Started by upstream project "BIOFORMATS-test-repo" build number 131
originally caused by:
Started by upstream project "Trigger" build number 148
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8
[BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins9199525354496488477.sh
+ '[' gatan-dm2 = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_20540_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] 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] 01:42:55,453 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:42:55,455 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 01:42:55,455 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:42:55,456 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:42:55,456 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:42:55,456 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:42:55,457 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:42:55,457 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:42:55,457 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:42:55,457 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:42:55,458 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:42:55,458 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:42:55,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:42:55,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:42:55,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:42:55,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:42:55,656 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:42:55,656 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:42:55,656 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:42:55,657 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:42:55,657 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 01:42:55,657 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 01:42:55,658 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 201 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-07-24 01:42:55,666] [main] java.version = 17.0.2
[testng] 01:42:55,669 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:42:55,669 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:55,707 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-24_01-42-55.log]
[testng] 01:42:55,708 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-07-24 01:42:55,710] [main] testng.directory = /data
[testng] [2024-07-24 01:42:55,710] [main] testng.configDirectory = /config
[testng] [2024-07-24 01:42:55,718] [main] testng.multiplier = 1.0
[testng] [2024-07-24 01:42:55,719] [main] testng.in-memory = false
[testng] [2024-07-24 01:42:55,719] [main] testng.allow-missing = false
[testng] [2024-07-24 01:42:55,719] [main] user.language = en
[testng] [2024-07-24 01:42:55,719] [main] user.country = ${user.country}
[testng] [2024-07-24 01:42:55,719] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-07-24 01:42:56,451] [main] ----------------------------------------
[testng] [2024-07-24 01:42:56,451] [main] Total files: 25
[testng] [2024-07-24 01:42:56,452] [main] Scan time: 0.732 s (29 ms/file)
[testng] [2024-07-24 01:42:56,452] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 18 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-07-24 01:42:57,359] [pool-1-thread-1] Initializing /data/pang/screen capture of metadata/tem_dm_microscope_info.png:
[testng] 01:42:57,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:42:57,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:57,362 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-24_01-42-57.log]
[testng] 01:42:57,363 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42702a80 - End of configuration.
[testng] [2024-07-24 01:42:57,373] [pool-1-thread-12] Initializing /data/imagic/13008.dm2:
[testng] 01:42:57,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:42:57,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:57,375 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-24_01-42-57.log]
[testng] 01:42:57,375 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39ccd99b - End of configuration.
[testng] [2024-07-24 01:42:57,394] [pool-1-thread-11] Initializing /data/pang/screen capture of metadata/tem_dm_keywords_info.png:
[testng] 01:42:57,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:42:57,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:57,395 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-24_01-42-57.log]
[testng] 01:42:57,395 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bcc4d80 - End of configuration.
[testng] [2024-07-24 01:42:57,400] [pool-1-thread-10] Initializing /data/imagic/not read correctly/Zucchini_preview.png:
[testng] 01:42:57,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:42:57,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:57,401 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-24_01-42-57.log]
[testng] 01:42:57,401 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b2b50f8 - End of configuration.
[testng] [2024-07-24 01:42:57,405] [pool-1-thread-9] Initializing /data/imagic/not read correctly/Zucchini.dm2:
[testng] 01:42:57,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:42:57,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:57,406 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-24_01-42-57.log]
[testng] 01:42:57,406 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c31a518 - End of configuration.
[testng] [2024-07-24 01:42:57,418] [pool-1-thread-8] Initializing /data/imagic/Histiocyte in Skin Dermis.dm2:
[testng] 01:42:57,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:42:57,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:57,419 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-24_01-42-57.log]
[testng] 01:42:57,419 |-INFO in ch.qos.logback.core.sift.SiftProcessor@750659fa - End of configuration.
[testng] [2024-07-24 01:42:57,431] [pool-1-thread-7] Initializing /data/pang/screen capture of metadata/tem_dm_general_info.png:
[testng] 01:42:57,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:42:57,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:57,433 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-24_01-42-57.log]
[testng] 01:42:57,433 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ef58ccc - End of configuration.
[testng] [2024-07-24 01:42:57,438] [pool-1-thread-6] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info1.png:
[testng] 01:42:57,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:42:57,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:57,439 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-24_01-42-57.log]
[testng] 01:42:57,439 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28c05bca - End of configuration.
[testng] [2024-07-24 01:42:57,444] [pool-1-thread-5] Initializing /data/imagic/1-1.dm2:
[testng] 01:42:57,444 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:42:57,444 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:57,445 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-24_01-42-57.log]
[testng] 01:42:57,445 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34ef661 - End of configuration.
[testng] [2024-07-24 01:42:57,459] [pool-1-thread-4] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info2.png:
[testng] 01:42:57,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:42:57,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:57,460 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-24_01-42-57.log]
[testng] 01:42:57,460 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1af301b8 - End of configuration.
[testng] [2024-07-24 01:42:57,464] [pool-1-thread-3] Initializing /data/imagic/not read correctly/Abeta Moon_preview.png:
[testng] 01:42:57,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:42:57,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:57,466 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-24_01-42-57.log]
[testng] 01:42:57,466 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5635b8ef - End of configuration.
[testng] [2024-07-24 01:42:57,480] [pool-1-thread-2] Initializing /data/imagic/not read correctly/Abeta Moon.dm2:
[testng] 01:42:57,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:42:57,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:57,481 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-24_01-42-57.log]
[testng] 01:42:57,482 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a3650b6 - End of configuration.
[testng] [2024-07-24 01:42:58,692] [pool-1-thread-2] Initializing /data/pang/10500x-o4:
[testng] [2024-07-24 01:42:58,781] [pool-1-thread-3] Initializing /data/pang/signed:
[testng] [2024-07-24 01:42:58,793] [pool-1-thread-10] Initializing /data/pang/grating025k.dm2:
[testng] [2024-07-24 01:42:58,801] [pool-1-thread-11] Initializing /data/pang/unproc-auto:
[testng] [2024-07-24 01:42:58,810] [pool-1-thread-4] Initializing /data/pang/DLMeD2E1_010500x03.dm2:
[testng] [2024-07-24 01:42:58,823] [pool-1-thread-7] Initializing /data/imagic/TEM 10118.dm2:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 954, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 8 seconds
Finished: SUCCESS