Started by upstream project "BIOFORMATS-test-repo" build number 201
originally caused by:
Started by upstream project "Trigger" build number 226
originally caused by:
Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder
[BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins4435844604833780892.sh
+ '[' flex = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_31853_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 12:33:55,396 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 12:33:55,397 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service.
[testng] 12:33:55,397 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 12:33:55,398 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 12:33:55,399 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 12:33:55,399 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 12:33:55,399 |-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] 12:33:55,399 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 12:33:55,400 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 12:33:55,400 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 12:33:55,401 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 12:33:55,401 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 12:33:55,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 12:33:55,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 12:33:55,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 12:33:55,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 12:33:55,667 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 12:33:55,667 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 12:33:55,667 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 12:33:55,667 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 12:33:55,667 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration.
[testng] 12:33:55,668 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point
[testng] 12:33:55,668 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 268 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-09-26 12:33:55,677] [main] java.version = 21
[testng] 12:33:55,681 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 12:33:55,681 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:33:55,723 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-26_12-33-55.log]
[testng] 12:33:55,724 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration.
[testng] [2024-09-26 12:33:55,726] [main] testng.directory = /data
[testng] [2024-09-26 12:33:55,726] [main] testng.configDirectory = /config
[testng] [2024-09-26 12:33:55,735] [main] testng.multiplier = 1.0
[testng] [2024-09-26 12:33:55,736] [main] testng.in-memory = false
[testng] [2024-09-26 12:33:55,736] [main] testng.allow-missing = false
[testng] [2024-09-26 12:33:55,737] [main] user.language = en
[testng] [2024-09-26 12:33:55,737] [main] user.country = ${user.country}
[testng] [2024-09-26 12:33:55,737] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-09-26 12:34:45,857] [main] ----------------------------------------
[testng] [2024-09-26 12:34:45,857] [main] Total files: 791
[testng] [2024-09-26 12:34:45,857] [main] Scan time: 50.12 s (63 ms/file)
[testng] [2024-09-26 12:34:45,858] [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 12:39:30,704] [pool-1-thread-1] Initializing /data/qa-18096/002003001.flex:
[testng] 12:39:30,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 12:39:30,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:39:30,706 |-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_12-39-30.log]
[testng] 12:39:30,707 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cfac8a0 - End of configuration.
[testng] [2024-09-26 12:39:31,340] [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] 12:39:31,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 12:39:31,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:39:31,341 |-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_12-39-31.log]
[testng] 12:39:31,341 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70ff39d1 - End of configuration.
[testng] [2024-09-26 12:39:31,966] [pool-1-thread-11] Initializing /data/stephane/002007000.flex:
[testng] 12:39:31,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 12:39:31,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:39:31,967 |-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_12-39-31.log]
[testng] 12:39:31,967 |-INFO in ch.qos.logback.core.sift.SiftProcessor@369ff5ed - End of configuration.
[testng] [2024-09-26 12:39:32,556] [pool-1-thread-10] Initializing /data/public/idr0007/Plate1/001001000.flex:
[testng] 12:39:32,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 12:39:32,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:39:32,557 |-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_12-39-32.log]
[testng] 12:39:32,558 |-INFO in ch.qos.logback.core.sift.SiftProcessor@825a17 - End of configuration.
[testng] [2024-09-26 12:39:37,387] [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] 12:39:37,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 12:39:37,388 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:39:37,389 |-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_12-39-37.log]
[testng] 12:39:37,390 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d98bd7e - End of configuration.
[testng] [2024-09-26 12:39:38,194] [pool-1-thread-8] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex:
[testng] 12:39:38,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 12:39:38,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:39:38,195 |-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_12-39-38.log]
[testng] 12:39:38,196 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12b45d9a - End of configuration.
[testng] [2024-09-26 12:39:39,861] [pool-1-thread-7] Initializing /data/tony/test.tiff:
[testng] 12:39:39,861 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 12:39:39,861 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:39:39,862 |-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_12-39-39.log]
[testng] 12:39:39,862 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10ec712d - End of configuration.
[testng] [2024-09-26 12:39:41,652] [pool-1-thread-6] Initializing /data/tamjid/006005000.flex:
[testng] 12:39:41,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 12:39:41,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:39:41,653 |-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_12-39-41.log]
[testng] 12:39:41,654 |-INFO in ch.qos.logback.core.sift.SiftProcessor@764513e5 - End of configuration.
[testng] [2024-09-26 12:39:42,483] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex:
[testng] 12:39:42,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 12:39:42,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:39:42,484 |-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_12-39-42.log]
[testng] 12:39:42,484 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f648f92 - End of configuration.
[testng] [2024-09-26 12:39:43,256] [pool-1-thread-4] Initializing /data/qa-18096/002002001.flex:
[testng] 12:39:43,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 12:39:43,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:39:43,257 |-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_12-39-43.log]
[testng] 12:39:43,257 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a6fc8dd - End of configuration.
[testng] [2024-09-26 12:39:44,062] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex:
[testng] 12:39:44,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 12:39:44,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:39:44,063 |-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_12-39-44.log]
[testng] 12:39:44,064 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c7b312d - End of configuration.
[testng] [2024-09-26 12:39:50,169] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex:
[testng] 12:39:50,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 12:39:50,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:39:50,170 |-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_12-39-50.log]
[testng] 12:39:50,170 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4eb25d8b - End of configuration.
[testng] [2024-09-26 12:40:09,103] [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 12:40:10,341] [pool-1-thread-5] Initializing /data/achim/003003000.flex:
[testng] [2024-09-26 12:40:11,431] [pool-1-thread-1] Initializing /data/tony/000101400 - from PE sofwatre.tif:
[testng] [2024-09-26 12:40:13,744] [pool-1-thread-4] Initializing /data/anatole/001004000.flex:
[testng] [2024-09-26 12:40:15,070] [pool-1-thread-11] Initializing /data/qa-2983/004007000.flex:
[testng] [2024-09-26 12:40:16,031] [pool-1-thread-6] Initializing /data/qa-17190/002002011.flex:
[testng] [2024-09-26 12:40:22,766] [pool-1-thread-12] Initializing /data/tony/001001000_objects.flex:
[testng] [2024-09-26 12:40:26,925] [pool-1-thread-1] 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 12:40:28,826] [pool-1-thread-6] Initializing /data/ghislain/test.flex:
[testng] [2024-09-26 12:40:29,824] [pool-1-thread-11] Initializing /data/tony/003003000.tiff:
[testng] [2024-09-26 12:40:33,853] [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 12:40:42,936] [pool-1-thread-5] Initializing /data/manuel/003003001.flex:
[testng] [2024-09-26 12:40:44,184] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex:
[testng] [2024-09-26 12:40:52,270] [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 12:40:58,952] [pool-1-thread-6] 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 12:41:00,226] [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 12:41:01,532] [pool-1-thread-11] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex:
[testng] [2024-09-26 12:41:02,829] [pool-1-thread-4] Initializing /data/tamjid/006003000.flex:
[testng] [2024-09-26 12:41:14,884] [pool-1-thread-4] Initializing /data/tony/001014000 - from flex.tif:
[testng] [2024-09-26 12:41:19,205] [pool-1-thread-12] Initializing /data/tony/test1.flex:
[testng] [2024-09-26 12:41:20,318] [pool-1-thread-6] 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 12:41:21,434] [pool-1-thread-5] Initializing /data/stephane/006013000.flex:
[testng] [2024-09-26 12:41:22,731] [pool-1-thread-1] Initializing /data/tony/003008000.flex:
[testng] [2024-09-26 12:41:28,405] [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 12:41:36,423] [pool-1-thread-12] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex:
[testng] [2024-09-26 12:41:37,880] [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 12:41:52,713] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex:
[testng] [2024-09-26 12:42:03,099] [pool-1-thread-5] 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 12:42:06,812] [pool-1-thread-1] Initializing /data/tony/015002000.tiff:
[testng] [2024-09-26 12:42:16,317] [pool-1-thread-12] 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: 18 minutes 2 seconds
Finished: SUCCESS