Started by upstream project "BIOFORMATS-test-repo" build number 244
originally caused by:
Started by upstream project "Trigger" build number 268
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3
[BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins632300875806921757.sh
+ '[' tillvision = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_38406_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] 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] 01:25:42,431 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:25:42,432 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 01:25:42,432 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:25:42,433 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:25:42,433 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:25:42,434 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:25:42,434 |-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] 01:25:42,434 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:25:42,435 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:25:42,435 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:25:42,435 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:25:42,436 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:25:42,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:25:42,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:25:42,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:25:42,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:25:42,632 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:25:42,632 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:25:42,632 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:25:42,633 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:25:42,633 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 01:25:42,633 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 01:25:42,633 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 198 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-03 01:25:42,643] [main] java.version = 17.0.2
[testng] 01:25:42,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:25:42,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:25:42,687 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-03_01-25-42.log]
[testng] 01:25:42,688 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-11-03 01:25:42,690] [main] testng.directory = /data
[testng] [2024-11-03 01:25:42,690] [main] testng.configDirectory = /config
[testng] [2024-11-03 01:25:42,699] [main] testng.multiplier = 1.0
[testng] [2024-11-03 01:25:42,700] [main] testng.in-memory = false
[testng] [2024-11-03 01:25:42,700] [main] testng.allow-missing = false
[testng] [2024-11-03 01:25:42,700] [main] user.language = en
[testng] [2024-11-03 01:25:42,700] [main] user.country = ${user.country}
[testng] [2024-11-03 01:25:42,700] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-11-03 01:25:53,486] [main] ----------------------------------------
[testng] [2024-11-03 01:25:53,486] [main] Total files: 46
[testng] [2024-11-03 01:25:53,486] [main] Scan time: 10.786 s (234 ms/file)
[testng] [2024-11-03 01:25:53,486] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 25 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-03 01:26:35,651] [pool-1-thread-1] Initializing /data/venu/060310/drug addition _BAM.vws:
[testng] 01:26:35,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:26:35,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:26:35,653 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-03_01-26-35.log]
[testng] 01:26:35,653 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10834028 - End of configuration.
[testng] [2024-11-03 01:26:36,169] [pool-1-thread-12] Initializing /data/gerhard/test.vws:
[testng] 01:26:36,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:26:36,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:26:36,170 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-03_01-26-36.log]
[testng] 01:26:36,171 |-INFO in ch.qos.logback.core.sift.SiftProcessor@697b8b88 - End of configuration.
[testng] [2024-11-03 01:26:36,597] [pool-1-thread-11] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif:
[testng] 01:26:36,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:26:36,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:26:36,598 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-03_01-26-36.log]
[testng] 01:26:36,599 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66ebce75 - End of configuration.
[testng] [2024-11-03 01:26:37,996] [pool-1-thread-10] Initializing /data/ian/non_working_tillvision_vws/20120404.vws:
[testng] 01:26:37,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:26:37,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:26:37,997 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-03_01-26-37.log]
[testng] 01:26:37,997 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72addcd6 - End of configuration.
[testng] [2024-11-03 01:26:41,962] [pool-1-thread-9] Initializing /data/samples/fibre.vws:
[testng] 01:26:41,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:26:41,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:26:41,963 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-03_01-26-41.log]
[testng] 01:26:41,963 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1aa3dedf - End of configuration.
[testng] [2024-11-03 01:26:42,365] [pool-1-thread-8] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws:
[testng] 01:26:42,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:26:42,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:26:42,366 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-03_01-26-42.log]
[testng] 01:26:42,366 |-INFO in ch.qos.logback.core.sift.SiftProcessor@369ff5ed - End of configuration.
[testng] [2024-11-03 01:26:43,398] [pool-1-thread-7] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws:
[testng] 01:26:43,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:26:43,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:26:43,399 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-03_01-26-43.log]
[testng] 01:26:43,399 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fb549d2 - End of configuration.
[testng] [2024-11-03 01:26:43,891] [pool-1-thread-6] Initializing /data/christian/080807epi/080807epi2.vws:
[testng] 01:26:43,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:26:43,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:26:43,892 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-03_01-26-43.log]
[testng] 01:26:43,893 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58432731 - End of configuration.
[testng] [2024-11-03 01:26:44,319] [pool-1-thread-5] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws:
[testng] 01:26:44,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:26:44,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:26:44,319 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-03_01-26-44.log]
[testng] 01:26:44,320 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cd14542 - End of configuration.
[testng] [2024-11-03 01:26:46,099] [pool-1-thread-4] Initializing /data/christian/080807ionophore/080807ionophore3.vws:
[testng] 01:26:46,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:26:46,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:26:46,100 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-03_01-26-46.log]
[testng] 01:26:46,100 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bfe966b - End of configuration.
[testng] [2024-11-03 01:26:46,516] [pool-1-thread-3] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws:
[testng] 01:26:46,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:26:46,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:26:46,517 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-03_01-26-46.log]
[testng] 01:26:46,517 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18145002 - End of configuration.
[testng] [2024-11-03 01:26:47,008] [pool-1-thread-2] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws:
[testng] 01:26:47,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:26:47,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:26:47,009 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-03_01-26-47.log]
[testng] 01:26:47,009 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6068bc1e - End of configuration.
[testng] [2024-11-03 01:26:54,561] [pool-1-thread-9] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws:
[testng] [2024-11-03 01:26:55,892] [pool-1-thread-12] Initializing /data/imagesc-84715/not working.vws:
[testng] [2024-11-03 01:26:56,743] [pool-1-thread-11] Initializing /data/andreas/090811E1.vws:
[testng] [2024-11-03 01:27:10,227] [pool-1-thread-6] Initializing /data/imagesc-84715/working.vws:
[testng] [2024-11-03 01:27:11,209] [pool-1-thread-4] Initializing /data/stephan/two sequences.vws:
[testng] [2024-11-03 01:27:14,967] [pool-1-thread-2] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws:
[testng] [2024-11-03 01:27:15,689] [pool-1-thread-7] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif:
[testng] [2024-11-03 01:27:17,214] [pool-1-thread-1] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif:
[testng] [2024-11-03 01:27:26,305] [pool-1-thread-7] Initializing /data/ian/working_tillvision_vws/20120322.vws:
[testng] [2024-11-03 01:27:30,197] [pool-1-thread-1] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws:
[testng] [2024-11-03 01:27:31,977] [pool-1-thread-12] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif:
[testng] [2024-11-03 01:27:39,031] [pool-1-thread-9] Initializing /data/andreas/090812E4.vws:
[testng] [2024-11-03 01:27:43,365] [pool-1-thread-12] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1325, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 15 minutes 46 seconds
Finished: SUCCESS