Started by upstream project "BIOFORMATS-test-repo" build number 101
originally caused by:
Started by upstream project "Trigger" build number 112
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4
[BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins16765989313132264620.sh
+ '[' amira = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_15577_merge_ci -v /uod/idr/repos/curated/amira:/data -v /uod/idr-scratch/merge-ci/curated/amira:/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] 01:21:52,748 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:21:52,749 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 01:21:52,749 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:21:52,750 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:21:52,751 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:21:52,751 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:21:52,751 |-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] 01:21:52,751 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:21:52,752 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:21:52,752 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:21:52,753 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:21:52,753 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:21:52,928 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:21:52,928 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:21:52,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:21:52,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:21:52,958 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:21:52,958 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:21:52,958 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:21:52,959 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:21:52,959 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 01:21:52,960 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 01:21:52,960 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 208 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-23 01:21:52,971] [main] java.version = 17.0.2
[testng] 01:21:52,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:21:52,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:53,025 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-23_01-21-52.log]
[testng] 01:21:53,027 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-06-23 01:21:53,029] [main] testng.directory = /data
[testng] [2024-06-23 01:21:53,030] [main] testng.configDirectory = /config
[testng] [2024-06-23 01:21:53,043] [main] testng.multiplier = 1.0
[testng] [2024-06-23 01:21:53,044] [main] testng.in-memory = false
[testng] [2024-06-23 01:21:53,044] [main] testng.allow-missing = false
[testng] [2024-06-23 01:21:53,044] [main] user.language = en
[testng] [2024-06-23 01:21:53,044] [main] user.country = ${user.country}
[testng] [2024-06-23 01:21:53,044] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-06-23 01:21:53,641] [main] ----------------------------------------
[testng] [2024-06-23 01:21:53,641] [main] Total files: 15
[testng] [2024-06-23 01:21:53,641] [main] Scan time: 0.596 s (39 ms/file)
[testng] [2024-06-23 01:21:53,641] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 12 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-23 01:21:54,745] [pool-1-thread-1] Initializing /data/johannes/template.labels:
[testng] 01:21:54,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:21:54,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:54,747 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-23_01-21-54.log]
[testng] 01:21:54,748 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28316d5a - End of configuration.
[testng] [2024-06-23 01:21:54,773] [pool-1-thread-12] Initializing /data/jeremy/Virus_Membrane7.am:
[testng] 01:21:54,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:21:54,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:54,774 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-23_01-21-54.log]
[testng] 01:21:54,774 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27cb65b8 - End of configuration.
[testng] [2024-06-23 01:21:54,811] [pool-1-thread-11] Initializing /data/public/ignacio/test.am:
[testng] 01:21:54,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:21:54,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:54,812 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-23_01-21-54.log]
[testng] 01:21:54,813 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2653f72b - End of configuration.
[testng] [2024-06-23 01:21:54,826] [pool-1-thread-10] Initializing /data/public/imagesc-50585/BF_CheckAmira.am:
[testng] 01:21:54,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:21:54,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:54,827 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-23_01-21-54.log]
[testng] 01:21:54,828 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cb74978 - End of configuration.
[testng] [2024-06-23 01:21:54,844] [pool-1-thread-9] Initializing /data/jeremy/Hiv_spikes.am:
[testng] 01:21:54,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:21:54,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:54,845 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-23_01-21-54.log]
[testng] 01:21:54,846 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d3c5000 - End of configuration.
[testng] [2024-06-23 01:21:54,882] [pool-1-thread-8] Initializing /data/samples/emptykey/test.am:
[testng] 01:21:54,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:21:54,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:54,885 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-23_01-21-54.log]
[testng] 01:21:54,886 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9c27da4 - End of configuration.
[testng] [2024-06-23 01:21:54,905] [pool-1-thread-7] Initializing /data/jcb/201108088/Haberman-Fig4A-original.am:
[testng] 01:21:54,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:21:54,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:54,906 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-23_01-21-54.log]
[testng] 01:21:54,907 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1dc24ef9 - End of configuration.
[testng] [2024-06-23 01:21:54,971] [pool-1-thread-6] Initializing /data/jeremy/Virus_Membrane7-screenshot.PNG:
[testng] 01:21:54,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:21:54,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:54,973 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-23_01-21-54.log]
[testng] 01:21:54,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d654a70 - End of configuration.
[testng] [2024-06-23 01:21:54,982] [pool-1-thread-5] Initializing /data/public/imagesc-50585/BF_CheckMIB.am:
[testng] 01:21:54,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:21:54,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:54,983 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-23_01-21-54.log]
[testng] 01:21:54,984 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48ef9df7 - End of configuration.
[testng] [2024-06-23 01:21:54,996] [pool-1-thread-4] Initializing /data/ilya/test.am:
[testng] 01:21:54,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:21:54,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:54,997 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-23_01-21-54.log]
[testng] 01:21:54,998 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3206a7c8 - End of configuration.
[testng] [2024-06-23 01:21:55,044] [pool-1-thread-3] Initializing /data/public/imagesc-50585/BF_Check.tif:
[testng] 01:21:55,045 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:21:55,045 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:55,047 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-23_01-21-55.log]
[testng] 01:21:55,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22ebec66 - End of configuration.
[testng] [2024-06-23 01:21:55,091] [pool-1-thread-2] Initializing /data/johannes/template.grey:
[testng] 01:21:55,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:21:55,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:55,095 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-23_01-21-55.log]
[testng] 01:21:55,096 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2daa70fe - End of configuration.
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 636, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 11 seconds
Finished: SUCCESS