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Started by upstream project "BIOFORMATS-test-repo" build number 203 originally caused by: Started by upstream project "Trigger" build number 229 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins10998900402741588429.sh + '[' bruker = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_32259_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] 03:53:46,725 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:53:46,727 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 03:53:46,727 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:53:46,728 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:53:46,728 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:53:46,729 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:53:46,729 |-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] 03:53:46,729 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:53:46,729 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:53:46,730 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:53:46,730 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:53:46,731 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:53:46,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:53:46,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:53:46,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:53:46,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:53:46,929 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:53:46,929 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:53:46,930 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:53:46,930 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:53:46,930 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 03:53:46,931 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 03:53:46,931 |-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] [2024-09-28 03:53:46,940] [main] java.version = 11.0.16 [testng] 03:53:46,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:53:46,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:53:46,985 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-28_03-53-46.log] [testng] 03:53:46,986 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-09-28 03:53:46,989] [main] testng.directory = /data [testng] [2024-09-28 03:53:46,989] [main] testng.configDirectory = /config [testng] [2024-09-28 03:53:46,999] [main] testng.multiplier = 1.0 [testng] [2024-09-28 03:53:47,000] [main] testng.in-memory = false [testng] [2024-09-28 03:53:47,000] [main] testng.allow-missing = false [testng] [2024-09-28 03:53:47,000] [main] user.language = en [testng] [2024-09-28 03:53:47,000] [main] user.country = ${user.country} [testng] [2024-09-28 03:53:47,000] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-28 04:13:45,645] [main] ---------------------------------------- [testng] [2024-09-28 04:13:45,645] [main] Total files: 826 [testng] [2024-09-28 04:13:45,645] [main] Scan time: 1198.645 s (1451 ms/file) [testng] [2024-09-28 04:13:45,645] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-28 04:14:48,277] [pool-1-thread-1] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif: [testng] 04:14:48,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:14:48,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:48,280 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-28_04-14-48.log] [testng] 04:14:48,281 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42c1ba4a - End of configuration. [testng] [2024-09-28 04:14:49,697] [pool-1-thread-12] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif: [testng] 04:14:49,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:14:49,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:49,698 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-28_04-14-49.log] [testng] 04:14:49,699 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f31f68d - End of configuration. [testng] [2024-09-28 04:14:51,089] [pool-1-thread-11] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif: [testng] 04:14:51,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:14:51,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:51,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-28_04-14-51.log] [testng] 04:14:51,091 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7996bb6b - End of configuration. [testng] [2024-09-28 04:14:52,619] [pool-1-thread-10] Initializing /data/samples/dimension-mismatch/1/acqp: [testng] 04:14:52,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:14:52,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:52,620 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-28_04-14-52.log] [testng] 04:14:52,620 |-INFO in ch.qos.logback.core.sift.SiftProcessor@84029e7 - End of configuration. [testng] [2024-09-28 04:14:54,149] [pool-1-thread-9] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif: [testng] 04:14:54,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:14:54,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:54,149 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-28_04-14-54.log] [testng] 04:14:54,150 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40110b20 - End of configuration. [testng] [2024-09-28 04:14:55,563] [pool-1-thread-8] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif: [testng] 04:14:55,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:14:55,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:55,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-28_04-14-55.log] [testng] 04:14:55,565 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22da5fc4 - End of configuration. [testng] [2024-09-28 04:14:56,980] [pool-1-thread-7] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif: [testng] 04:14:56,980 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:14:56,980 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:56,981 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-28_04-14-56.log] [testng] 04:14:56,981 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5068b96f - End of configuration. [testng] [2024-09-28 04:14:58,413] [pool-1-thread-6] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif: [testng] 04:14:58,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:14:58,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:58,414 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-28_04-14-58.log] [testng] 04:14:58,415 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56b7b3ce - End of configuration. [testng] [2024-09-28 04:14:59,779] [pool-1-thread-5] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif: [testng] 04:14:59,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:14:59,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:59,780 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-28_04-14-59.log] [testng] 04:14:59,781 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f0da17 - End of configuration. [testng] [2024-09-28 04:15:00,986] [pool-1-thread-4] Initializing /data/wis/RA_060110.051/1/acqp: [testng] 04:15:00,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:15:00,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:15:00,987 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-28_04-15-00.log] [testng] 04:15:00,987 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6cb6e7eb - End of configuration. [testng] [2024-09-28 04:15:04,390] [pool-1-thread-3] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif: [testng] 04:15:04,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:15:04,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:15:04,390 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-28_04-15-04.log] [testng] 04:15:04,391 |-INFO in ch.qos.logback.core.sift.SiftProcessor@954fb2a - End of configuration. [testng] [2024-09-28 04:15:05,712] [pool-1-thread-2] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif: [testng] 04:15:05,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:15:05,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:15:05,713 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-28_04-15-05.log] [testng] 04:15:05,713 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55d3b552 - End of configuration. [testng] [2024-09-28 04:15:16,989] [pool-1-thread-5] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif: [testng] [2024-09-28 04:15:18,669] [pool-1-thread-6] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif: [testng] [2024-09-28 04:15:20,614] [pool-1-thread-9] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif: [testng] [2024-09-28 04:15:22,325] [pool-1-thread-12] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif: [testng] [2024-09-28 04:15:23,958] [pool-1-thread-11] Initializing /data/wis/RA_240912_m1.g71/1/acqp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 36 minutes 31 seconds Finished: SUCCESS