Started by upstream project "BIOFORMATS-test-repo" build number 313
originally caused by:
Started by upstream project "Trigger" build number 335
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/jenkins13776595594667807878.sh
+ '[' tillvision = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_49617_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 02:29:54,845 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:29:54,846 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service.
[testng] 02:29:54,846 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:29:54,847 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:29:54,847 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:29:54,848 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:29:54,848 |-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] 02:29:54,848 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:29:54,848 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:29:54,849 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:29:54,849 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:29:54,849 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:29:55,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:29:55,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:29:55,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:29:55,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:29:55,041 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:29:55,041 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:29:55,041 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:29:55,042 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:29:55,042 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration.
[testng] 02:29:55,043 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point
[testng] 02:29:55,043 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 195 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2025-01-09 02:29:55,052] [main] java.version = 21
[testng] 02:29:55,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:29:55,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:29:55,097 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-09_02-29-55.log]
[testng] 02:29:55,099 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration.
[testng] [2025-01-09 02:29:55,100] [main] testng.directory = /data
[testng] [2025-01-09 02:29:55,101] [main] testng.configDirectory = /config
[testng] [2025-01-09 02:29:55,110] [main] testng.multiplier = 1.0
[testng] [2025-01-09 02:29:55,111] [main] testng.in-memory = false
[testng] [2025-01-09 02:29:55,111] [main] testng.allow-missing = false
[testng] [2025-01-09 02:29:55,111] [main] user.language = en
[testng] [2025-01-09 02:29:55,111] [main] user.country = ${user.country}
[testng] [2025-01-09 02:29:55,111] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2025-01-09 02:30:09,468] [main] ----------------------------------------
[testng] [2025-01-09 02:30:09,468] [main] Total files: 46
[testng] [2025-01-09 02:30:09,468] [main] Scan time: 14.357 s (312 ms/file)
[testng] [2025-01-09 02:30:09,469] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 25 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2025-01-09 02:30:57,851] [pool-1-thread-1] Initializing /data/imagesc-84715/not working.vws:
[testng] 02:30:57,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:30:57,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:30:57,856 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-09_02-30-57.log]
[testng] 02:30:57,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c8affb7 - End of configuration.
[testng] [2025-01-09 02:30:58,424] [pool-1-thread-12] Initializing /data/andreas/090811E1.vws:
[testng] 02:30:58,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:30:58,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:30:58,425 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-09_02-30-58.log]
[testng] 02:30:58,426 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c7bde09 - End of configuration.
[testng] [2025-01-09 02:31:04,519] [pool-1-thread-11] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws:
[testng] 02:31:04,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:31:04,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:31:04,520 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-09_02-31-04.log]
[testng] 02:31:04,521 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59c48302 - End of configuration.
[testng] [2025-01-09 02:31:05,056] [pool-1-thread-10] Initializing /data/andreas/090812E4.vws:
[testng] 02:31:05,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:31:05,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:31:05,057 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-09_02-31-05.log]
[testng] 02:31:05,057 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b31582d - End of configuration.
[testng] [2025-01-09 02:31:07,858] [pool-1-thread-9] Initializing /data/gerhard/test.vws:
[testng] 02:31:07,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:31:07,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:31:07,859 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-09_02-31-07.log]
[testng] 02:31:07,859 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6475b136 - End of configuration.
[testng] [2025-01-09 02:31:08,380] [pool-1-thread-8] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif:
[testng] 02:31:08,381 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:31:08,381 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:31:08,382 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-09_02-31-08.log]
[testng] 02:31:08,382 |-INFO in ch.qos.logback.core.sift.SiftProcessor@461603bd - End of configuration.
[testng] [2025-01-09 02:31:09,812] [pool-1-thread-7] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws:
[testng] 02:31:09,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:31:09,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:31:09,813 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-09_02-31-09.log]
[testng] 02:31:09,813 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f1ad6e4 - End of configuration.
[testng] [2025-01-09 02:31:10,448] [pool-1-thread-6] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif:
[testng] 02:31:10,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:31:10,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:31:10,449 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-09_02-31-10.log]
[testng] 02:31:10,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@260903aa - End of configuration.
[testng] [2025-01-09 02:31:12,471] [pool-1-thread-5] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws:
[testng] 02:31:12,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:31:12,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:31:12,473 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-09_02-31-12.log]
[testng] 02:31:12,473 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fb216bc - End of configuration.
[testng] [2025-01-09 02:31:14,497] [pool-1-thread-4] Initializing /data/christian/080807ionophore/080807ionophore3.vws:
[testng] 02:31:14,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:31:14,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:31:14,498 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-09_02-31-14.log]
[testng] 02:31:14,498 |-INFO in ch.qos.logback.core.sift.SiftProcessor@629fa43d - End of configuration.
[testng] [2025-01-09 02:31:15,027] [pool-1-thread-3] Initializing /data/ian/non_working_tillvision_vws/20120404.vws:
[testng] 02:31:15,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:31:15,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:31:15,028 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-09_02-31-15.log]
[testng] 02:31:15,028 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a10c7ca - End of configuration.
[testng] [2025-01-09 02:31:19,255] [pool-1-thread-2] Initializing /data/samples/fibre.vws:
[testng] 02:31:19,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:31:19,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:31:19,256 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-09_02-31-19.log]
[testng] 02:31:19,256 |-INFO in ch.qos.logback.core.sift.SiftProcessor@148c9c87 - End of configuration.
[testng] [2025-01-09 02:31:27,156] [pool-1-thread-2] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif:
[testng] [2025-01-09 02:31:29,877] [pool-1-thread-9] Initializing /data/ian/working_tillvision_vws/20120322.vws:
[testng] [2025-01-09 02:31:35,500] [pool-1-thread-8] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif:
[testng] [2025-01-09 02:31:37,437] [pool-1-thread-6] Initializing /data/venu/060310/drug addition _BAM.vws:
[testng] [2025-01-09 02:31:46,017] [pool-1-thread-2] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws:
[testng] [2025-01-09 02:31:47,841] [pool-1-thread-4] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws:
[testng] [2025-01-09 02:31:51,552] [pool-1-thread-8] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws:
[testng] [2025-01-09 02:31:53,121] [pool-1-thread-1] Initializing /data/stephan/two sequences.vws:
[testng] [2025-01-09 02:31:57,363] [pool-1-thread-11] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws:
[testng] [2025-01-09 02:32:17,297] [pool-1-thread-6] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws:
[testng] [2025-01-09 02:32:25,959] [pool-1-thread-2] Initializing /data/imagesc-84715/working.vws:
[testng] [2025-01-09 02:32:36,478] [pool-1-thread-7] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws:
[testng] [2025-01-09 02:32:39,049] [pool-1-thread-11] Initializing /data/christian/080807epi/080807epi2.vws:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1325, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 18 minutes 4 seconds
Finished: SUCCESS