Started by upstream project "BIOFORMATS-test-repo" build number 78
originally caused by:
Started by upstream project "Trigger" build number 86
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder
[BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins11359277299278070089.sh
+ '[' tillvision = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_11855_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] 01:44:18,067 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:44:18,068 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 01:44:18,068 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:44:18,069 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:44:18,069 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:44:18,069 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:44:18,070 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:44:18,070 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:44:18,070 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:44:18,071 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:44:18,071 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:44:18,071 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:44:18,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:44:18,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:44:18,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:44:18,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:44:18,275 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:44:18,276 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:44:18,276 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:44:18,276 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:44:18,276 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 01:44:18,277 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 01:44:18,277 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 207 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-05-29 01:44:18,289] [main] java.version = 17.0.2
[testng] 01:44:18,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:44:18,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:18,358 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-29_01-44-18.log]
[testng] 01:44:18,360 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-05-29 01:44:18,363] [main] testng.directory = /data
[testng] [2024-05-29 01:44:18,363] [main] testng.configDirectory = /config
[testng] [2024-05-29 01:44:18,375] [main] testng.multiplier = 1.0
[testng] [2024-05-29 01:44:18,377] [main] testng.in-memory = false
[testng] [2024-05-29 01:44:18,377] [main] testng.allow-missing = false
[testng] [2024-05-29 01:44:18,377] [main] user.language = en
[testng] [2024-05-29 01:44:18,377] [main] user.country = ${user.country}
[testng] [2024-05-29 01:44:18,377] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-05-29 01:44:19,891] [main] ----------------------------------------
[testng] [2024-05-29 01:44:19,891] [main] Total files: 46
[testng] [2024-05-29 01:44:19,891] [main] Scan time: 1.514 s (32 ms/file)
[testng] [2024-05-29 01:44:19,891] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 25 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-05-29 01:44:40,851] [pool-1-thread-1] Initializing /data/christian/080807ionophore/080807ionophore3.vws:
[testng] 01:44:40,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:44:40,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:40,853 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-29_01-44-40.log]
[testng] 01:44:40,853 |-INFO in ch.qos.logback.core.sift.SiftProcessor@647b6f6a - End of configuration.
[testng] [2024-05-29 01:44:40,956] [pool-1-thread-12] Initializing /data/andreas/090812E4.vws:
[testng] 01:44:40,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:44:40,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:40,958 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-29_01-44-40.log]
[testng] 01:44:40,959 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7acb96c3 - End of configuration.
[testng] [2024-05-29 01:44:42,034] [pool-1-thread-11] Initializing /data/imagesc-84715/working.vws:
[testng] 01:44:42,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:44:42,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:42,035 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-29_01-44-42.log]
[testng] 01:44:42,035 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23e21520 - End of configuration.
[testng] [2024-05-29 01:44:42,502] [pool-1-thread-10] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws:
[testng] 01:44:42,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:44:42,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:42,503 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-29_01-44-42.log]
[testng] 01:44:42,504 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c47ab5 - End of configuration.
[testng] [2024-05-29 01:44:42,733] [pool-1-thread-9] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws:
[testng] 01:44:42,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:44:42,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:42,734 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-29_01-44-42.log]
[testng] 01:44:42,735 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37d85a51 - End of configuration.
[testng] [2024-05-29 01:44:42,753] [pool-1-thread-8] Initializing /data/andreas/090811E1.vws:
[testng] 01:44:42,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:44:42,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:42,754 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-29_01-44-42.log]
[testng] 01:44:42,754 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c05f47a - End of configuration.
[testng] [2024-05-29 01:44:45,976] [pool-1-thread-7] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws:
[testng] 01:44:45,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:44:45,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:45,980 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-29_01-44-45.log]
[testng] 01:44:45,983 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a6daf5c - End of configuration.
[testng] [2024-05-29 01:44:46,019] [pool-1-thread-6] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws:
[testng] 01:44:46,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:44:46,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:46,020 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-29_01-44-46.log]
[testng] 01:44:46,021 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56c0c053 - End of configuration.
[testng] [2024-05-29 01:44:48,154] [pool-1-thread-5] Initializing /data/ian/working_tillvision_vws/20120322.vws:
[testng] 01:44:48,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:44:48,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:48,155 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-29_01-44-48.log]
[testng] 01:44:48,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b22364f - End of configuration.
[testng] [2024-05-29 01:44:52,461] [pool-1-thread-4] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws:
[testng] 01:44:52,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:44:52,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:52,463 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-29_01-44-52.log]
[testng] 01:44:52,464 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e60e8ec - End of configuration.
[testng] [2024-05-29 01:44:53,201] [pool-1-thread-3] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws:
[testng] 01:44:53,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:44:53,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:53,202 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-29_01-44-53.log]
[testng] 01:44:53,203 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e77f532 - End of configuration.
[testng] [2024-05-29 01:44:53,216] [pool-1-thread-2] Initializing /data/ian/non_working_tillvision_vws/20120404.vws:
[testng] 01:44:53,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:44:53,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:53,217 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-29_01-44-53.log]
[testng] 01:44:53,218 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fa03425 - End of configuration.
[testng] [2024-05-29 01:44:59,941] [pool-1-thread-3] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif:
[testng] [2024-05-29 01:44:59,970] [pool-1-thread-9] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif:
[testng] [2024-05-29 01:44:59,999] [pool-1-thread-7] Initializing /data/imagesc-84715/not working.vws:
[testng] [2024-05-29 01:45:00,819] [pool-1-thread-1] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif:
[testng] [2024-05-29 01:45:00,851] [pool-1-thread-9] Initializing /data/samples/fibre.vws:
[testng] [2024-05-29 01:45:00,907] [pool-1-thread-3] Initializing /data/venu/060310/drug addition _BAM.vws:
[testng] [2024-05-29 01:45:01,394] [pool-1-thread-9] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws:
[testng] [2024-05-29 01:45:01,513] [pool-1-thread-1] Initializing /data/christian/080807epi/080807epi2.vws:
[testng] [2024-05-29 01:45:03,651] [pool-1-thread-10] Initializing /data/gerhard/test.vws:
[testng] [2024-05-29 01:45:03,733] [pool-1-thread-1] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif:
[testng] [2024-05-29 01:45:04,304] [pool-1-thread-1] Initializing /data/stephan/two sequences.vws:
[testng] [2024-05-29 01:45:04,769] [pool-1-thread-9] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws:
[testng] [2024-05-29 01:45:05,577] [pool-1-thread-7] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1325, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 7 minutes 4 seconds
Finished: SUCCESS