Started by upstream project "BIOFORMATS-test-repo" build number 194
originally caused by:
Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9
[BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins14069051302620110871.sh
+ '[' mrc = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_30708_merge_ci -v /uod/idr/repos/curated/mrc:/data -v /uod/idr-scratch/merge-ci/curated/mrc:/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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 11:41:04,943 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 11:41:04,944 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service.
[testng] 11:41:04,944 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 11:41:04,945 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 11:41:04,945 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 11:41:04,945 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 11:41:04,946 |-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] 11:41:04,946 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 11:41:04,946 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 11:41:04,947 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 11:41:04,947 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 11:41:04,947 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 11:41:05,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 11:41:05,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 11:41:05,129 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 11:41:05,129 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 11:41:05,135 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 11:41:05,136 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 11:41:05,136 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 11:41:05,136 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 11:41:05,136 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration.
[testng] 11:41:05,137 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point
[testng] 11:41:05,137 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 191 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-09-19 11:41:05,146] [main] java.version = 21
[testng] 11:41:05,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 11:41:05,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:41:05,191 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-19_11-41-05.log]
[testng] 11:41:05,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration.
[testng] [2024-09-19 11:41:05,194] [main] testng.directory = /data
[testng] [2024-09-19 11:41:05,194] [main] testng.configDirectory = /config
[testng] [2024-09-19 11:41:05,203] [main] testng.multiplier = 1.0
[testng] [2024-09-19 11:41:05,203] [main] testng.in-memory = false
[testng] [2024-09-19 11:41:05,203] [main] testng.allow-missing = false
[testng] [2024-09-19 11:41:05,203] [main] user.language = en
[testng] [2024-09-19 11:41:05,204] [main] user.country = ${user.country}
[testng] [2024-09-19 11:41:05,204] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-09-19 11:41:10,564] [main] ----------------------------------------
[testng] [2024-09-19 11:41:10,564] [main] Total files: 20
[testng] [2024-09-19 11:41:10,564] [main] Scan time: 5.36 s (268 ms/file)
[testng] [2024-09-19 11:41:10,565] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 20 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-09-19 11:41:15,157] [pool-1-thread-1] Initializing /data/bioformats2raw-198/test_uint8.mrc:
[testng] 11:41:15,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 11:41:15,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:41:15,159 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-19_11-41-15.log]
[testng] 11:41:15,159 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e21c232 - End of configuration.
[testng] [2024-09-19 11:41:15,337] [pool-1-thread-12] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc:
[testng] 11:41:15,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 11:41:15,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:41:15,338 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-19_11-41-15.log]
[testng] 11:41:15,339 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18a26865 - End of configuration.
[testng] [2024-09-19 11:41:15,532] [pool-1-thread-11] Initializing /data/dan/three.mrc:
[testng] 11:41:15,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 11:41:15,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:41:15,533 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-19_11-41-15.log]
[testng] 11:41:15,534 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ff4dbb3 - End of configuration.
[testng] [2024-09-19 11:41:15,729] [pool-1-thread-10] Initializing /data/samples/golgi.mrc:
[testng] 11:41:15,729 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 11:41:15,729 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:41:15,730 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-19_11-41-15.log]
[testng] 11:41:15,730 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b1497d - End of configuration.
[testng] [2024-09-19 11:41:16,164] [pool-1-thread-9] Initializing /data/jcb/thylakoid5.rec:
[testng] 11:41:16,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 11:41:16,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:41:16,165 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-19_11-41-16.log]
[testng] 11:41:16,165 |-INFO in ch.qos.logback.core.sift.SiftProcessor@644f4ccc - End of configuration.
[testng] [2024-09-19 11:41:16,576] [pool-1-thread-8] Initializing /data/ticket-10073/wtjoin4.rec:
[testng] 11:41:16,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 11:41:16,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:41:16,577 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-19_11-41-16.log]
[testng] 11:41:16,577 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bbc3868 - End of configuration.
[testng] [2024-09-19 11:41:16,782] [pool-1-thread-7] Initializing /data/ascb/c191ali.mrc:
[testng] 11:41:16,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 11:41:16,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:41:16,783 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-19_11-41-16.log]
[testng] 11:41:16,783 |-INFO in ch.qos.logback.core.sift.SiftProcessor@342a5d84 - End of configuration.
[testng] [2024-09-19 11:41:17,004] [pool-1-thread-6] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc:
[testng] 11:41:17,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 11:41:17,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:41:17,005 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-19_11-41-17.log]
[testng] 11:41:17,006 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f395f6 - End of configuration.
[testng] [2024-09-19 11:41:17,323] [pool-1-thread-5] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map:
[testng] 11:41:17,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 11:41:17,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:41:17,324 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-19_11-41-17.log]
[testng] 11:41:17,325 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b7e14b1 - End of configuration.
[testng] [2024-09-19 11:41:17,565] [pool-1-thread-4] Initializing /data/ascb/cfa1071.mrc:
[testng] 11:41:17,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 11:41:17,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:41:17,566 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-19_11-41-17.log]
[testng] 11:41:17,566 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a5ee39c - End of configuration.
[testng] [2024-09-19 11:41:17,857] [pool-1-thread-3] Initializing /data/strand/Series1_A.mrc:
[testng] 11:41:17,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 11:41:17,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:41:17,858 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-19_11-41-17.log]
[testng] 11:41:17,858 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dabef9a - End of configuration.
[testng] [2024-09-19 11:41:18,079] [pool-1-thread-2] Initializing /data/samples/1160.mrc:
[testng] 11:41:18,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 11:41:18,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:41:18,080 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-19_11-41-18.log]
[testng] 11:41:18,081 |-INFO in ch.qos.logback.core.sift.SiftProcessor@141e7d0c - End of configuration.
[testng] [2024-09-19 11:41:22,271] [pool-1-thread-1] Initializing /data/ascb/c191.st:
[testng] [2024-09-19 11:41:22,489] [pool-1-thread-5] Initializing /data/ascb/514_9903.mrc:
[testng] [2024-09-19 11:41:22,695] [pool-1-thread-10] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc:
[testng] [2024-09-19 11:41:22,937] [pool-1-thread-7] Initializing /data/dan/one.mrc:
[testng] [2024-09-19 11:41:23,530] [pool-1-thread-6] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc:
[testng] [2024-09-19 11:41:23,785] [pool-1-thread-9] Initializing /data/jcb/thyl-apr23-4.rec:
[testng] [2024-09-19 11:41:24,321] [pool-1-thread-8] Initializing /data/dan/two.mrc:
[testng] [2024-09-19 11:41:24,565] [pool-1-thread-11] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1060, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 26 seconds
Finished: SUCCESS