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:55:19,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:19,172 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-27_01-55-19.log]
[testng] 01:55:19,172 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28afa215 - End of configuration.
[testng] [2024-10-27 01:55:23,328] [pool-1-thread-5] Initializing /data/qa-2983/004007000.flex:
[testng] 01:55:23,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:55:23,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:23,330 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-27_01-55-23.log]
[testng] 01:55:23,330 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a284b4e - End of configuration.
[testng] [2024-10-27 01:55:23,837] [pool-1-thread-4] Initializing /data/tony/003003000.tiff:
[testng] 01:55:23,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:55:23,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:23,837 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-27_01-55-23.log]
[testng] 01:55:23,838 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51bea189 - End of configuration.
[testng] [2024-10-27 01:55:24,968] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex:
[testng] 01:55:24,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:55:24,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:24,969 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-27_01-55-24.log]
[testng] 01:55:24,969 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d2a71b0 - End of configuration.
[testng] [2024-10-27 01:55:29,584] [pool-1-thread-2] Initializing /data/manuel/003003001.flex:
[testng] 01:55:29,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:55:29,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:29,585 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-27_01-55-29.log]
[testng] 01:55:29,585 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65a71622 - End of configuration.
[testng] [2024-10-27 01:55:37,975] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex:
[testng] [2024-10-27 01:55:43,527] [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] [2024-10-27 01:55:44,235] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex:
[testng] [2024-10-27 01:55:44,902] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex:
[testng] [2024-10-27 01:55:45,520] [pool-1-thread-1] Initializing /data/stephane/002007000.flex:
[testng] [2024-10-27 01:55:49,664] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex:
[testng] [2024-10-27 01:55:50,341] [pool-1-thread-9] Initializing /data/qa-18096/002002001.flex:
[testng] [2024-10-27 01:55:51,018] [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] [2024-10-27 01:55:54,963] [pool-1-thread-8] Initializing /data/tony/test.tiff:
[testng] [2024-10-27 01:55:56,339] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex:
[testng] [2024-10-27 01:56:01,612] [pool-1-thread-5] Initializing /data/tony/001001000_objects.flex:
[testng] [2024-10-27 01:56:02,239] [pool-1-thread-1] Initializing /data/achim/003003000.flex:
[testng] [2024-10-27 01:56:06,336] [pool-1-thread-9] Initializing /data/tamjid/006005000.flex:
[testng] [2024-10-27 01:56:07,029] [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] [2024-10-27 01:56:08,736] [pool-1-thread-8] Initializing /data/qa-18096/002003001.flex:
[testng] [2024-10-27 01:56:12,117] [pool-1-thread-12] Initializing /data/anatole/001004000.flex:
[testng] [2024-10-27 01:56:13,071] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex:
[testng] [2024-10-27 01:56:13,854] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex:
[testng] [2024-10-27 01:56:23,579] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex:
[testng] [2024-10-27 01:56:24,437] [pool-1-thread-1] Initializing /data/stephane/006013000.flex:
[testng] [2024-10-27 01:56:26,090] [pool-1-thread-8] Initializing /data/tony/000101400 - from PE sofwatre.tif:
[testng] [2024-10-27 01:56:30,647] [pool-1-thread-4] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex:
[testng] [2024-10-27 01:56:36,827] [pool-1-thread-8] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex:
[testng] [2024-10-27 01:56:38,009] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex:
[testng] [2024-10-27 01:56:44,313] [pool-1-thread-9] Initializing /data/tony/015002000.tiff:
[testng] [2024-10-27 01:56:46,166] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex:
[testng] [2024-10-27 01:56:52,612] [pool-1-thread-12] Initializing /data/qa-17190/002002011.flex:
[testng] [2024-10-27 01:56:54,380] [pool-1-thread-9] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex:
[testng] [2024-10-27 01:57:01,668] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex:
[testng] [2024-10-27 01:57:12,464] [pool-1-thread-9] 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: 12 minutes 33 seconds
Finished: SUCCESS