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Started by upstream project "BIOFORMATS-test-repo" build number 93 originally caused by: Started by upstream project "Trigger" build number 104 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins5572170370358663268.sh + '[' bruker = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_14376_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] 02:31:39,729 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:31:39,731 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 02:31:39,731 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:31:39,732 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:31:39,732 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:31:39,732 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:31:39,733 |-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] 02:31:39,733 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:31:39,733 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:31:39,734 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:31:39,734 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:31:39,735 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:31:39,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:31:39,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:31:39,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:31:39,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:31:39,935 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:31:39,935 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:31:39,935 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:31:39,936 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:31:39,936 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 02:31:39,937 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 02:31:39,937 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 204 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-15 02:31:39,946] [main] java.version = 11.0.16 [testng] 02:31:39,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:31:39,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:31:39,991 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-15_02-31-39.log] [testng] 02:31:39,992 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-06-15 02:31:39,994] [main] testng.directory = /data [testng] [2024-06-15 02:31:39,995] [main] testng.configDirectory = /config [testng] [2024-06-15 02:31:40,004] [main] testng.multiplier = 1.0 [testng] [2024-06-15 02:31:40,006] [main] testng.in-memory = false [testng] [2024-06-15 02:31:40,006] [main] testng.allow-missing = false [testng] [2024-06-15 02:31:40,006] [main] user.language = en [testng] [2024-06-15 02:31:40,006] [main] user.country = ${user.country} [testng] [2024-06-15 02:31:40,006] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-15 02:32:17,586] [main] ---------------------------------------- [testng] [2024-06-15 02:32:17,586] [main] Total files: 826 [testng] [2024-06-15 02:32:17,586] [main] Scan time: 37.58 s (45 ms/file) [testng] [2024-06-15 02:32:17,586] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-15 02:32:20,565] [pool-1-thread-1] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif: [testng] 02:32:20,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:32:20,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:20,567 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-15_02-32-20.log] [testng] 02:32:20,568 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f874ec3 - End of configuration. [testng] [2024-06-15 02:32:20,616] [pool-1-thread-12] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif: [testng] 02:32:20,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:32:20,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:20,617 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-15_02-32-20.log] [testng] 02:32:20,618 |-INFO in ch.qos.logback.core.sift.SiftProcessor@178a1e09 - End of configuration. [testng] [2024-06-15 02:32:20,674] [pool-1-thread-11] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif: [testng] 02:32:20,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:32:20,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:20,675 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-15_02-32-20.log] [testng] 02:32:20,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17189322 - End of configuration. [testng] [2024-06-15 02:32:20,724] [pool-1-thread-10] Initializing /data/wis/RA_240912_m1.g71/1/acqp: [testng] 02:32:20,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:32:20,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:20,725 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-15_02-32-20.log] [testng] 02:32:20,726 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34d8a34 - End of configuration. [testng] [2024-06-15 02:32:20,846] [pool-1-thread-9] Initializing /data/samples/dimension-mismatch/1/acqp: [testng] 02:32:20,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:32:20,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:20,847 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-15_02-32-20.log] [testng] 02:32:20,847 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35e27e30 - End of configuration. [testng] [2024-06-15 02:32:20,874] [pool-1-thread-8] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif: [testng] 02:32:20,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:32:20,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:20,875 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-15_02-32-20.log] [testng] 02:32:20,876 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76a2c23a - End of configuration. [testng] [2024-06-15 02:32:20,935] [pool-1-thread-7] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif: [testng] 02:32:20,935 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:32:20,935 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:20,936 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-15_02-32-20.log] [testng] 02:32:20,936 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c5e3291 - End of configuration. [testng] [2024-06-15 02:32:20,974] [pool-1-thread-6] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif: [testng] 02:32:20,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:32:20,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:20,975 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-15_02-32-20.log] [testng] 02:32:20,976 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b33f7f4 - End of configuration. [testng] [2024-06-15 02:32:21,023] [pool-1-thread-5] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif: [testng] 02:32:21,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:32:21,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:21,024 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-15_02-32-21.log] [testng] 02:32:21,024 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20df9bd1 - End of configuration. [testng] [2024-06-15 02:32:21,061] [pool-1-thread-4] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif: [testng] 02:32:21,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:32:21,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:21,062 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-15_02-32-21.log] [testng] 02:32:21,062 |-INFO in ch.qos.logback.core.sift.SiftProcessor@233264b8 - End of configuration. [testng] [2024-06-15 02:32:21,101] [pool-1-thread-3] Initializing /data/wis/RA_060110.051/1/acqp: [testng] 02:32:21,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:32:21,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:21,101 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-15_02-32-21.log] [testng] 02:32:21,102 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ce848d3 - End of configuration. [testng] [2024-06-15 02:32:21,184] [pool-1-thread-2] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif: [testng] 02:32:21,184 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:32:21,184 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:21,185 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-15_02-32-21.log] [testng] 02:32:21,185 |-INFO in ch.qos.logback.core.sift.SiftProcessor@726f83b7 - End of configuration. [testng] [2024-06-15 02:32:23,203] [pool-1-thread-8] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif: [testng] [2024-06-15 02:32:23,248] [pool-1-thread-5] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif: [testng] [2024-06-15 02:32:23,297] [pool-1-thread-6] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif: [testng] [2024-06-15 02:32:23,340] [pool-1-thread-12] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif: [testng] [2024-06-15 02:32:23,389] [pool-1-thread-9] 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 4 seconds Finished: SUCCESS