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Started by upstream project "BIOFORMATS-test-repo" build number 210 originally caused by: Started by upstream project "Trigger" build number 236 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins15402962819633526370.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_33398_merge_ci -v /uod/idr/repos/curated/scanr:/data -v /uod/idr-scratch/merge-ci/curated/scanr:/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] 03:31:59,316 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:31:59,318 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 03:31:59,318 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:31:59,319 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:31:59,319 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:31:59,319 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:31:59,320 |-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] 03:31:59,320 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:31:59,320 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:31:59,321 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:31:59,321 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:31:59,321 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:31:59,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:31:59,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:31:59,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:31:59,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:31:59,520 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:31:59,520 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:31:59,520 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:31:59,521 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:31:59,521 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 03:31:59,522 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 03:31:59,522 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 202 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-05 03:31:59,531] [main] java.version = 11.0.16 [testng] 03:31:59,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:31:59,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:31:59,577 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-05_03-31-59.log] [testng] 03:31:59,579 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-10-05 03:31:59,581] [main] testng.directory = /data [testng] [2024-10-05 03:31:59,581] [main] testng.configDirectory = /config [testng] [2024-10-05 03:31:59,591] [main] testng.multiplier = 1.0 [testng] [2024-10-05 03:31:59,592] [main] testng.in-memory = false [testng] [2024-10-05 03:31:59,593] [main] testng.allow-missing = false [testng] [2024-10-05 03:31:59,593] [main] user.language = en [testng] [2024-10-05 03:31:59,593] [main] user.country = ${user.country} [testng] [2024-10-05 03:31:59,593] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-05 03:36:13,338] [main] ---------------------------------------- [testng] [2024-10-05 03:36:13,339] [main] Total files: 2169 [testng] [2024-10-05 03:36:13,339] [main] Scan time: 253.745 s (116 ms/file) [testng] [2024-10-05 03:36:13,339] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-05 03:54:54,579] [pool-1-thread-1] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 03:54:54,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:54:54,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:54,582 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-05_03-54-54.log] [testng] 03:54:54,583 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c4eacd6 - End of configuration. [testng] [2024-10-05 03:54:55,245] [pool-1-thread-12] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 03:54:55,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:54:55,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:55,247 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-05_03-54-55.log] [testng] 03:54:55,247 |-INFO in ch.qos.logback.core.sift.SiftProcessor@585393a0 - End of configuration. [testng] [2024-10-05 03:54:55,931] [pool-1-thread-11] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 03:54:55,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:54:55,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:55,932 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-05_03-54-55.log] [testng] 03:54:55,933 |-INFO in ch.qos.logback.core.sift.SiftProcessor@111974d4 - End of configuration. [testng] [2024-10-05 03:55:02,758] [pool-1-thread-10] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 03:55:02,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:55:02,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:55:02,760 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-05_03-55-02.log] [testng] 03:55:02,760 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5cff6066 - End of configuration. [testng] [2024-10-05 03:57:01,930] [pool-1-thread-9] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 03:57:01,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:57:01,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:57:01,931 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-05_03-57-01.log] [testng] 03:57:01,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c10f9e3 - End of configuration. [testng] [2024-10-05 03:58:57,546] [pool-1-thread-8] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 03:58:57,546 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:58:57,546 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:58:57,547 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-05_03-58-57.log] [testng] 03:58:57,548 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c436ad - End of configuration. [testng] [2024-10-05 03:59:46,783] [pool-1-thread-7] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 03:59:46,783 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:59:46,783 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:59:46,784 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-05_03-59-46.log] [testng] 03:59:46,785 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e5c40f3 - End of configuration. [testng] [2024-10-05 04:00:07,961] [pool-1-thread-6] Initializing /data/gideon/experiment_descriptor.xml: [testng] 04:00:07,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:00:07,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:00:07,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-05_04-00-07.log] [testng] 04:00:07,962 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78059d46 - End of configuration. [testng] [2024-10-05 04:00:37,393] [pool-1-thread-5] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 04:00:37,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:00:37,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:00:37,395 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-05_04-00-37.log] [testng] 04:00:37,395 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a1e9d4e - End of configuration. [testng] [2024-10-05 04:00:45,175] [pool-1-thread-4] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 04:00:45,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:00:45,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:00:45,176 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-05_04-00-45.log] [testng] 04:00:45,177 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79942086 - End of configuration. [testng] [2024-10-05 04:00:46,801] [pool-1-thread-3] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 04:00:46,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:00:46,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:00:46,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-05_04-00-46.log] [testng] 04:00:46,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fd6522 - End of configuration. [testng] [2024-10-05 04:02:31,846] [pool-1-thread-2] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 04:02:31,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:02:31,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:31,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-05_04-02-31.log] [testng] 04:02:31,848 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7da2a984 - End of configuration. [testng] [2024-10-05 04:04:58,174] [pool-1-thread-1] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] [2024-10-05 04:05:56,802] [pool-1-thread-12] Initializing /data/nadine/experiment_descriptor.xml: [testng] [2024-10-05 04:06:23,016] [pool-1-thread-12] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] [2024-10-05 04:06:59,226] [pool-1-thread-4] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] [2024-10-05 04:09:25,229] [pool-1-thread-5] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 04:55:05,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:55:05,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:55:05,218 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-05_04-55-05.log] [testng] 04:55:05,218 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14f8ca45 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 83 minutes 11 seconds Finished: SUCCESS