Started by upstream project "BIOFORMATS-test-repo" build number 32
originally caused by:
Started by upstream project "Trigger" build number 36
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/jenkins1827419380672511083.sh
+ '[' gatan-dm2 = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_4303_merge_ci -v /uod/idr/repos/curated/gatan-dm2:/data -v /uod/idr-scratch/merge-ci/curated/gatan-dm2:/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] 01:44:47,961 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:44:47,962 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 01:44:47,962 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:44:47,963 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:44:47,964 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:44:47,964 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:44:47,965 |-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] 01:44:47,965 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:44:47,965 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:44:47,966 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:44:47,966 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:44:47,967 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:44:48,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:44:48,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:44:48,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:44:48,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:44:48,182 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:44:48,182 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:44:48,182 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:44:48,183 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:44:48,183 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 01:44:48,184 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 01:44:48,184 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 219 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-04-13 01:44:48,194] [main] java.version = 11.0.16
[testng] 01:44:48,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:44:48,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:48,242 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-13_01-44-48.log]
[testng] 01:44:48,244 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-04-13 01:44:48,246] [main] testng.directory = /data
[testng] [2024-04-13 01:44:48,246] [main] testng.configDirectory = /config
[testng] [2024-04-13 01:44:48,256] [main] testng.multiplier = 1.0
[testng] [2024-04-13 01:44:48,258] [main] testng.in-memory = false
[testng] [2024-04-13 01:44:48,258] [main] testng.allow-missing = false
[testng] [2024-04-13 01:44:48,258] [main] user.language = en
[testng] [2024-04-13 01:44:48,258] [main] user.country = ${user.country}
[testng] [2024-04-13 01:44:48,258] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-04-13 01:44:49,267] [main] ----------------------------------------
[testng] [2024-04-13 01:44:49,267] [main] Total files: 25
[testng] [2024-04-13 01:44:49,267] [main] Scan time: 1.008 s (40 ms/file)
[testng] [2024-04-13 01:44:49,267] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 18 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-04-13 01:44:50,494] [pool-1-thread-1] Initializing /data/imagic/Histiocyte in Skin Dermis.dm2:
[testng] 01:44:50,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:44:50,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:50,497 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-13_01-44-50.log]
[testng] 01:44:50,498 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64428fe3 - End of configuration.
[testng] [2024-04-13 01:44:50,521] [pool-1-thread-12] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info1.png:
[testng] 01:44:50,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:44:50,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:50,523 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-13_01-44-50.log]
[testng] 01:44:50,523 |-INFO in ch.qos.logback.core.sift.SiftProcessor@112ae57a - End of configuration.
[testng] [2024-04-13 01:44:50,530] [pool-1-thread-11] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info2.png:
[testng] 01:44:50,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:44:50,531 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:50,532 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-13_01-44-50.log]
[testng] 01:44:50,532 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bac0eee - End of configuration.
[testng] [2024-04-13 01:44:50,538] [pool-1-thread-10] Initializing /data/pang/grating025k.dm2:
[testng] 01:44:50,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:44:50,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:50,539 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-13_01-44-50.log]
[testng] 01:44:50,540 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43043779 - End of configuration.
[testng] [2024-04-13 01:44:50,560] [pool-1-thread-9] Initializing /data/pang/10500x-o4:
[testng] 01:44:50,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:44:50,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:50,562 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-13_01-44-50.log]
[testng] 01:44:50,562 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9a24a15 - End of configuration.
[testng] [2024-04-13 01:44:50,582] [pool-1-thread-8] Initializing /data/imagic/13008.dm2:
[testng] 01:44:50,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:44:50,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:50,583 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-13_01-44-50.log]
[testng] 01:44:50,584 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12c95f2e - End of configuration.
[testng] [2024-04-13 01:44:50,600] [pool-1-thread-7] Initializing /data/imagic/not read correctly/Zucchini_preview.png:
[testng] 01:44:50,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:44:50,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:50,601 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-13_01-44-50.log]
[testng] 01:44:50,602 |-INFO in ch.qos.logback.core.sift.SiftProcessor@145d8751 - End of configuration.
[testng] [2024-04-13 01:44:50,608] [pool-1-thread-6] Initializing /data/pang/screen capture of metadata/tem_dm_general_info.png:
[testng] 01:44:50,609 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:44:50,609 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:50,610 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-13_01-44-50.log]
[testng] 01:44:50,611 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30a27bb9 - End of configuration.
[testng] [2024-04-13 01:44:50,618] [pool-1-thread-5] Initializing /data/pang/unproc-auto:
[testng] 01:44:50,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:44:50,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:50,619 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-13_01-44-50.log]
[testng] 01:44:50,619 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b4fb4dd - End of configuration.
[testng] [2024-04-13 01:44:50,632] [pool-1-thread-4] Initializing /data/pang/screen capture of metadata/tem_dm_keywords_info.png:
[testng] 01:44:50,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:44:50,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:50,633 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-13_01-44-50.log]
[testng] 01:44:50,634 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7496284a - End of configuration.
[testng] [2024-04-13 01:44:50,638] [pool-1-thread-3] Initializing /data/imagic/TEM 10118.dm2:
[testng] 01:44:50,638 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:44:50,638 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:50,639 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-13_01-44-50.log]
[testng] 01:44:50,640 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61d5776a - End of configuration.
[testng] [2024-04-13 01:44:50,653] [pool-1-thread-2] Initializing /data/pang/screen capture of metadata/tem_dm_microscope_info.png:
[testng] 01:44:50,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:44:50,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:50,654 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-13_01-44-50.log]
[testng] 01:44:50,655 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34ee2ce0 - End of configuration.
[testng] [2024-04-13 01:44:52,820] [pool-1-thread-6] Initializing /data/imagic/not read correctly/Abeta Moon_preview.png:
[testng] [2024-04-13 01:44:52,824] [pool-1-thread-5] Initializing /data/pang/signed:
[testng] [2024-04-13 01:44:52,836] [pool-1-thread-10] Initializing /data/imagic/not read correctly/Zucchini.dm2:
[testng] [2024-04-13 01:44:52,848] [pool-1-thread-9] Initializing /data/imagic/not read correctly/Abeta Moon.dm2:
[testng] [2024-04-13 01:44:52,868] [pool-1-thread-8] Initializing /data/pang/DLMeD2E1_010500x03.dm2:
[testng] [2024-04-13 01:44:52,885] [pool-1-thread-3] Initializing /data/imagic/1-1.dm2:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 954, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 9 seconds
Finished: SUCCESS