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Started by upstream project "BIOFORMATS-test-repo" build number 264 originally caused by: Started by upstream project "Trigger" build number 287 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/jenkins12157267731440936.sh + '[' bruker = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41747_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 test-automated: [testng] File leak detector installed [testng] 04:35:02,535 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 04:35:02,537 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 04:35:02,537 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:35:02,538 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:35:02,538 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:35:02,538 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:35:02,538 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 04:35:02,538 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:35:02,539 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:35:02,539 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:35:02,539 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:35:02,539 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:35:02,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:35:02,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:35:02,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:35:02,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:35:02,795 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:35:02,795 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:35:02,796 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:35:02,796 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:35:02,796 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 04:35:02,797 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 04:35:02,797 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 258 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-22 04:35:02,806] [main] java.version = 1.8.0_342 [testng] 04:35:02,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:35:02,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:35:02,854 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-22_04-35-02.log] [testng] 04:35:02,855 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-22 04:35:02,857] [main] testng.directory = /data [testng] [2024-11-22 04:35:02,857] [main] testng.configDirectory = /config [testng] [2024-11-22 04:35:02,870] [main] testng.multiplier = 1.0 [testng] [2024-11-22 04:35:02,871] [main] testng.in-memory = false [testng] [2024-11-22 04:35:02,871] [main] testng.allow-missing = false [testng] [2024-11-22 04:35:02,871] [main] user.language = en [testng] [2024-11-22 04:35:02,871] [main] user.country = ${user.country} [testng] [2024-11-22 04:35:02,871] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-22 05:11:38,854] [main] ---------------------------------------- [testng] [2024-11-22 05:11:38,854] [main] Total files: 826 [testng] [2024-11-22 05:11:38,854] [main] Scan time: 2195.983 s (2658 ms/file) [testng] [2024-11-22 05:11:38,854] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-22 05:13:43,038] [pool-1-thread-1] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif: [testng] 05:13:43,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:13:43,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:13:43,039 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-22_05-13-43.log] [testng] 05:13:43,040 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23f1747b - End of configuration. [testng] [2024-11-22 05:13:45,913] [pool-1-thread-12] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif: [testng] 05:13:45,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:13:45,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:13:45,914 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-22_05-13-45.log] [testng] 05:13:45,914 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f0c722a - End of configuration. [testng] [2024-11-22 05:13:48,768] [pool-1-thread-11] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif: [testng] 05:13:48,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:13:48,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:13:48,769 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-22_05-13-48.log] [testng] 05:13:48,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f1cddd2 - End of configuration. [testng] [2024-11-22 05:13:51,616] [pool-1-thread-10] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif: [testng] 05:13:51,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:13:51,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:13:51,617 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-22_05-13-51.log] [testng] 05:13:51,618 |-INFO in ch.qos.logback.core.sift.SiftProcessor@524827bd - End of configuration. [testng] [2024-11-22 05:13:54,467] [pool-1-thread-9] Initializing /data/samples/dimension-mismatch/1/acqp: [testng] 05:13:54,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:13:54,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:13:54,468 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-22_05-13-54.log] [testng] 05:13:54,468 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3273d65 - End of configuration. [testng] [2024-11-22 05:13:57,621] [pool-1-thread-8] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif: [testng] 05:13:57,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:13:57,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:13:57,622 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-22_05-13-57.log] [testng] 05:13:57,623 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22b399a7 - End of configuration. [testng] [2024-11-22 05:14:00,515] [pool-1-thread-7] Initializing /data/wis/RA_060110.051/1/acqp: [testng] 05:14:00,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:14:00,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:14:00,516 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-22_05-14-00.log] [testng] 05:14:00,516 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32c2c412 - End of configuration. [testng] [2024-11-22 05:14:07,613] [pool-1-thread-6] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif: [testng] 05:14:07,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:14:07,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:14:07,614 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-22_05-14-07.log] [testng] 05:14:07,615 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a9ba184 - End of configuration. [testng] [2024-11-22 05:14:10,554] [pool-1-thread-5] Initializing /data/wis/RA_240912_m1.g71/1/acqp: [testng] 05:14:10,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:14:10,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:14:10,554 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-22_05-14-10.log] [testng] 05:14:10,555 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d2a0409 - End of configuration. [testng] [2024-11-22 05:14:20,186] [pool-1-thread-4] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif: [testng] 05:14:20,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:14:20,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:14:20,187 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-22_05-14-20.log] [testng] 05:14:20,188 |-INFO in ch.qos.logback.core.sift.SiftProcessor@549f5727 - End of configuration. [testng] [2024-11-22 05:14:23,080] [pool-1-thread-3] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif: [testng] 05:14:23,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:14:23,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:14:23,080 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-22_05-14-23.log] [testng] 05:14:23,081 |-INFO in ch.qos.logback.core.sift.SiftProcessor@dd919c1 - End of configuration. [testng] [2024-11-22 05:14:25,875] [pool-1-thread-2] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif: [testng] 05:14:25,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:14:25,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:14:25,876 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-22_05-14-25.log] [testng] 05:14:25,876 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bd9c7df - End of configuration. [testng] [2024-11-22 05:14:48,262] [pool-1-thread-8] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif: [testng] [2024-11-22 05:14:51,166] [pool-1-thread-6] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif: [testng] [2024-11-22 05:14:54,424] [pool-1-thread-10] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif: [testng] [2024-11-22 05:14:57,427] [pool-1-thread-12] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif: [testng] [2024-11-22 05:15:00,470] [pool-1-thread-4] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_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: 66 minutes 27 seconds Finished: SUCCESS