Started by upstream project "BIOFORMATS-test-repo" build number 42
originally caused by:
Started by upstream project "Trigger" build number 49
originally caused by:
Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2
[BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins7813727193731534018.sh
+ '[' mrc = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_5936_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] 1 warning
test-automated:
[testng] WARNING: An illegal reflective access operation has occurred
[testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket
[testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener
[testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
[testng] WARNING: All illegal access operations will be denied in a future release
[testng] File leak detector installed
[testng] 06:24:06,563 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 06:24:06,565 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 06:24:06,565 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 06:24:06,566 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 06:24:06,567 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 06:24:06,567 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 06:24:06,568 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 06:24:06,568 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 06:24:06,568 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 06:24:06,569 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 06:24:06,569 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 06:24:06,570 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 06:24:06,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 06:24:06,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 06:24:06,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 06:24:06,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 06:24:06,806 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 06:24:06,806 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 06:24:06,806 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 06:24:06,806 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 06:24:06,807 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 06:24:06,807 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 06:24:06,808 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 240 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-04-23 06:24:06,819] [main] java.version = 11.0.16
[testng] 06:24:06,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 06:24:06,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:24:06,872 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-23_06-24-06.log]
[testng] 06:24:06,874 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-04-23 06:24:06,877] [main] testng.directory = /data
[testng] [2024-04-23 06:24:06,877] [main] testng.configDirectory = /config
[testng] [2024-04-23 06:24:06,889] [main] testng.multiplier = 1.0
[testng] [2024-04-23 06:24:06,891] [main] testng.in-memory = false
[testng] [2024-04-23 06:24:06,892] [main] testng.allow-missing = false
[testng] [2024-04-23 06:24:06,892] [main] user.language = en
[testng] [2024-04-23 06:24:06,892] [main] user.country = ${user.country}
[testng] [2024-04-23 06:24:06,892] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-04-23 06:24:08,176] [main] ----------------------------------------
[testng] [2024-04-23 06:24:08,177] [main] Total files: 20
[testng] [2024-04-23 06:24:08,177] [main] Scan time: 1.284 s (64 ms/file)
[testng] [2024-04-23 06:24:08,177] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 20 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-04-23 06:24:08,764] [pool-1-thread-1] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc:
[testng] 06:24:08,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 06:24:08,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:24:08,776 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-23_06-24-08.log]
[testng] 06:24:08,776 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c4a67da - End of configuration.
[testng] [2024-04-23 06:24:08,797] [pool-1-thread-12] Initializing /data/ascb/c191.st:
[testng] 06:24:08,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 06:24:08,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:24:08,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-23_06-24-08.log]
[testng] 06:24:08,802 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42e60e0c - End of configuration.
[testng] [2024-04-23 06:24:08,818] [pool-1-thread-11] Initializing /data/dan/two.mrc:
[testng] 06:24:08,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 06:24:08,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:24:08,819 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-23_06-24-08.log]
[testng] 06:24:08,819 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dedd677 - End of configuration.
[testng] [2024-04-23 06:24:08,839] [pool-1-thread-10] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc:
[testng] 06:24:08,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 06:24:08,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:24:08,841 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-23_06-24-08.log]
[testng] 06:24:08,841 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b89bd71 - End of configuration.
[testng] [2024-04-23 06:24:08,859] [pool-1-thread-9] Initializing /data/samples/golgi.mrc:
[testng] 06:24:08,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 06:24:08,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:24:08,860 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-23_06-24-08.log]
[testng] 06:24:08,860 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b0c73f5 - End of configuration.
[testng] [2024-04-23 06:24:08,916] [pool-1-thread-8] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc:
[testng] 06:24:08,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 06:24:08,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:24:08,917 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-23_06-24-08.log]
[testng] 06:24:08,918 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b1076e3 - End of configuration.
[testng] [2024-04-23 06:24:08,986] [pool-1-thread-7] Initializing /data/bioformats2raw-198/test_uint8.mrc:
[testng] 06:24:08,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 06:24:08,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:24:08,987 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-23_06-24-08.log]
[testng] 06:24:08,987 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41a89e1c - End of configuration.
[testng] [2024-04-23 06:24:09,000] [pool-1-thread-6] Initializing /data/ascb/514_9903.mrc:
[testng] 06:24:09,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 06:24:09,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:24:09,002 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-23_06-24-09.log]
[testng] 06:24:09,002 |-INFO in ch.qos.logback.core.sift.SiftProcessor@748b43a3 - End of configuration.
[testng] [2024-04-23 06:24:09,038] [pool-1-thread-5] Initializing /data/jcb/thyl-apr23-4.rec:
[testng] 06:24:09,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 06:24:09,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:24:09,039 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-23_06-24-09.log]
[testng] 06:24:09,040 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b37b149 - End of configuration.
[testng] [2024-04-23 06:24:09,069] [pool-1-thread-4] Initializing /data/jcb/thylakoid5.rec:
[testng] 06:24:09,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 06:24:09,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:24:09,070 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-23_06-24-09.log]
[testng] 06:24:09,071 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59e33c32 - End of configuration.
[testng] [2024-04-23 06:24:09,086] [pool-1-thread-3] Initializing /data/dan/one.mrc:
[testng] 06:24:09,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 06:24:09,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:24:09,087 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-23_06-24-09.log]
[testng] 06:24:09,087 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a9a3d49 - End of configuration.
[testng] [2024-04-23 06:24:09,107] [pool-1-thread-2] Initializing /data/ascb/cfa1071.mrc:
[testng] 06:24:09,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 06:24:09,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:24:09,108 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-23_06-24-09.log]
[testng] 06:24:09,109 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a182810 - End of configuration.
[testng] [2024-04-23 06:24:10,778] [pool-1-thread-7] Initializing /data/ascb/c191ali.mrc:
[testng] [2024-04-23 06:24:10,793] [pool-1-thread-9] Initializing /data/dan/three.mrc:
[testng] [2024-04-23 06:24:10,802] [pool-1-thread-8] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc:
[testng] [2024-04-23 06:24:10,813] [pool-1-thread-12] Initializing /data/ticket-10073/wtjoin4.rec:
[testng] [2024-04-23 06:24:10,822] [pool-1-thread-5] Initializing /data/strand/Series1_A.mrc:
[testng] [2024-04-23 06:24:10,837] [pool-1-thread-1] Initializing /data/samples/1160.mrc:
[testng] [2024-04-23 06:24:11,218] [pool-1-thread-4] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map:
[testng] [2024-04-23 06:24:11,403] [pool-1-thread-3] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1060, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 13 seconds
Finished: SUCCESS