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Started by upstream project "BIOFORMATS-test-repo" build number 89 originally caused by: Started by upstream project "Trigger" build number 100 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins10422069961259163081.sh + '[' bruker = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_13720_merge_ci -v /uod/idr/repos/curated/bruker:/data -v /uod/idr-scratch/merge-ci/curated/bruker:/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] 02:26:58,402 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:26:58,403 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 02:26:58,403 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:26:58,405 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:26:58,405 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:26:58,406 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:26:58,406 |-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] 02:26:58,406 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:26:58,407 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:26:58,408 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:26:58,408 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:26:58,408 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:26:58,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:26:58,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:26:58,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:26:58,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:26:58,676 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:26:58,676 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:26:58,676 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:26:58,677 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:26:58,677 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 02:26:58,678 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 02:26:58,678 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 271 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-11 02:26:58,689] [main] java.version = 11.0.16 [testng] 02:26:58,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:26:58,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:26:58,753 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-11_02-26-58.log] [testng] 02:26:58,755 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-06-11 02:26:58,758] [main] testng.directory = /data [testng] [2024-06-11 02:26:58,758] [main] testng.configDirectory = /config [testng] [2024-06-11 02:26:58,770] [main] testng.multiplier = 1.0 [testng] [2024-06-11 02:26:58,773] [main] testng.in-memory = false [testng] [2024-06-11 02:26:58,773] [main] testng.allow-missing = false [testng] [2024-06-11 02:26:58,773] [main] user.language = en [testng] [2024-06-11 02:26:58,773] [main] user.country = ${user.country} [testng] [2024-06-11 02:26:58,773] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-11 02:27:47,751] [main] ---------------------------------------- [testng] [2024-06-11 02:27:47,751] [main] Total files: 826 [testng] [2024-06-11 02:27:47,751] [main] Scan time: 48.978 s (59 ms/file) [testng] [2024-06-11 02:27:47,751] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-11 02:27:51,902] [pool-1-thread-1] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif: [testng] 02:27:51,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:27:51,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:51,905 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-11_02-27-51.log] [testng] 02:27:51,906 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c37af7e - End of configuration. [testng] [2024-06-11 02:27:51,997] [pool-1-thread-12] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif: [testng] 02:27:51,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:27:51,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:52,002 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-11_02-27-52.log] [testng] 02:27:52,003 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f50f29e - End of configuration. [testng] [2024-06-11 02:27:52,146] [pool-1-thread-11] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif: [testng] 02:27:52,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:27:52,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:52,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-11_02-27-52.log] [testng] 02:27:52,148 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f5b0988 - End of configuration. [testng] [2024-06-11 02:27:52,241] [pool-1-thread-10] Initializing /data/wis/RA_240912_m1.g71/1/acqp: [testng] 02:27:52,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:27:52,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:52,245 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-11_02-27-52.log] [testng] 02:27:52,246 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d816635 - End of configuration. [testng] [2024-06-11 02:27:52,542] [pool-1-thread-9] Initializing /data/samples/dimension-mismatch/1/acqp: [testng] 02:27:52,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:27:52,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:52,544 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-11_02-27-52.log] [testng] 02:27:52,544 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6af3c04a - End of configuration. [testng] [2024-06-11 02:27:52,575] [pool-1-thread-8] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif: [testng] 02:27:52,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:27:52,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:52,577 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-11_02-27-52.log] [testng] 02:27:52,577 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22a535ba - End of configuration. [testng] [2024-06-11 02:27:52,629] [pool-1-thread-7] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif: [testng] 02:27:52,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:27:52,630 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:52,630 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-11_02-27-52.log] [testng] 02:27:52,631 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c37c7e8 - End of configuration. [testng] [2024-06-11 02:27:52,679] [pool-1-thread-6] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif: [testng] 02:27:52,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:27:52,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:52,681 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-11_02-27-52.log] [testng] 02:27:52,681 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ae6d0cc - End of configuration. [testng] [2024-06-11 02:27:52,750] [pool-1-thread-5] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif: [testng] 02:27:52,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:27:52,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:52,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-11_02-27-52.log] [testng] 02:27:52,752 |-INFO in ch.qos.logback.core.sift.SiftProcessor@437ddcf1 - End of configuration. [testng] [2024-06-11 02:27:52,808] [pool-1-thread-4] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif: [testng] 02:27:52,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:27:52,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:52,809 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-11_02-27-52.log] [testng] 02:27:52,810 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5953adbd - End of configuration. [testng] [2024-06-11 02:27:52,876] [pool-1-thread-3] Initializing /data/wis/RA_060110.051/1/acqp: [testng] 02:27:52,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:27:52,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:52,878 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-11_02-27-52.log] [testng] 02:27:52,878 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16bda97e - End of configuration. [testng] [2024-06-11 02:27:52,985] [pool-1-thread-2] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif: [testng] 02:27:52,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:27:52,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:52,986 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-11_02-27-52.log] [testng] 02:27:52,987 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20ecf0dc - End of configuration. [testng] [2024-06-11 02:27:56,876] [pool-1-thread-9] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif: [testng] [2024-06-11 02:27:56,955] [pool-1-thread-1] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif: [testng] [2024-06-11 02:27:57,006] [pool-1-thread-4] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif: [testng] [2024-06-11 02:27:57,073] [pool-1-thread-8] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif: [testng] [2024-06-11 02:27:57,112] [pool-1-thread-11] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 1 minute 21 seconds Finished: SUCCESS