Started by upstream project "BIOFORMATS-test-repo" build number 67
originally caused by:
Started by upstream project "Trigger" build number 75
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4
[BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins6800403955466899353.sh
+ '[' flex = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_10034_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] WARNING: An illegal reflective access operation has occurred
[testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket
[testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener
[testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
[testng] WARNING: All illegal access operations will be denied in a future release
[testng] File leak detector installed
[testng] 01:32:32,419 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:32:32,421 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 01:32:32,421 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:32:32,422 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:32:32,423 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:32:32,423 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:32:32,423 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:32:32,423 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:32:32,424 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:32:32,424 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:32:32,425 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:32:32,425 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:32:32,610 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:32:32,610 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:32:32,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:32:32,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:32:32,638 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:32:32,639 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:32:32,639 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:32:32,639 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:32:32,639 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 01:32:32,640 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 01:32:32,640 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 216 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-05-18 01:32:32,649] [main] java.version = 11.0.16
[testng] 01:32:32,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:32:32,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:32:32,697 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-18_01-32-32.log]
[testng] 01:32:32,699 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-05-18 01:32:32,701] [main] testng.directory = /data
[testng] [2024-05-18 01:32:32,701] [main] testng.configDirectory = /config
[testng] [2024-05-18 01:32:32,712] [main] testng.multiplier = 1.0
[testng] [2024-05-18 01:32:32,713] [main] testng.in-memory = false
[testng] [2024-05-18 01:32:32,713] [main] testng.allow-missing = false
[testng] [2024-05-18 01:32:32,713] [main] user.language = en
[testng] [2024-05-18 01:32:32,713] [main] user.country = ${user.country}
[testng] [2024-05-18 01:32:32,713] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-05-18 01:32:45,648] [main] ----------------------------------------
[testng] [2024-05-18 01:32:45,648] [main] Total files: 791
[testng] [2024-05-18 01:32:45,648] [main] Scan time: 12.934 s (16 ms/file)
[testng] [2024-05-18 01:32:45,649] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 42 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-05-18 01:38:40,713] [pool-1-thread-1] Initializing /data/qa-18096/002003001.flex:
[testng] 01:38:40,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:38:40,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:40,715 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-18_01-38-40.log]
[testng] 01:38:40,716 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b71b00f - End of configuration.
[testng] [2024-05-18 01:38:40,804] [pool-1-thread-12] Initializing /data/tony/003003000.tiff:
[testng] 01:38:40,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:38:40,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:40,805 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-18_01-38-40.log]
[testng] 01:38:40,805 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a1687e9 - End of configuration.
[testng] [2024-05-18 01:38:40,939] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex:
[testng] 01:38:40,939 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:38:40,939 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:40,940 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-18_01-38-40.log]
[testng] 01:38:40,940 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e362cb5 - End of configuration.
[testng] [2024-05-18 01:38:41,545] [pool-1-thread-10] Initializing /data/achim/003003000.flex:
[testng] 01:38:41,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:38:41,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:41,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-18_01-38-41.log]
[testng] 01:38:41,546 |-INFO in ch.qos.logback.core.sift.SiftProcessor@261e4ae3 - End of configuration.
[testng] [2024-05-18 01:38:41,990] [pool-1-thread-9] Initializing /data/manuel/003003001.flex:
[testng] 01:38:41,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:38:41,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:41,992 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-18_01-38-41.log]
[testng] 01:38:41,992 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27f733b0 - End of configuration.
[testng] [2024-05-18 01:38:42,070] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex:
[testng] 01:38:42,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:38:42,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:42,071 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-18_01-38-42.log]
[testng] 01:38:42,072 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26b86d93 - End of configuration.
[testng] [2024-05-18 01:38:42,107] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex:
[testng] 01:38:42,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:38:42,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:42,108 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-18_01-38-42.log]
[testng] 01:38:42,108 |-INFO in ch.qos.logback.core.sift.SiftProcessor@171f0d - End of configuration.
[testng] [2024-05-18 01:38:42,137] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex:
[testng] 01:38:42,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:38:42,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:42,138 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-18_01-38-42.log]
[testng] 01:38:42,138 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1998f9fd - End of configuration.
[testng] [2024-05-18 01:38:42,598] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex:
[testng] 01:38:42,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:38:42,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:42,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-18_01-38-42.log]
[testng] 01:38:42,600 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27efc7a3 - End of configuration.
[testng] [2024-05-18 01:38:43,082] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex:
[testng] 01:38:43,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:38:43,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:43,083 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-18_01-38-43.log]
[testng] 01:38:43,084 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31ae7556 - End of configuration.
[testng] [2024-05-18 01:38:43,118] [pool-1-thread-3] Initializing /data/tony/003008000.flex:
[testng] 01:38:43,119 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:38:43,119 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:43,119 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-18_01-38-43.log]
[testng] 01:38:43,120 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19d89179 - End of configuration.
[testng] [2024-05-18 01:38:43,174] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex:
[testng] 01:38:43,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:38:43,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:43,174 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-18_01-38-43.log]
[testng] 01:38:43,175 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b6882a5 - End of configuration.
[testng] [2024-05-18 01:38:45,623] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex:
[testng] [2024-05-18 01:38:45,702] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex:
[testng] [2024-05-18 01:38:45,788] [pool-1-thread-1] Initializing /data/tony/001014000 - from flex.tif:
[testng] [2024-05-18 01:38:45,858] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex:
[testng] [2024-05-18 01:38:45,983] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex:
[testng] [2024-05-18 01:38:46,920] [pool-1-thread-4] Initializing /data/tony/test.tiff:
[testng] [2024-05-18 01:38:47,003] [pool-1-thread-9] Initializing /data/qa-17190/002002011.flex:
[testng] [2024-05-18 01:38:47,567] [pool-1-thread-1] Initializing /data/tony/015002000.tiff:
[testng] [2024-05-18 01:38:47,750] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex:
[testng] [2024-05-18 01:38:48,131] [pool-1-thread-10] Initializing /data/qa-18096/002002001.flex:
[testng] [2024-05-18 01:38:48,185] [pool-1-thread-4] Initializing /data/stephane/006013000.flex:
[testng] [2024-05-18 01:38:48,532] [pool-1-thread-1] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex:
[testng] [2024-05-18 01:38:48,816] [pool-1-thread-10] Initializing /data/ghislain/test.flex:
[testng] [2024-05-18 01:38:49,194] [pool-1-thread-9] Initializing /data/tamjid/006004000.flex:
[testng] [2024-05-18 01:38:49,758] [pool-1-thread-10] Initializing /data/tamjid/006005000.flex:
[testng] [2024-05-18 01:38:49,841] [pool-1-thread-9] Initializing /data/qa-2983/004007000.flex:
[testng] [2024-05-18 01:38:49,969] [pool-1-thread-3] Initializing /data/tony/000101400 - from PE sofwatre.tif:
[testng] [2024-05-18 01:38:50,391] [pool-1-thread-7] Initializing /data/tony/test1.flex:
[testng] [2024-05-18 01:38:50,520] [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] [2024-05-18 01:38:50,567] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex:
[testng] [2024-05-18 01:38:51,213] [pool-1-thread-3] Initializing /data/stephane/002007000.flex:
[testng] [2024-05-18 01:38:51,371] [pool-1-thread-7] Initializing /data/anatole/001004000.flex:
[testng] [2024-05-18 01:38:52,426] [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] [2024-05-18 01:38:52,477] [pool-1-thread-8] Initializing /data/qa-7469/002002.flex:
[testng] [2024-05-18 01:38:53,031] [pool-1-thread-8] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex:
[testng] [2024-05-18 01:39:02,380] [pool-1-thread-1] Initializing /data/tony/001001000_objects.flex:
[testng] [2024-05-18 01:39:02,524] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex:
[testng] [2024-05-18 01:39:03,710] [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] [2024-05-18 01:39:03,766] [pool-1-thread-4] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex:
[testng] [2024-05-18 01:39:05,673] [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]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2226, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 9 minutes 57 seconds
Finished: SUCCESS