Started by upstream project "BIOFORMATS-test-repo" build number 309
originally caused by:
Started by upstream project "Trigger" build number 331
originally caused by:
Started by timer
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/jenkins5142018435947771519.sh
+ '[' flex = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_48940_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] 00:51:11,950 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 00:51:11,952 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 00:51:11,952 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:51:11,953 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:51:11,953 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:51:11,953 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:51:11,954 |-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] 00:51:11,954 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:51:11,954 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:51:11,955 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:51:11,955 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:51:11,955 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:51:12,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:51:12,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:51:12,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:51:12,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:51:12,142 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:51:12,142 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:51:12,142 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:51:12,142 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:51:12,142 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 00:51:12,143 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 00:51:12,143 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 189 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2025-01-05 00:51:12,152] [main] java.version = 17.0.2
[testng] 00:51:12,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:51:12,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:51:12,193 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-05_00-51-12.log]
[testng] 00:51:12,194 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2025-01-05 00:51:12,196] [main] testng.directory = /data
[testng] [2025-01-05 00:51:12,197] [main] testng.configDirectory = /config
[testng] [2025-01-05 00:51:12,205] [main] testng.multiplier = 1.0
[testng] [2025-01-05 00:51:12,205] [main] testng.in-memory = false
[testng] [2025-01-05 00:51:12,205] [main] testng.allow-missing = false
[testng] [2025-01-05 00:51:12,206] [main] user.language = en
[testng] [2025-01-05 00:51:12,206] [main] user.country = ${user.country}
[testng] [2025-01-05 00:51:12,206] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2025-01-05 00:52:13,507] [main] ----------------------------------------
[testng] [2025-01-05 00:52:13,507] [main] Total files: 791
[testng] [2025-01-05 00:52:13,508] [main] Scan time: 61.301 s (77 ms/file)
[testng] [2025-01-05 00:52:13,508] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 42 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2025-01-05 00:57:10,568] [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] 00:57:10,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:57:10,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:57:10,573 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-05_00-57-10.log]
[testng] 00:57:10,573 |-INFO in ch.qos.logback.core.sift.SiftProcessor@376da750 - End of configuration.
[testng] [2025-01-05 00:57:11,278] [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] 00:57:11,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:57:11,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:57:11,279 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-05_00-57-11.log]
[testng] 00:57:11,280 |-INFO in ch.qos.logback.core.sift.SiftProcessor@495f603 - End of configuration.
[testng] [2025-01-05 00:57:12,266] [pool-1-thread-11] Initializing /data/ghislain/test.flex:
[testng] 00:57:12,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:57:12,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:57:12,267 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-05_00-57-12.log]
[testng] 00:57:12,267 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c07cf29 - End of configuration.
[testng] [2025-01-05 00:57:14,328] [pool-1-thread-10] Initializing /data/tamjid/006005000.flex:
[testng] 00:57:14,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:57:14,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:57:14,329 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-05_00-57-14.log]
[testng] 00:57:14,330 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6686711f - End of configuration.
[testng] [2025-01-05 00:57:14,964] [pool-1-thread-9] Initializing /data/tamjid/006003000.flex:
[testng] 00:57:14,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:57:14,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:57:14,965 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-05_00-57-14.log]
[testng] 00:57:14,965 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16350833 - End of configuration.
[testng] [2025-01-05 00:57:15,552] [pool-1-thread-8] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex:
[testng] 00:57:15,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:57:15,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:57:15,552 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-05_00-57-15.log]
[testng] 00:57:15,553 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cf4d45 - End of configuration.
[testng] [2025-01-05 00:57:16,372] [pool-1-thread-7] Initializing /data/qa-2983/004007000.flex:
[testng] 00:57:16,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:57:16,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:57:16,373 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-05_00-57-16.log]
[testng] 00:57:16,373 |-INFO in ch.qos.logback.core.sift.SiftProcessor@567f307 - End of configuration.
[testng] [2025-01-05 00:57:16,959] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex:
[testng] 00:57:16,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:57:16,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:57:16,960 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-05_00-57-16.log]
[testng] 00:57:16,961 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3888386c - End of configuration.
[testng] [2025-01-05 00:57:21,913] [pool-1-thread-5] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex:
[testng] 00:57:21,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:57:21,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:57:21,914 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-05_00-57-21.log]
[testng] 00:57:21,914 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32f7604 - End of configuration.
[testng] [2025-01-05 00:57:22,578] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex:
[testng] 00:57:22,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:57:22,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:57:22,580 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-05_00-57-22.log]
[testng] 00:57:22,581 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ad238b1 - End of configuration.
[testng] [2025-01-05 00:57:28,104] [pool-1-thread-3] Initializing /data/tamjid/006004000.flex:
[testng] 00:57:28,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:57:28,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:57:28,105 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-05_00-57-28.log]
[testng] 00:57:28,105 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48ba7317 - End of configuration.
[testng] [2025-01-05 00:57:28,838] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex:
[testng] 00:57:28,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:57:28,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:57:28,839 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-05_00-57-28.log]
[testng] 00:57:28,839 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15e80250 - End of configuration.
[testng] [2025-01-05 00:57:48,218] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex:
[testng] [2025-01-05 00:57:49,117] [pool-1-thread-3] Initializing /data/qa-17190/002002011.flex:
[testng] [2025-01-05 00:57:50,011] [pool-1-thread-10] Initializing /data/qa-18096/002003001.flex:
[testng] [2025-01-05 00:57:50,741] [pool-1-thread-7] Initializing /data/public/idr0007/Plate1/001001000.flex:
[testng] [2025-01-05 00:57:57,536] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex:
[testng] [2025-01-05 00:58:03,688] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex:
[testng] [2025-01-05 00:58:04,603] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex:
[testng] [2025-01-05 00:58:17,303] [pool-1-thread-3] Initializing /data/tony/001001000_objects.flex:
[testng] [2025-01-05 00:58:18,345] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex:
[testng] [2025-01-05 00:58:22,959] [pool-1-thread-9] Initializing /data/stephane/006013000.flex:
[testng] [2025-01-05 00:58:26,486] [pool-1-thread-1] Initializing /data/tony/test1.flex:
[testng] [2025-01-05 00:58:33,284] [pool-1-thread-3] Initializing /data/qa-7469/002002.flex:
[testng] [2025-01-05 00:58:38,321] [pool-1-thread-10] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex:
[testng] [2025-01-05 00:58:40,451] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex:
[testng] [2025-01-05 00:58:47,774] [pool-1-thread-12] Initializing /data/tony/015002000.tiff:
[testng] [2025-01-05 00:58:50,534] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex:
[testng] [2025-01-05 00:58:55,953] [pool-1-thread-9] Initializing /data/manuel/003003001.flex:
[testng] [2025-01-05 00:58:59,046] [pool-1-thread-3] Initializing /data/anatole/001004000.flex:
[testng] [2025-01-05 00:59:07,183] [pool-1-thread-12] Initializing /data/qa-18096/002002001.flex:
[testng] [2025-01-05 00:59:16,496] [pool-1-thread-5] Initializing /data/stephane/002007000.flex:
[testng] [2025-01-05 00:59:17,577] [pool-1-thread-8] Initializing /data/tony/test.tiff:
[testng] [2025-01-05 00:59:21,979] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex:
[testng] [2025-01-05 00:59:25,723] [pool-1-thread-9] Initializing /data/tony/000101400 - from PE sofwatre.tif:
[testng] [2025-01-05 00:59:33,242] [pool-1-thread-8] Initializing /data/tony/003003000.tiff:
[testng] [2025-01-05 00:59:36,691] [pool-1-thread-5] Initializing /data/achim/003003000.flex:
[testng] [2025-01-05 00:59:41,766] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex:
[testng] [2025-01-05 00:59:50,283] [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] [2025-01-05 00:59:53,321] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex:
[testng] [2025-01-05 00:59:57,034] [pool-1-thread-8] Initializing /data/tony/003008000.flex:
[testng] [2025-01-05 01:00:03,515] [pool-1-thread-5] Initializing /data/tony/001014000 - from flex.tif:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2226, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 16 minutes 6 seconds
Finished: SUCCESS