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Started by upstream project "BIOFORMATS-test-repo" build number 253 originally caused by: Started by upstream project "Trigger" build number 277 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/jenkins11988222824623197831.sh + '[' bruker = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_39943_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] 04:27:59,937 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 04:27:59,938 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 04:27:59,938 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:27:59,939 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:27:59,940 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:27:59,940 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:27:59,940 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 04:27:59,940 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:27:59,941 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:27:59,942 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:27:59,942 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:27:59,942 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:28:00,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:28:00,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:28:00,129 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:28:00,129 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:28:00,135 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:28:00,135 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:28:00,135 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:28:00,135 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:28:00,136 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 04:28:00,136 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 04:28:00,136 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 195 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-12 04:28:00,145] [main] java.version = 11.0.16 [testng] 04:28:00,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:28:00,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:00,189 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-12_04-28-00.log] [testng] 04:28:00,191 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-12 04:28:00,193] [main] testng.directory = /data [testng] [2024-11-12 04:28:00,193] [main] testng.configDirectory = /config [testng] [2024-11-12 04:28:00,202] [main] testng.multiplier = 1.0 [testng] [2024-11-12 04:28:00,203] [main] testng.in-memory = false [testng] [2024-11-12 04:28:00,203] [main] testng.allow-missing = false [testng] [2024-11-12 04:28:00,204] [main] user.language = en [testng] [2024-11-12 04:28:00,204] [main] user.country = ${user.country} [testng] [2024-11-12 04:28:00,204] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-12 05:05:49,953] [main] ---------------------------------------- [testng] [2024-11-12 05:05:49,953] [main] Total files: 826 [testng] [2024-11-12 05:05:49,953] [main] Scan time: 2269.749 s (2747 ms/file) [testng] [2024-11-12 05:05:49,953] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-12 05:07:58,937] [pool-1-thread-1] Initializing /data/wis/RA_060110.051/1/acqp: [testng] 05:07:58,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:07:58,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:58,940 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-12_05-07-58.log] [testng] 05:07:58,940 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48784042 - End of configuration. [testng] [2024-11-12 05:08:07,259] [pool-1-thread-12] Initializing /data/wis/RA_240912_m1.g71/1/acqp: [testng] 05:08:07,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:08:07,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:07,261 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-12_05-08-07.log] [testng] 05:08:07,261 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b2c2862 - End of configuration. [testng] [2024-11-12 05:08:18,843] [pool-1-thread-11] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif: [testng] 05:08:18,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:08:18,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:18,844 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-12_05-08-18.log] [testng] 05:08:18,844 |-INFO in ch.qos.logback.core.sift.SiftProcessor@139e39f9 - End of configuration. [testng] [2024-11-12 05:08:22,072] [pool-1-thread-10] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif: [testng] 05:08:22,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:08:22,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:22,073 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-12_05-08-22.log] [testng] 05:08:22,073 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50e9e934 - End of configuration. [testng] [2024-11-12 05:08:25,226] [pool-1-thread-9] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif: [testng] 05:08:25,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:08:25,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:25,227 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-12_05-08-25.log] [testng] 05:08:25,227 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65e110a5 - End of configuration. [testng] [2024-11-12 05:08:28,412] [pool-1-thread-8] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif: [testng] 05:08:28,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:08:28,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:28,413 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-12_05-08-28.log] [testng] 05:08:28,413 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e21ad8d - End of configuration. [testng] [2024-11-12 05:08:31,588] [pool-1-thread-7] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif: [testng] 05:08:31,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:08:31,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:31,589 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-12_05-08-31.log] [testng] 05:08:31,589 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f8e3087 - End of configuration. [testng] [2024-11-12 05:08:34,809] [pool-1-thread-6] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif: [testng] 05:08:34,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:08:34,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:34,810 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-12_05-08-34.log] [testng] 05:08:34,811 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ebcaf6c - End of configuration. [testng] [2024-11-12 05:08:38,098] [pool-1-thread-5] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif: [testng] 05:08:38,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:08:38,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:38,098 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-12_05-08-38.log] [testng] 05:08:38,099 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d21b2c3 - End of configuration. [testng] [2024-11-12 05:08:41,220] [pool-1-thread-4] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif: [testng] 05:08:41,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:08:41,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:41,221 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-12_05-08-41.log] [testng] 05:08:41,221 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f374ea1 - End of configuration. [testng] [2024-11-12 05:08:44,382] [pool-1-thread-3] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif: [testng] 05:08:44,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:08:44,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:44,383 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-12_05-08-44.log] [testng] 05:08:44,383 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d3f9a20 - End of configuration. [testng] [2024-11-12 05:08:47,635] [pool-1-thread-2] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif: [testng] 05:08:47,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:08:47,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:47,635 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-12_05-08-47.log] [testng] 05:08:47,636 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b1e2e18 - End of configuration. [testng] [2024-11-12 05:09:11,055] [pool-1-thread-10] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif: [testng] [2024-11-12 05:09:14,231] [pool-1-thread-4] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif: [testng] [2024-11-12 05:09:17,592] [pool-1-thread-11] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif: [testng] [2024-11-12 05:09:20,872] [pool-1-thread-3] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif: [testng] [2024-11-12 05:09:24,186] [pool-1-thread-7] Initializing /data/samples/dimension-mismatch/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: 68 minutes 3 seconds Finished: SUCCESS