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Started by upstream project "BIOFORMATS-test-repo" build number 25 originally caused by: Started by upstream project "Trigger" build number 28 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins10869008973353892945.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_3222_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] 02:30:53,028 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:30:53,029 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 02:30:53,029 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:30:53,030 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:30:53,031 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:30:53,031 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:30:53,032 |-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] 02:30:53,032 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:30:53,033 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:30:53,033 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:30:53,034 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:30:53,034 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:30:53,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:30:53,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:30:53,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:30:53,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:30:53,325 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:30:53,325 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:30:53,325 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:30:53,326 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:30:53,326 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 02:30:53,327 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 02:30:53,327 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 294 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-06 02:30:53,341] [main] java.version = 11.0.16 [testng] 02:30:53,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:30:53,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:30:53,390 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-06_02-30-53.log] [testng] 02:30:53,391 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-04-06 02:30:53,393] [main] testng.directory = /data [testng] [2024-04-06 02:30:53,393] [main] testng.configDirectory = /config [testng] [2024-04-06 02:30:53,405] [main] testng.multiplier = 1.0 [testng] [2024-04-06 02:30:53,407] [main] testng.in-memory = false [testng] [2024-04-06 02:30:53,407] [main] testng.allow-missing = false [testng] [2024-04-06 02:30:53,407] [main] user.language = en [testng] [2024-04-06 02:30:53,407] [main] user.country = ${user.country} [testng] [2024-04-06 02:30:53,407] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-06 02:30:54,363] [main] ---------------------------------------- [testng] [2024-04-06 02:30:54,363] [main] Total files: 32 [testng] [2024-04-06 02:30:54,363] [main] Scan time: 0.955 s (29 ms/file) [testng] [2024-04-06 02:30:54,363] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-06 02:30:58,709] [pool-1-thread-1] Initializing /data/keith/test.1sc: [testng] 02:30:58,710 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:30:58,710 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:30:58,711 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-06_02-30-58.log] [testng] 02:30:58,712 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ce14380 - End of configuration. [testng] [2024-04-06 02:30:58,738] [pool-1-thread-12] Initializing /data/geert/bad example1.1sc: [testng] 02:30:58,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:30:58,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:30:58,739 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-06_02-30-58.log] [testng] 02:30:58,739 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68d2828e - End of configuration. [testng] [2024-04-06 02:30:58,778] [pool-1-thread-11] Initializing /data/samples/imagesEight.1sc: [testng] 02:30:58,778 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:30:58,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:30:58,779 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-06_02-30-58.log] [testng] 02:30:58,780 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60cd6a15 - End of configuration. [testng] [2024-04-06 02:30:58,800] [pool-1-thread-10] Initializing /data/qa-29469/bad3.1sc: [testng] 02:30:58,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:30:58,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:30:58,801 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-06_02-30-58.log] [testng] 02:30:58,802 |-INFO in ch.qos.logback.core.sift.SiftProcessor@189bf787 - End of configuration. [testng] [2024-04-06 02:30:58,833] [pool-1-thread-9] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] 02:30:58,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:30:58,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:30:58,834 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-06_02-30-58.log] [testng] 02:30:58,835 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43f26c1a - End of configuration. [testng] [2024-04-06 02:30:58,901] [pool-1-thread-8] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 02:30:58,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:30:58,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:30:58,902 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-06_02-30-58.log] [testng] 02:30:58,902 |-INFO in ch.qos.logback.core.sift.SiftProcessor@790c254f - End of configuration. [testng] [2024-04-06 02:30:58,969] [pool-1-thread-7] Initializing /data/qa-16880/c-src v7.1sc: [testng] 02:30:58,969 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:30:58,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:30:58,970 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-06_02-30-58.log] [testng] 02:30:58,970 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7dd5b8de - End of configuration. [testng] [2024-04-06 02:30:58,996] [pool-1-thread-6] Initializing /data/keith/test2.1sc: [testng] 02:30:58,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:30:58,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:30:58,997 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-06_02-30-58.log] [testng] 02:30:58,998 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ef8da72 - End of configuration. [testng] [2024-04-06 02:30:59,015] [pool-1-thread-5] Initializing /data/keith/pg020410saur3.1sc: [testng] 02:30:59,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:30:59,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:30:59,016 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-06_02-30-59.log] [testng] 02:30:59,017 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ebc8c21 - End of configuration. [testng] [2024-04-06 02:30:59,030] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] 02:30:59,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:30:59,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:30:59,031 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-06_02-30-59.log] [testng] 02:30:59,031 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49878f15 - End of configuration. [testng] [2024-04-06 02:30:59,054] [pool-1-thread-3] Initializing /data/david/Opened in imageJ.tiff: [testng] 02:30:59,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:30:59,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:30:59,054 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-06_02-30-59.log] [testng] 02:30:59,055 |-INFO in ch.qos.logback.core.sift.SiftProcessor@334054d - End of configuration. [testng] [2024-04-06 02:30:59,096] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] 02:30:59,096 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:30:59,096 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:30:59,096 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-06_02-30-59.log] [testng] 02:30:59,097 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19dcf47c - End of configuration. [testng] [2024-04-06 02:31:01,870] [pool-1-thread-1] Initializing /data/geert/good example1.1sc: [testng] [2024-04-06 02:31:01,911] [pool-1-thread-7] Initializing /data/qa-29469/good.1sc: [testng] [2024-04-06 02:31:01,937] [pool-1-thread-11] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2024-04-06 02:31:01,972] [pool-1-thread-6] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] [2024-04-06 02:31:01,992] [pool-1-thread-5] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [2024-04-06 02:31:02,007] [pool-1-thread-10] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] [2024-04-06 02:31:02,052] [pool-1-thread-3] Initializing /data/samples/Criterion.1sc: [testng] [2024-04-06 02:31:02,077] [pool-1-thread-12] Initializing /data/geert/bad example1.jpg: [testng] [2024-04-06 02:31:02,108] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] [2024-04-06 02:31:02,172] [pool-1-thread-8] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-04-06 02:31:02,196] [pool-1-thread-2] Initializing /data/qa-29459/bad.1sc: [testng] [2024-04-06 02:31:02,226] [pool-1-thread-9] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-04-06 02:31:02,716] [pool-1-thread-5] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] [2024-04-06 02:31:03,088] [pool-1-thread-2] Initializing /data/qa-29459/bad.jpg: [testng] [2024-04-06 02:31:03,114] [pool-1-thread-8] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] [2024-04-06 02:31:03,187] [pool-1-thread-11] Initializing /data/qa-29469/bad2.1sc: [testng] [2024-04-06 02:31:03,434] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-04-06 02:31:03,488] [pool-1-thread-7] Initializing /data/keith/PF020328saur v3.1sc: [testng] [2024-04-06 02:31:03,501] [pool-1-thread-6] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-04-06 02:31:03,546] [pool-1-thread-5] 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: 15 seconds Finished: SUCCESS