Started by upstream project "BIOFORMATS-test-repo" build number 365
originally caused by:
Started by upstream project "Trigger" build number 391
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2
[BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins12738141393786358737.sh
+ '[' tillvision = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_58202_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] 01:38:08,484 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15
[testng] 01:38:08,486 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service.
[testng] 01:38:08,486 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:38:08,486 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:38:08,487 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:38:08,487 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:38:08,488 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:38:08,488 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:38:08,488 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:38:08,488 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:38:08,489 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:38:08,489 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:38:08,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:38:08,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:38:08,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:38:08,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:38:08,686 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:38:08,686 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:38:08,686 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:38:08,687 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:38:08,687 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration.
[testng] 01:38:08,687 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point
[testng] 01:38:08,688 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 200 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2025-03-05 01:38:08,696] [main] java.version = 17.0.2
[testng] 01:38:08,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:38:08,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:38:08,739 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-05_01-38-08.log]
[testng] 01:38:08,741 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration.
[testng] [2025-03-05 01:38:08,743] [main] testng.directory = /data
[testng] [2025-03-05 01:38:08,743] [main] testng.configDirectory = /config
[testng] [2025-03-05 01:38:08,752] [main] testng.multiplier = 1.0
[testng] [2025-03-05 01:38:08,753] [main] testng.in-memory = false
[testng] [2025-03-05 01:38:08,753] [main] testng.allow-missing = false
[testng] [2025-03-05 01:38:08,753] [main] user.language = en
[testng] [2025-03-05 01:38:08,754] [main] user.country = ${user.country}
[testng] [2025-03-05 01:38:08,754] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2025-03-05 01:38:24,371] [main] ----------------------------------------
[testng] [2025-03-05 01:38:24,371] [main] Total files: 46
[testng] [2025-03-05 01:38:24,371] [main] Scan time: 15.617 s (339 ms/file)
[testng] [2025-03-05 01:38:24,371] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 25 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2025-03-05 01:39:18,915] [pool-1-thread-1] Initializing /data/andreas/090811E1.vws:
[testng] 01:39:18,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:39:18,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:18,917 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-05_01-39-18.log]
[testng] 01:39:18,917 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e71c6c1 - End of configuration.
[testng] [2025-03-05 01:39:24,905] [pool-1-thread-12] Initializing /data/gerhard/test.vws:
[testng] 01:39:24,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:39:24,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:24,907 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-05_01-39-24.log]
[testng] 01:39:24,907 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cc9158d - End of configuration.
[testng] [2025-03-05 01:39:25,470] [pool-1-thread-11] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws:
[testng] 01:39:25,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:39:25,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:25,471 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-05_01-39-25.log]
[testng] 01:39:25,471 |-INFO in ch.qos.logback.core.sift.SiftProcessor@705f4ee - End of configuration.
[testng] [2025-03-05 01:39:27,449] [pool-1-thread-10] Initializing /data/ian/non_working_tillvision_vws/20120404.vws:
[testng] 01:39:27,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:39:27,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:27,450 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-05_01-39-27.log]
[testng] 01:39:27,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64ee74a4 - End of configuration.
[testng] [2025-03-05 01:39:31,889] [pool-1-thread-9] Initializing /data/imagesc-84715/not working.vws:
[testng] 01:39:31,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:39:31,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:31,891 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-05_01-39-31.log]
[testng] 01:39:31,891 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1298b0d1 - End of configuration.
[testng] [2025-03-05 01:39:32,579] [pool-1-thread-8] Initializing /data/venu/060310/drug addition _BAM.vws:
[testng] 01:39:32,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:39:32,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:32,580 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-05_01-39-32.log]
[testng] 01:39:32,581 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18c500a3 - End of configuration.
[testng] [2025-03-05 01:39:33,331] [pool-1-thread-7] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif:
[testng] 01:39:33,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:39:33,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:33,332 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-05_01-39-33.log]
[testng] 01:39:33,332 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2750c33 - End of configuration.
[testng] [2025-03-05 01:39:35,065] [pool-1-thread-6] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws:
[testng] 01:39:35,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:39:35,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:35,066 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-05_01-39-35.log]
[testng] 01:39:35,066 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5503af77 - End of configuration.
[testng] [2025-03-05 01:39:35,784] [pool-1-thread-5] Initializing /data/christian/080807ionophore/080807ionophore3.vws:
[testng] 01:39:35,784 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:39:35,784 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:35,785 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-05_01-39-35.log]
[testng] 01:39:35,786 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45d02c99 - End of configuration.
[testng] [2025-03-05 01:39:36,349] [pool-1-thread-4] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws:
[testng] 01:39:36,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:39:36,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:36,350 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-05_01-39-36.log]
[testng] 01:39:36,350 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ccb31f1 - End of configuration.
[testng] [2025-03-05 01:39:36,931] [pool-1-thread-3] Initializing /data/samples/fibre.vws:
[testng] 01:39:36,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:39:36,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:36,932 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-05_01-39-36.log]
[testng] 01:39:36,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70ff39d1 - End of configuration.
[testng] [2025-03-05 01:39:37,386] [pool-1-thread-2] Initializing /data/christian/080807epi/080807epi2.vws:
[testng] 01:39:37,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:39:37,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:39:37,387 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-05_01-39-37.log]
[testng] 01:39:37,388 |-INFO in ch.qos.logback.core.sift.SiftProcessor@771b9c35 - End of configuration.
[testng] [2025-03-05 01:39:45,728] [pool-1-thread-3] Initializing /data/stephan/two sequences.vws:
[testng] [2025-03-05 01:39:46,712] [pool-1-thread-12] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif:
[testng] [2025-03-05 01:39:50,365] [pool-1-thread-7] Initializing /data/imagesc-84715/working.vws:
[testng] [2025-03-05 01:40:00,456] [pool-1-thread-12] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif:
[testng] [2025-03-05 01:40:03,850] [pool-1-thread-2] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws:
[testng] [2025-03-05 01:40:04,706] [pool-1-thread-5] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws:
[testng] [2025-03-05 01:40:10,102] [pool-1-thread-9] Initializing /data/andreas/090812E4.vws:
[testng] [2025-03-05 01:40:17,283] [pool-1-thread-12] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws:
[testng] [2025-03-05 01:40:20,567] [pool-1-thread-4] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws:
[testng] [2025-03-05 01:40:21,701] [pool-1-thread-8] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws:
[testng] [2025-03-05 01:40:24,823] [pool-1-thread-6] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws:
[testng] [2025-03-05 01:40:37,686] [pool-1-thread-7] Initializing /data/ian/working_tillvision_vws/20120322.vws:
[testng] [2025-03-05 01:40:48,659] [pool-1-thread-3] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1325, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 19 minutes 45 seconds
Finished: SUCCESS