Started by upstream project "BIOFORMATS-test-repo" build number 284
originally caused by:
Started by upstream project "Trigger" build number 303
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/jenkins17933862161191594592.sh
+ '[' flex = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_44822_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] 00:53:27,231 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 00:53:27,233 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 00:53:27,233 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:53:27,234 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:53:27,234 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:53:27,234 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:53:27,235 |-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] 00:53:27,235 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:53:27,235 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:53:27,236 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:53:27,236 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:53:27,236 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:53:27,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:53:27,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:53:27,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:53:27,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:53:27,438 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:53:27,438 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:53:27,438 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:53:27,438 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:53:27,438 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 00:53:27,439 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 00:53:27,439 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 204 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-12-08 00:53:27,448] [main] java.version = 17.0.2
[testng] 00:53:27,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:53:27,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:53:27,492 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-08_00-53-27.log]
[testng] 00:53:27,494 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-12-08 00:53:27,496] [main] testng.directory = /data
[testng] [2024-12-08 00:53:27,496] [main] testng.configDirectory = /config
[testng] [2024-12-08 00:53:27,505] [main] testng.multiplier = 1.0
[testng] [2024-12-08 00:53:27,506] [main] testng.in-memory = false
[testng] [2024-12-08 00:53:27,506] [main] testng.allow-missing = false
[testng] [2024-12-08 00:53:27,506] [main] user.language = en
[testng] [2024-12-08 00:53:27,506] [main] user.country = ${user.country}
[testng] [2024-12-08 00:53:27,506] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-12-08 00:54:51,010] [main] ----------------------------------------
[testng] [2024-12-08 00:54:51,010] [main] Total files: 791
[testng] [2024-12-08 00:54:51,010] [main] Scan time: 83.504 s (105 ms/file)
[testng] [2024-12-08 00:54:51,010] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 42 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-12-08 01:00:21,511] [pool-1-thread-1] Initializing /data/ghislain/test.flex:
[testng] 01:00:21,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:00:21,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:00:21,513 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-08_01-00-21.log]
[testng] 01:00:21,513 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60eb9ea - End of configuration.
[testng] [2024-12-08 01:00:22,059] [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] 01:00:22,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:00:22,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:00:22,060 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-08_01-00-22.log]
[testng] 01:00:22,061 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d416c16 - End of configuration.
[testng] [2024-12-08 01:00:22,589] [pool-1-thread-11] Initializing /data/tony/003008000.flex:
[testng] 01:00:22,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:00:22,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:00:22,590 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-08_01-00-22.log]
[testng] 01:00:22,590 |-INFO in ch.qos.logback.core.sift.SiftProcessor@492fdcde - End of configuration.
[testng] [2024-12-08 01:00:23,822] [pool-1-thread-10] Initializing /data/tony/001014000 - from flex.tif:
[testng] 01:00:23,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:00:23,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:00:23,823 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-08_01-00-23.log]
[testng] 01:00:23,824 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6eb24782 - End of configuration.
[testng] [2024-12-08 01:00:24,950] [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] 01:00:24,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:00:24,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:00:24,951 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-08_01-00-24.log]
[testng] 01:00:24,951 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f094931 - End of configuration.
[testng] [2024-12-08 01:00:25,499] [pool-1-thread-8] Initializing /data/tamjid/006004000.flex:
[testng] 01:00:25,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:00:25,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:00:25,500 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-08_01-00-25.log]
[testng] 01:00:25,500 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30dc634 - End of configuration.
[testng] [2024-12-08 01:00:26,119] [pool-1-thread-7] Initializing /data/public/idr0007/Plate1/001001000.flex:
[testng] 01:00:26,119 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:00:26,119 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:00:26,120 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-08_01-00-26.log]
[testng] 01:00:26,120 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f06a2b2 - End of configuration.
[testng] [2024-12-08 01:00:31,800] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex:
[testng] 01:00:31,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:00:31,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:00:31,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-08_01-00-31.log]
[testng] 01:00:31,802 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c5bb950 - End of configuration.
[testng] [2024-12-08 01:00:37,457] [pool-1-thread-5] Initializing /data/qa-2983/004007000.flex:
[testng] 01:00:37,457 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:00:37,457 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:00:37,458 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-08_01-00-37.log]
[testng] 01:00:37,458 |-INFO in ch.qos.logback.core.sift.SiftProcessor@741703f5 - End of configuration.
[testng] [2024-12-08 01:00:38,438] [pool-1-thread-4] Initializing /data/tony/003003000.tiff:
[testng] 01:00:38,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:00:38,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:00:38,439 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-08_01-00-38.log]
[testng] 01:00:38,440 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6efb14cb - End of configuration.
[testng] [2024-12-08 01:00:39,855] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex:
[testng] 01:00:39,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:00:39,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:00:39,856 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-08_01-00-39.log]
[testng] 01:00:39,856 |-INFO in ch.qos.logback.core.sift.SiftProcessor@563e357e - End of configuration.
[testng] [2024-12-08 01:00:47,220] [pool-1-thread-2] Initializing /data/manuel/003003001.flex:
[testng] 01:00:47,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:00:47,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:00:47,221 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-08_01-00-47.log]
[testng] 01:00:47,221 |-INFO in ch.qos.logback.core.sift.SiftProcessor@521e5250 - End of configuration.
[testng] [2024-12-08 01:01:00,609] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex:
[testng] [2024-12-08 01:01:10,666] [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] [2024-12-08 01:01:11,551] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex:
[testng] [2024-12-08 01:01:12,730] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex:
[testng] [2024-12-08 01:01:13,605] [pool-1-thread-1] Initializing /data/stephane/002007000.flex:
[testng] [2024-12-08 01:01:18,515] [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] [2024-12-08 01:01:19,434] [pool-1-thread-12] Initializing /data/qa-18096/002002001.flex:
[testng] [2024-12-08 01:01:20,288] [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] [2024-12-08 01:01:26,497] [pool-1-thread-2] Initializing /data/tony/test.tiff:
[testng] [2024-12-08 01:01:29,647] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex:
[testng] [2024-12-08 01:01:38,499] [pool-1-thread-5] Initializing /data/tony/001001000_objects.flex:
[testng] [2024-12-08 01:01:40,367] [pool-1-thread-1] Initializing /data/achim/003003000.flex:
[testng] [2024-12-08 01:01:41,537] [pool-1-thread-4] Initializing /data/tamjid/006005000.flex:
[testng] [2024-12-08 01:01:48,189] [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] [2024-12-08 01:01:52,226] [pool-1-thread-2] Initializing /data/qa-18096/002003001.flex:
[testng] [2024-12-08 01:01:53,284] [pool-1-thread-11] Initializing /data/anatole/001004000.flex:
[testng] [2024-12-08 01:01:54,599] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex:
[testng] [2024-12-08 01:01:58,229] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex:
[testng] [2024-12-08 01:02:10,925] [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] [2024-12-08 01:02:15,231] [pool-1-thread-1] Initializing /data/stephane/006013000.flex:
[testng] [2024-12-08 01:02:19,229] [pool-1-thread-12] Initializing /data/tony/000101400 - from PE sofwatre.tif:
[testng] [2024-12-08 01:02:21,388] [pool-1-thread-2] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex:
[testng] [2024-12-08 01:02:25,080] [pool-1-thread-9] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex:
[testng] [2024-12-08 01:02:38,120] [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] [2024-12-08 01:02:42,507] [pool-1-thread-5] Initializing /data/tony/015002000.tiff:
[testng] [2024-12-08 01:02:44,971] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex:
[testng] [2024-12-08 01:02:46,352] [pool-1-thread-1] Initializing /data/qa-17190/002002011.flex:
[testng] [2024-12-08 01:03:01,944] [pool-1-thread-5] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex:
[testng] [2024-12-08 01:03:03,301] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex:
[testng] [2024-12-08 01:03:29,559] [pool-1-thread-5] 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: 17 minutes 8 seconds
Finished: SUCCESS