Started by upstream project "BIOFORMATS-test-repo" build number 60
originally caused by:
Started by upstream project "Trigger" build number 67
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/jenkins9725812620201468576.sh
+ '[' biorad-gel = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_8963_merge_ci -v /uod/idr/repos/curated/biorad-gel:/data -v /uod/idr-scratch/merge-ci/curated/biorad-gel:/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] 02:27:25,874 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:27:25,876 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 02:27:25,876 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:27:25,877 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:27:25,878 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:27:25,878 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:27:25,879 |-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] 02:27:25,879 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:27:25,879 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:27:25,880 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:27:25,880 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:27:25,881 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:27:26,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:27:26,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:27:26,231 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:27:26,231 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:27:26,350 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:27:26,351 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:27:26,351 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:27:26,351 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:27:26,351 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 02:27:26,352 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 02:27:26,352 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 473 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-05-11 02:27:26,367] [main] java.version = 11.0.16
[testng] 02:27:26,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:27:26,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:26,474 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-11_02-27-26.log]
[testng] 02:27:26,475 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-05-11 02:27:26,498] [main] testng.directory = /data
[testng] [2024-05-11 02:27:26,498] [main] testng.configDirectory = /config
[testng] [2024-05-11 02:27:26,537] [main] testng.multiplier = 1.0
[testng] [2024-05-11 02:27:26,539] [main] testng.in-memory = false
[testng] [2024-05-11 02:27:26,539] [main] testng.allow-missing = false
[testng] [2024-05-11 02:27:26,539] [main] user.language = en
[testng] [2024-05-11 02:27:26,539] [main] user.country = ${user.country}
[testng] [2024-05-11 02:27:26,539] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-05-11 02:27:27,577] [main] ----------------------------------------
[testng] [2024-05-11 02:27:27,577] [main] Total files: 32
[testng] [2024-05-11 02:27:27,577] [main] Scan time: 1.038 s (32 ms/file)
[testng] [2024-05-11 02:27:27,577] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 32 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-05-11 02:27:31,790] [pool-1-thread-1] Initializing /data/keith/test.1sc:
[testng] 02:27:31,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:27:31,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:31,793 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-11_02-27-31.log]
[testng] 02:27:31,794 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e7aa6ab - End of configuration.
[testng] [2024-05-11 02:27:31,850] [pool-1-thread-12] Initializing /data/geert/bad example1.1sc:
[testng] 02:27:31,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:27:31,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:31,853 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-11_02-27-31.log]
[testng] 02:27:31,853 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3059fdcd - End of configuration.
[testng] [2024-05-11 02:27:31,910] [pool-1-thread-11] Initializing /data/samples/imagesEight.1sc:
[testng] 02:27:31,910 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:27:31,910 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:31,911 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-11_02-27-31.log]
[testng] 02:27:31,912 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47f74159 - End of configuration.
[testng] [2024-05-11 02:27:31,930] [pool-1-thread-10] Initializing /data/qa-29469/bad3.1sc:
[testng] 02:27:31,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:27:31,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:31,931 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-11_02-27-31.log]
[testng] 02:27:31,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1076417c - End of configuration.
[testng] [2024-05-11 02:27:31,984] [pool-1-thread-9] Initializing /data/sylvain/2009-10-23 12hr 18min.tif:
[testng] 02:27:31,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:27:31,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:31,986 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-11_02-27-31.log]
[testng] 02:27:31,987 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b58a79d - End of configuration.
[testng] [2024-05-11 02:27:32,087] [pool-1-thread-8] Initializing /data/sylvain/2009-10-26 14hr 59min.tif:
[testng] 02:27:32,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:27:32,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:32,088 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-11_02-27-32.log]
[testng] 02:27:32,088 |-INFO in ch.qos.logback.core.sift.SiftProcessor@189bf787 - End of configuration.
[testng] [2024-05-11 02:27:32,177] [pool-1-thread-7] Initializing /data/qa-16880/c-src v7.1sc:
[testng] 02:27:32,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:27:32,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:32,178 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-11_02-27-32.log]
[testng] 02:27:32,178 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43f26c1a - End of configuration.
[testng] [2024-05-11 02:27:32,217] [pool-1-thread-6] Initializing /data/keith/test2.1sc:
[testng] 02:27:32,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:27:32,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:32,218 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-11_02-27-32.log]
[testng] 02:27:32,218 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a0bdd8b - End of configuration.
[testng] [2024-05-11 02:27:32,236] [pool-1-thread-5] Initializing /data/keith/pg020410saur3.1sc:
[testng] 02:27:32,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:27:32,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:32,237 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-11_02-27-32.log]
[testng] 02:27:32,237 |-INFO in ch.qos.logback.core.sift.SiftProcessor@180ee78 - End of configuration.
[testng] [2024-05-11 02:27:32,258] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 57min:
[testng] 02:27:32,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:27:32,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:32,259 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-11_02-27-32.log]
[testng] 02:27:32,259 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2749237c - End of configuration.
[testng] [2024-05-11 02:27:32,283] [pool-1-thread-3] Initializing /data/david/Opened in imageJ.tiff:
[testng] 02:27:32,283 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:27:32,283 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:32,284 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-11_02-27-32.log]
[testng] 02:27:32,285 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a7f584c - End of configuration.
[testng] [2024-05-11 02:27:32,328] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 56min:
[testng] 02:27:32,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:27:32,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:27:32,329 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-11_02-27-32.log]
[testng] 02:27:32,329 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26bf0497 - End of configuration.
[testng] [2024-05-11 02:27:34,195] [pool-1-thread-11] Initializing /data/geert/good example1.1sc:
[testng] [2024-05-11 02:27:34,251] [pool-1-thread-12] Initializing /data/sylvain/2009-10-26 14hr 57min.tif:
[testng] [2024-05-11 02:27:34,310] [pool-1-thread-5] Initializing /data/samples/Criterion.1sc:
[testng] [2024-05-11 02:27:34,337] [pool-1-thread-1] Initializing /data/geert/bad example1.jpg:
[testng] [2024-05-11 02:27:34,371] [pool-1-thread-6] Initializing /data/sylvain/2009-10-26 14hr 56min.tif:
[testng] [2024-05-11 02:27:34,432] [pool-1-thread-3] Initializing /data/sylvain/2009-10-23 12hr 18min:
[testng] [2024-05-11 02:27:34,457] [pool-1-thread-7] Initializing /data/qa-29459/bad.1sc:
[testng] [2024-05-11 02:27:34,495] [pool-1-thread-10] Initializing /data/sylvain/2009-10-23 12hr 19min.tif:
[testng] [2024-05-11 02:27:34,612] [pool-1-thread-2] Initializing /data/keith/PF020426MRSA v2.1sc:
[testng] [2024-05-11 02:27:34,718] [pool-1-thread-4] Initializing /data/sylvain/2009-10-23 12hr 19min:
[testng] [2024-05-11 02:27:34,819] [pool-1-thread-8] Initializing /data/geert/bad example1.1sc.jpg:
[testng] [2024-05-11 02:27:34,963] [pool-1-thread-9] Initializing /data/qa-29469/good.1sc:
[testng] [2024-05-11 02:27:35,146] [pool-1-thread-2] Initializing /data/david/Converted in Quantity One (Biorad).tiff:
[testng] [2024-05-11 02:27:35,405] [pool-1-thread-7] Initializing /data/qa-29459/bad.jpg:
[testng] [2024-05-11 02:27:35,459] [pool-1-thread-5] Initializing /data/david/Original Biorad Gel format file.1sc:
[testng] [2024-05-11 02:27:35,750] [pool-1-thread-2] Initializing /data/qa-29469/bad2.1sc:
[testng] [2024-05-11 02:27:35,877] [pool-1-thread-5] Initializing /data/sylvain/2009-10-26 14hr 59min:
[testng] [2024-05-11 02:27:35,900] [pool-1-thread-7] Initializing /data/geert/good example1.1sc.jpg:
[testng] [2024-05-11 02:27:35,925] [pool-1-thread-3] Initializing /data/keith/PF020328saur v3.1sc:
[testng] [2024-05-11 02:27:35,941] [pool-1-thread-1] Initializing /data/adrian/test_img.1sc:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1696, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 14 seconds
Finished: SUCCESS