Started by upstream project "BIOFORMATS-test-repo" build number 390
originally caused by:
Started by upstream project "Trigger" build number 414
originally caused by:
Started by user devspace
Restarted from build #413, stage Bio-Formats
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/jenkins13296417035273601631.sh
+ '[' flex = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_61709_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] 01:25:43,079 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15
[testng] 01:25:43,080 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service.
[testng] 01:25:43,080 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:25:43,081 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:25:43,082 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:25:43,082 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:25:43,083 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:25:43,083 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:25:43,083 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:25:43,084 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:25:43,084 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:25:43,084 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:25:43,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:25:43,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:25:43,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:25:43,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:25:43,288 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:25:43,288 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:25:43,288 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:25:43,288 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:25:43,288 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration.
[testng] 01:25:43,289 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point
[testng] 01:25:43,289 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 206 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2025-03-25 01:25:43,299] [main] java.version = 11.0.16
[testng] 01:25:43,302 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:25:43,302 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:25:43,344 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-25_01-25-43.log]
[testng] 01:25:43,346 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration.
[testng] [2025-03-25 01:25:43,348] [main] testng.directory = /data
[testng] [2025-03-25 01:25:43,348] [main] testng.configDirectory = /config
[testng] [2025-03-25 01:25:43,358] [main] testng.multiplier = 1.0
[testng] [2025-03-25 01:25:43,359] [main] testng.in-memory = false
[testng] [2025-03-25 01:25:43,360] [main] testng.allow-missing = false
[testng] [2025-03-25 01:25:43,360] [main] user.language = en
[testng] [2025-03-25 01:25:43,360] [main] user.country = ${user.country}
[testng] [2025-03-25 01:25:43,360] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2025-03-25 01:33:51,749] [main] ----------------------------------------
[testng] [2025-03-25 01:33:51,750] [main] Total files: 791
[testng] [2025-03-25 01:33:51,750] [main] Scan time: 488.389 s (617 ms/file)
[testng] [2025-03-25 01:33:51,750] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 42 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2025-03-25 01:49:47,028] [pool-1-thread-1] Initializing /data/public/idr0007/Plate1/001001000.flex:
[testng] 01:49:47,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:49:47,029 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:49:47,030 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-25_01-49-47.log]
[testng] 01:49:47,031 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c1900de - End of configuration.
[testng] [2025-03-25 01:50:16,458] [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] 01:50:16,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:50:16,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:50:16,461 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-25_01-50-16.log]
[testng] 01:50:16,461 |-INFO in ch.qos.logback.core.sift.SiftProcessor@595f9dee - End of configuration.
[testng] [2025-03-25 01:50:20,596] [pool-1-thread-11] Initializing /data/tony/000101400 - from PE sofwatre.tif:
[testng] 01:50:20,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:50:20,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:50:20,597 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-25_01-50-20.log]
[testng] 01:50:20,597 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58b870f6 - End of configuration.
[testng] [2025-03-25 01:50:28,138] [pool-1-thread-10] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex:
[testng] 01:50:28,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:50:28,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:50:28,139 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-25_01-50-28.log]
[testng] 01:50:28,139 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71dc3bd - End of configuration.
[testng] [2025-03-25 01:50:31,826] [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] 01:50:31,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:50:31,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:50:31,827 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-25_01-50-31.log]
[testng] 01:50:31,828 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72a35721 - End of configuration.
[testng] [2025-03-25 01:50:35,416] [pool-1-thread-8] Initializing /data/qa-7469/002002.flex:
[testng] 01:50:35,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:50:35,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:50:35,417 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-25_01-50-35.log]
[testng] 01:50:35,418 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ace0ee3 - End of configuration.
[testng] [2025-03-25 01:50:38,673] [pool-1-thread-7] Initializing /data/ghislain/test.flex:
[testng] 01:50:38,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:50:38,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:50:38,673 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-25_01-50-38.log]
[testng] 01:50:38,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@229cd53e - End of configuration.
[testng] [2025-03-25 01:50:41,899] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex:
[testng] 01:50:41,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:50:41,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:50:41,900 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-25_01-50-41.log]
[testng] 01:50:41,901 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b249504 - End of configuration.
[testng] [2025-03-25 01:50:45,480] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex:
[testng] 01:50:45,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:50:45,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:50:45,481 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-25_01-50-45.log]
[testng] 01:50:45,481 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fb2eb6 - End of configuration.
[testng] [2025-03-25 01:51:14,653] [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] 01:51:14,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:51:14,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:51:14,654 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-25_01-51-14.log]
[testng] 01:51:14,654 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f1452ec - End of configuration.
[testng] [2025-03-25 01:51:18,653] [pool-1-thread-3] Initializing /data/tony/001001000_objects.flex:
[testng] 01:51:18,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:51:18,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:51:18,654 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-25_01-51-18.log]
[testng] 01:51:18,654 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b80793b - End of configuration.
[testng] [2025-03-25 01:51:23,259] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex:
[testng] 01:51:23,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:51:23,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:51:23,261 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-25_01-51-23.log]
[testng] 01:51:23,261 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29b08ea8 - End of configuration.
[testng] [2025-03-25 01:52:46,328] [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] [2025-03-25 01:52:50,811] [pool-1-thread-8] Initializing /data/tamjid/006005000.flex:
[testng] [2025-03-25 01:52:55,054] [pool-1-thread-10] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex:
[testng] [2025-03-25 01:52:59,240] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex:
[testng] [2025-03-25 01:53:31,313] [pool-1-thread-7] Initializing /data/tony/003003000.tiff:
[testng] [2025-03-25 01:53:56,663] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex:
[testng] [2025-03-25 01:54:22,547] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex:
[testng] [2025-03-25 01:54:26,077] [pool-1-thread-4] Initializing /data/tony/001014000 - from flex.tif:
[testng] [2025-03-25 01:54:33,076] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex:
[testng] [2025-03-25 01:55:25,244] [pool-1-thread-8] Initializing /data/qa-2983/004007000.flex:
[testng] [2025-03-25 01:55:29,392] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex:
[testng] [2025-03-25 01:55:48,631] [pool-1-thread-4] Initializing /data/anatole/001004000.flex:
[testng] [2025-03-25 01:56:11,735] [pool-1-thread-6] Initializing /data/tony/test1.flex:
[testng] [2025-03-25 01:56:15,601] [pool-1-thread-11] Initializing /data/stephane/002007000.flex:
[testng] [2025-03-25 01:56:23,336] [pool-1-thread-8] Initializing /data/stephane/006013000.flex:
[testng] [2025-03-25 01:57:02,508] [pool-1-thread-6] Initializing /data/qa-17190/002002011.flex:
[testng] [2025-03-25 01:57:06,009] [pool-1-thread-11] Initializing /data/tamjid/006003000.flex:
[testng] [2025-03-25 01:57:36,569] [pool-1-thread-8] Initializing /data/tony/003008000.flex:
[testng] [2025-03-25 01:57:52,743] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex:
[testng] [2025-03-25 01:57:59,270] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex:
[testng] [2025-03-25 01:58:31,443] [pool-1-thread-4] Initializing /data/tony/015002000.tiff:
[testng] [2025-03-25 01:58:45,276] [pool-1-thread-10] Initializing /data/qa-18096/002003001.flex:
[testng] [2025-03-25 01:59:05,929] [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] [2025-03-25 01:59:10,441] [pool-1-thread-8] Initializing /data/qa-18096/002002001.flex:
[testng] [2025-03-25 01:59:14,355] [pool-1-thread-6] Initializing /data/achim/003003000.flex:
[testng] [2025-03-25 01:59:26,908] [pool-1-thread-4] Initializing /data/tamjid/006004000.flex:
[testng] [2025-03-25 01:59:43,441] [pool-1-thread-10] Initializing /data/manuel/003003001.flex:
[testng] [2025-03-25 02:00:08,274] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex:
[testng] [2025-03-25 02:00:31,139] [pool-1-thread-4] Initializing /data/tony/test.tiff:
[testng] [2025-03-25 02:01:10,054] [pool-1-thread-6] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2226, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 70 minutes 47 seconds
Finished: SUCCESS