Started by upstream project "BIOFORMATS-test-repo" build number 103
originally caused by:
Started by upstream project "Trigger" build number 114
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7
[BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins1015672300962633444.sh
+ '[' leica-scn = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_16006_merge_ci -v /uod/idr/repos/curated/leica-scn:/data -v /uod/idr-scratch/merge-ci/curated/leica-scn:/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] 02:18:01,378 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:18:01,380 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 02:18:01,380 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:18:01,381 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:18:01,382 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:18:01,382 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:18:01,382 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 02:18:01,382 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:18:01,383 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:18:01,383 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:18:01,384 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:18:01,384 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:18:01,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:18:01,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:18:01,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:18:01,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:18:01,604 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:18:01,604 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:18:01,605 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:18:01,605 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:18:01,605 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 02:18:01,607 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 02:18:01,607 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 224 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-25 02:18:01,617] [main] java.version = 11.0.16
[testng] 02:18:01,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:18:01,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:01,672 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-25_02-18-01.log]
[testng] 02:18:01,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-06-25 02:18:01,678] [main] testng.directory = /data
[testng] [2024-06-25 02:18:01,678] [main] testng.configDirectory = /config
[testng] [2024-06-25 02:18:01,694] [main] testng.multiplier = 1.0
[testng] [2024-06-25 02:18:01,696] [main] testng.in-memory = false
[testng] [2024-06-25 02:18:01,697] [main] testng.allow-missing = false
[testng] [2024-06-25 02:18:01,697] [main] user.language = en
[testng] [2024-06-25 02:18:01,697] [main] user.country = ${user.country}
[testng] [2024-06-25 02:18:01,697] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-06-25 02:18:15,661] [main] ----------------------------------------
[testng] [2024-06-25 02:18:15,661] [main] Total files: 12
[testng] [2024-06-25 02:18:15,661] [main] Scan time: 13.964 s (1163 ms/file)
[testng] [2024-06-25 02:18:15,661] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 12 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-25 02:18:17,071] [pool-1-thread-1] Initializing /data/public/openslide/Leica-1/Leica-1.scn:
[testng] 02:18:17,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:18:17,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:17,074 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-25_02-18-17.log]
[testng] 02:18:17,074 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58b14ee2 - End of configuration.
[testng] [2024-06-25 02:18:17,167] [pool-1-thread-12] Initializing /data/scott/Oral_Biology_13 (1).scn:
[testng] 02:18:17,167 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:18:17,167 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:17,168 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-25_02-18-17.log]
[testng] 02:18:17,169 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44a75546 - End of configuration.
[testng] [2024-06-25 02:18:17,346] [pool-1-thread-11] Initializing /data/public/openslide/Leica-2/Leica-2.scn:
[testng] 02:18:17,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:18:17,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:17,347 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-25_02-18-17.log]
[testng] 02:18:17,347 |-INFO in ch.qos.logback.core.sift.SiftProcessor@669fbdad - End of configuration.
[testng] [2024-06-25 02:18:17,436] [pool-1-thread-10] Initializing /data/michael/collection_0000008286_2012-05-23 17_20_46 fullresolution.jpg:
[testng] 02:18:17,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:18:17,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:17,437 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-25_02-18-17.log]
[testng] 02:18:17,437 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2604837d - End of configuration.
[testng] [2024-06-25 02:18:17,494] [pool-1-thread-9] Initializing /data/mihaela/UCLAD_0000000280_2011-02-10 13_32_55Z.scn:
[testng] 02:18:17,494 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:18:17,494 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:17,495 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-25_02-18-17.log]
[testng] 02:18:17,495 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75cc45e7 - End of configuration.
[testng] [2024-06-25 02:18:17,564] [pool-1-thread-8] Initializing /data/qa-11049/HP15.4994_2015-04-28.scn:
[testng] 02:18:17,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:18:17,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:17,566 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-25_02-18-17.log]
[testng] 02:18:17,566 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a4f4629 - End of configuration.
[testng] [2024-06-25 02:18:17,658] [pool-1-thread-7] Initializing /data/michael/collection_0000008286_2012-05-23 17_20_46 opened usig LOCI.tif:
[testng] 02:18:17,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:18:17,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:17,659 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-25_02-18-17.log]
[testng] 02:18:17,659 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34dd50fa - End of configuration.
[testng] [2024-06-25 02:18:17,737] [pool-1-thread-6] Initializing /data/scott/ImageCollection_0000000418_2010-10-27 13_31_31Z.scn:
[testng] 02:18:17,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:18:17,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:17,739 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-25_02-18-17.log]
[testng] 02:18:17,739 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7747cd08 - End of configuration.
[testng] [2024-06-25 02:18:17,843] [pool-1-thread-5] Initializing /data/qa-17671/132223-12_022a1963-b32e-467f-8242-b51a5295951f.SCN:
[testng] 02:18:17,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:18:17,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:17,845 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-25_02-18-17.log]
[testng] 02:18:17,846 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cdbcba1 - End of configuration.
[testng] [2024-06-25 02:18:17,920] [pool-1-thread-4] Initializing /data/qa-10469/Slide_907790L_DAPI_Ki67.scn:
[testng] 02:18:17,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:18:17,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:17,921 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-25_02-18-17.log]
[testng] 02:18:17,922 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e4786c9 - End of configuration.
[testng] [2024-06-25 02:18:18,110] [pool-1-thread-3] Initializing /data/public/openslide/Leica-3/Leica-3.scn:
[testng] 02:18:18,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:18:18,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:18,111 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-25_02-18-18.log]
[testng] 02:18:18,112 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67fe8c48 - End of configuration.
[testng] [2024-06-25 02:18:18,216] [pool-1-thread-2] Initializing /data/michael/collection_0000008286_2012-05-23 17_20_46.scn:
[testng] 02:18:18,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:18:18,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:18:18,218 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-25_02-18-18.log]
[testng] 02:18:18,218 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c99b9fe - 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: 1 minute 39 seconds
Finished: SUCCESS