Started by upstream project "BIOFORMATS-test-repo" build number 104
originally caused by:
Started by upstream project "Trigger" build number 116
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8
[BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins3678498688327318630.sh
+ '[' tillvision = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_16119_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 01:45:06,583 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:45:06,585 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service.
[testng] 01:45:06,585 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:45:06,586 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:45:06,587 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:45:06,587 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:45:06,587 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:45:06,587 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:45:06,588 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:45:06,589 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:45:06,589 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:45:06,590 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:45:06,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:45:06,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:45:06,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:45:06,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:45:06,840 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:45:06,840 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:45:06,841 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:45:06,841 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:45:06,841 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration.
[testng] 01:45:06,842 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point
[testng] 01:45:06,842 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 254 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-27 01:45:06,855] [main] java.version = 21
[testng] 01:45:06,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:45:06,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:45:06,924 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-27_01-45-06.log]
[testng] 01:45:06,926 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration.
[testng] [2024-06-27 01:45:06,929] [main] testng.directory = /data
[testng] [2024-06-27 01:45:06,929] [main] testng.configDirectory = /config
[testng] [2024-06-27 01:45:06,942] [main] testng.multiplier = 1.0
[testng] [2024-06-27 01:45:06,943] [main] testng.in-memory = false
[testng] [2024-06-27 01:45:06,943] [main] testng.allow-missing = false
[testng] [2024-06-27 01:45:06,943] [main] user.language = en
[testng] [2024-06-27 01:45:06,943] [main] user.country = ${user.country}
[testng] [2024-06-27 01:45:06,943] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-06-27 01:45:08,719] [main] ----------------------------------------
[testng] [2024-06-27 01:45:08,719] [main] Total files: 46
[testng] [2024-06-27 01:45:08,719] [main] Scan time: 1.776 s (38 ms/file)
[testng] [2024-06-27 01:45:08,720] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 25 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-27 01:45:27,043] [pool-1-thread-1] Initializing /data/christian/080807epi/080807epi2.vws:
[testng] 01:45:27,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:45:27,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:45:27,045 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-27_01-45-27.log]
[testng] 01:45:27,046 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a94b608 - End of configuration.
[testng] [2024-06-27 01:45:27,128] [pool-1-thread-12] Initializing /data/samples/fibre.vws:
[testng] 01:45:27,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:45:27,129 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:45:27,129 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-27_01-45-27.log]
[testng] 01:45:27,130 |-INFO in ch.qos.logback.core.sift.SiftProcessor@301bd4e3 - End of configuration.
[testng] [2024-06-27 01:45:27,174] [pool-1-thread-11] Initializing /data/andreas/090812E4.vws:
[testng] 01:45:27,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:45:27,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:45:27,176 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-27_01-45-27.log]
[testng] 01:45:27,176 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ab030c2 - End of configuration.
[testng] [2024-06-27 01:45:28,163] [pool-1-thread-10] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws:
[testng] 01:45:28,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:45:28,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:45:28,164 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-27_01-45-28.log]
[testng] 01:45:28,165 |-INFO in ch.qos.logback.core.sift.SiftProcessor@195e827 - End of configuration.
[testng] [2024-06-27 01:45:29,778] [pool-1-thread-9] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif:
[testng] 01:45:29,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:45:29,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:45:29,782 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-27_01-45-29.log]
[testng] 01:45:29,783 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ae07d75 - End of configuration.
[testng] [2024-06-27 01:45:29,857] [pool-1-thread-8] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws:
[testng] 01:45:29,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:45:29,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:45:29,858 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-27_01-45-29.log]
[testng] 01:45:29,859 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a88d2bc - End of configuration.
[testng] [2024-06-27 01:45:29,918] [pool-1-thread-7] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws:
[testng] 01:45:29,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:45:29,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:45:29,919 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-27_01-45-29.log]
[testng] 01:45:29,920 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9fedd6a - End of configuration.
[testng] [2024-06-27 01:45:30,122] [pool-1-thread-6] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif:
[testng] 01:45:30,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:45:30,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:45:30,123 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-27_01-45-30.log]
[testng] 01:45:30,123 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44d0ac9e - End of configuration.
[testng] [2024-06-27 01:45:30,154] [pool-1-thread-5] Initializing /data/stephan/two sequences.vws:
[testng] 01:45:30,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:45:30,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:45:30,155 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-27_01-45-30.log]
[testng] 01:45:30,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63eee6d - End of configuration.
[testng] [2024-06-27 01:45:30,174] [pool-1-thread-4] Initializing /data/imagesc-84715/working.vws:
[testng] 01:45:30,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:45:30,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:45:30,175 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-27_01-45-30.log]
[testng] 01:45:30,175 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33b3a914 - End of configuration.
[testng] [2024-06-27 01:45:30,567] [pool-1-thread-3] Initializing /data/andreas/090811E1.vws:
[testng] 01:45:30,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:45:30,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:45:30,568 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-27_01-45-30.log]
[testng] 01:45:30,569 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1657217e - End of configuration.
[testng] [2024-06-27 01:45:33,379] [pool-1-thread-2] Initializing /data/ian/working_tillvision_vws/20120322.vws:
[testng] 01:45:33,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:45:33,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:45:33,380 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-27_01-45-33.log]
[testng] 01:45:33,380 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32e189c0 - End of configuration.
[testng] [2024-06-27 01:45:38,664] [pool-1-thread-12] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws:
[testng] [2024-06-27 01:45:38,682] [pool-1-thread-6] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif:
[testng] [2024-06-27 01:45:38,724] [pool-1-thread-9] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif:
[testng] [2024-06-27 01:45:39,174] [pool-1-thread-5] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws:
[testng] [2024-06-27 01:45:39,475] [pool-1-thread-1] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws:
[testng] [2024-06-27 01:45:39,517] [pool-1-thread-6] Initializing /data/imagesc-84715/not working.vws:
[testng] [2024-06-27 01:45:39,684] [pool-1-thread-9] Initializing /data/venu/060310/drug addition _BAM.vws:
[testng] [2024-06-27 01:45:39,845] [pool-1-thread-8] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws:
[testng] [2024-06-27 01:45:41,135] [pool-1-thread-12] Initializing /data/ian/non_working_tillvision_vws/20120404.vws:
[testng] [2024-06-27 01:45:45,609] [pool-1-thread-5] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws:
[testng] [2024-06-27 01:45:46,473] [pool-1-thread-7] Initializing /data/gerhard/test.vws:
[testng] [2024-06-27 01:45:46,689] [pool-1-thread-1] Initializing /data/christian/080807ionophore/080807ionophore3.vws:
[testng] [2024-06-27 01:45:46,885] [pool-1-thread-5] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1325, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 5 minutes 42 seconds
Finished: SUCCESS