Started by upstream project "BIOFORMATS-test-repo" build number 192 originally caused by: Started by upstream project "Trigger" build number 214 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins10353101543281867842.sh + '[' bruker = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_30455_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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 02:42:36,072 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:42:36,074 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:42:36,074 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:42:36,075 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:42:36,076 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:42:36,076 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:42:36,077 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:42:36,077 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:42:36,077 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:42:36,078 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:42:36,078 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:42:36,078 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:42:36,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:42:36,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:42:36,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:42:36,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:42:36,305 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:42:36,305 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:42:36,305 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:42:36,306 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:42:36,306 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:42:36,307 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:42:36,307 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 230 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-18 02:42:36,317] [main] java.version = 17.0.2 [testng] 02:42:36,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:42:36,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:42:36,366 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-18_02-42-36.log] [testng] 02:42:36,367 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-09-18 02:42:36,370] [main] testng.directory = /data [testng] [2024-09-18 02:42:36,370] [main] testng.configDirectory = /config [testng] [2024-09-18 02:42:36,380] [main] testng.multiplier = 1.0 [testng] [2024-09-18 02:42:36,381] [main] testng.in-memory = false [testng] [2024-09-18 02:42:36,381] [main] testng.allow-missing = false [testng] [2024-09-18 02:42:36,381] [main] user.language = en [testng] [2024-09-18 02:42:36,381] [main] user.country = ${user.country} [testng] [2024-09-18 02:42:36,381] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-18 02:44:44,727] [main] ---------------------------------------- [testng] [2024-09-18 02:44:44,727] [main] Total files: 826 [testng] [2024-09-18 02:44:44,727] [main] Scan time: 128.346 s (155 ms/file) [testng] [2024-09-18 02:44:44,727] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-18 02:44:51,308] [pool-1-thread-1] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif: [testng] 02:44:51,308 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:44:51,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:51,310 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-18_02-44-51.log] [testng] 02:44:51,310 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d8feaa1 - End of configuration. [testng] [2024-09-18 02:44:51,431] [pool-1-thread-12] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif: [testng] 02:44:51,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:44:51,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:51,433 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-18_02-44-51.log] [testng] 02:44:51,433 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a0aca3e - End of configuration. [testng] [2024-09-18 02:44:51,542] [pool-1-thread-11] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif: [testng] 02:44:51,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:44:51,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:51,543 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-18_02-44-51.log] [testng] 02:44:51,544 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6273f06a - End of configuration. [testng] [2024-09-18 02:44:51,631] [pool-1-thread-10] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif: [testng] 02:44:51,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:44:51,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:51,632 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-18_02-44-51.log] [testng] 02:44:51,633 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6057f525 - End of configuration. [testng] [2024-09-18 02:44:51,737] [pool-1-thread-9] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif: [testng] 02:44:51,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:44:51,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:51,738 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-18_02-44-51.log] [testng] 02:44:51,738 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18b33c67 - End of configuration. [testng] [2024-09-18 02:44:51,854] [pool-1-thread-8] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif: [testng] 02:44:51,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:44:51,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:51,855 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-18_02-44-51.log] [testng] 02:44:51,855 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ee4d5 - End of configuration. [testng] [2024-09-18 02:44:51,927] [pool-1-thread-7] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif: [testng] 02:44:51,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:44:51,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:51,928 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-18_02-44-51.log] [testng] 02:44:51,929 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b9276d7 - End of configuration. [testng] [2024-09-18 02:44:52,053] [pool-1-thread-6] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif: [testng] 02:44:52,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:44:52,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:52,054 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-18_02-44-52.log] [testng] 02:44:52,055 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bef57b1 - End of configuration. [testng] [2024-09-18 02:44:52,115] [pool-1-thread-5] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif: [testng] 02:44:52,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:44:52,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:52,116 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-18_02-44-52.log] [testng] 02:44:52,116 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49e61c4b - End of configuration. [testng] [2024-09-18 02:44:52,208] [pool-1-thread-4] Initializing /data/wis/RA_060110.051/1/acqp: [testng] 02:44:52,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:44:52,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:52,209 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-18_02-44-52.log] [testng] 02:44:52,210 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fdc1a62 - End of configuration. [testng] [2024-09-18 02:44:52,782] [pool-1-thread-3] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif: [testng] 02:44:52,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:44:52,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:52,783 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-18_02-44-52.log] [testng] 02:44:52,783 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ee168cb - End of configuration. [testng] [2024-09-18 02:44:52,853] [pool-1-thread-2] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif: [testng] 02:44:52,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:44:52,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:52,854 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-18_02-44-52.log] [testng] 02:44:52,854 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68b25825 - End of configuration. [testng] [2024-09-18 02:44:55,551] [pool-1-thread-3] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif: [testng] [2024-09-18 02:44:55,644] [pool-1-thread-10] Initializing /data/samples/dimension-mismatch/1/acqp: [testng] [2024-09-18 02:44:55,714] [pool-1-thread-5] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif: [testng] [2024-09-18 02:44:55,813] [pool-1-thread-7] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif: [testng] [2024-09-18 02:44:55,916] [pool-1-thread-12] 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: 3 minutes 19 seconds Finished: SUCCESS