Started by upstream project "BIOFORMATS-test-repo" build number 248
originally caused by:
Started by upstream project "Trigger" build number 272
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/jenkins12186671445773455792.sh
+ '[' tillvision = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_39062_merge_ci -v /uod/idr/repos/curated/tillvision:/data -v /uod/idr-scratch/merge-ci/curated/tillvision:/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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 01:46:09,658 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:46:09,660 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service.
[testng] 01:46:09,660 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:46:09,661 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:46:09,661 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:46:09,661 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:46:09,662 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:46:09,662 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:46:09,662 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:46:09,663 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:46:09,663 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:46:09,663 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:46:09,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:46:09,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:46:09,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:46:09,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:46:09,862 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:46:09,862 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:46:09,862 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:46:09,862 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:46:09,863 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration.
[testng] 01:46:09,863 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point
[testng] 01:46:09,863 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 201 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-07 01:46:09,873] [main] java.version = 21
[testng] 01:46:09,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:46:09,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:46:09,920 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-07_01-46-09.log]
[testng] 01:46:09,922 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration.
[testng] [2024-11-07 01:46:09,924] [main] testng.directory = /data
[testng] [2024-11-07 01:46:09,924] [main] testng.configDirectory = /config
[testng] [2024-11-07 01:46:09,933] [main] testng.multiplier = 1.0
[testng] [2024-11-07 01:46:09,934] [main] testng.in-memory = false
[testng] [2024-11-07 01:46:09,934] [main] testng.allow-missing = false
[testng] [2024-11-07 01:46:09,934] [main] user.language = en
[testng] [2024-11-07 01:46:09,934] [main] user.country = ${user.country}
[testng] [2024-11-07 01:46:09,934] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-11-07 01:46:29,050] [main] ----------------------------------------
[testng] [2024-11-07 01:46:29,051] [main] Total files: 46
[testng] [2024-11-07 01:46:29,051] [main] Scan time: 19.116 s (415 ms/file)
[testng] [2024-11-07 01:46:29,051] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 25 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-07 01:47:23,927] [pool-1-thread-1] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws:
[testng] 01:47:23,928 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:47:23,928 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:23,930 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-07_01-47-23.log]
[testng] 01:47:23,930 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d6db1bf - End of configuration.
[testng] [2024-11-07 01:47:24,729] [pool-1-thread-12] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws:
[testng] 01:47:24,729 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:47:24,729 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:24,730 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-07_01-47-24.log]
[testng] 01:47:24,731 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fe4ccdb - End of configuration.
[testng] [2024-11-07 01:47:25,395] [pool-1-thread-11] Initializing /data/christian/080807ionophore/080807ionophore3.vws:
[testng] 01:47:25,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:47:25,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:25,396 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-07_01-47-25.log]
[testng] 01:47:25,397 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c5b9c75 - End of configuration.
[testng] [2024-11-07 01:47:26,013] [pool-1-thread-10] Initializing /data/gerhard/test.vws:
[testng] 01:47:26,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:47:26,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:26,014 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-07_01-47-26.log]
[testng] 01:47:26,014 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a381df0 - End of configuration.
[testng] [2024-11-07 01:47:26,616] [pool-1-thread-9] Initializing /data/imagesc-84715/not working.vws:
[testng] 01:47:26,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:47:26,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:26,617 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-07_01-47-26.log]
[testng] 01:47:26,617 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43d182e2 - End of configuration.
[testng] [2024-11-07 01:47:27,329] [pool-1-thread-8] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif:
[testng] 01:47:27,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:47:27,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:27,330 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-07_01-47-27.log]
[testng] 01:47:27,331 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b329a50 - End of configuration.
[testng] [2024-11-07 01:47:29,167] [pool-1-thread-7] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws:
[testng] 01:47:29,167 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:47:29,167 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:29,168 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-07_01-47-29.log]
[testng] 01:47:29,169 |-INFO in ch.qos.logback.core.sift.SiftProcessor@595f955 - End of configuration.
[testng] [2024-11-07 01:47:29,856] [pool-1-thread-6] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif:
[testng] 01:47:29,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:47:29,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:29,857 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-07_01-47-29.log]
[testng] 01:47:29,858 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47bfbaa8 - End of configuration.
[testng] [2024-11-07 01:47:31,707] [pool-1-thread-5] Initializing /data/ian/working_tillvision_vws/20120322.vws:
[testng] 01:47:31,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:47:31,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:31,708 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-07_01-47-31.log]
[testng] 01:47:31,708 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59198ba9 - End of configuration.
[testng] [2024-11-07 01:47:35,736] [pool-1-thread-4] Initializing /data/imagesc-84715/working.vws:
[testng] 01:47:35,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:47:35,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:35,737 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-07_01-47-35.log]
[testng] 01:47:35,738 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11bb4551 - End of configuration.
[testng] [2024-11-07 01:47:36,691] [pool-1-thread-3] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws:
[testng] 01:47:36,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:47:36,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:36,692 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-07_01-47-36.log]
[testng] 01:47:36,692 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50ddf602 - End of configuration.
[testng] [2024-11-07 01:47:37,362] [pool-1-thread-2] Initializing /data/andreas/090812E4.vws:
[testng] 01:47:37,362 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:47:37,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:37,363 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-07_01-47-37.log]
[testng] 01:47:37,364 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3965c4cc - End of configuration.
[testng] [2024-11-07 01:47:48,957] [pool-1-thread-10] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws:
[testng] [2024-11-07 01:47:51,946] [pool-1-thread-8] Initializing /data/venu/060310/drug addition _BAM.vws:
[testng] [2024-11-07 01:47:52,812] [pool-1-thread-6] Initializing /data/christian/080807epi/080807epi2.vws:
[testng] [2024-11-07 01:48:04,242] [pool-1-thread-11] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws:
[testng] [2024-11-07 01:48:10,620] [pool-1-thread-9] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws:
[testng] [2024-11-07 01:48:17,247] [pool-1-thread-6] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws:
[testng] [2024-11-07 01:48:18,326] [pool-1-thread-3] Initializing /data/andreas/090811E1.vws:
[testng] [2024-11-07 01:48:25,442] [pool-1-thread-12] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif:
[testng] [2024-11-07 01:48:29,118] [pool-1-thread-1] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws:
[testng] [2024-11-07 01:48:31,564] [pool-1-thread-4] Initializing /data/stephan/two sequences.vws:
[testng] [2024-11-07 01:48:34,867] [pool-1-thread-7] Initializing /data/samples/fibre.vws:
[testng] [2024-11-07 01:48:41,958] [pool-1-thread-12] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif:
[testng] [2024-11-07 01:48:45,594] [pool-1-thread-7] Initializing /data/ian/non_working_tillvision_vws/20120404.vws:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1325, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 20 minutes 30 seconds
Finished: SUCCESS