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Started by upstream project "BIOFORMATS-test-repo" build number 4 originally caused by: Started by upstream project "Trigger" build number 5 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/jenkins16559925574709263065.sh + '[' bruker = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_597_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] 02:05:21,005 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:05:21,006 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:05:21,006 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:05:21,007 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:05:21,007 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:05:21,008 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:05:21,008 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:05:21,008 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:05:21,008 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:05:21,009 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:05:21,009 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:05:21,010 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:05:21,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:05:21,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:05:21,201 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:05:21,201 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:05:21,208 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:05:21,208 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:05:21,208 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:05:21,208 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:05:21,209 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:05:21,209 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:05:21,209 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 201 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-17 02:05:21,219] [main] java.version = 17.0.2 [testng] 02:05:21,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:05:21,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:05:21,266 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-17_02-05-21.log] [testng] 02:05:21,267 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-03-17 02:05:21,269] [main] testng.directory = /data [testng] [2024-03-17 02:05:21,269] [main] testng.configDirectory = /config [testng] [2024-03-17 02:05:21,278] [main] testng.multiplier = 1.0 [testng] [2024-03-17 02:05:21,279] [main] testng.in-memory = false [testng] [2024-03-17 02:05:21,279] [main] testng.allow-missing = false [testng] [2024-03-17 02:05:21,279] [main] user.language = en [testng] [2024-03-17 02:05:21,279] [main] user.country = ${user.country} [testng] [2024-03-17 02:05:21,279] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-17 02:14:45,370] [main] ---------------------------------------- [testng] [2024-03-17 02:14:45,370] [main] Total files: 826 [testng] [2024-03-17 02:14:45,370] [main] Scan time: 564.09 s (682 ms/file) [testng] [2024-03-17 02:14:45,370] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-17 02:15:10,998] [pool-1-thread-1] Initializing /data/wis/RA_240912_m1.g71/1/acqp: [testng] 02:15:10,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:15:10,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:10,999 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-17_02-15-10.log] [testng] 02:15:11,000 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e528442 - End of configuration. [testng] [2024-03-17 02:15:12,759] [pool-1-thread-12] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif: [testng] 02:15:12,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:15:12,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:12,760 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-17_02-15-12.log] [testng] 02:15:12,760 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5000dd6c - End of configuration. [testng] [2024-03-17 02:15:13,382] [pool-1-thread-11] Initializing /data/wis/RA_060110.051/1/acqp: [testng] 02:15:13,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:15:13,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:13,383 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-17_02-15-13.log] [testng] 02:15:13,383 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40215639 - End of configuration. [testng] [2024-03-17 02:15:14,784] [pool-1-thread-10] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif: [testng] 02:15:14,784 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:15:14,784 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:14,785 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-17_02-15-14.log] [testng] 02:15:14,785 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10033bd5 - End of configuration. [testng] [2024-03-17 02:15:15,309] [pool-1-thread-9] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif: [testng] 02:15:15,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:15:15,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:15,310 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-17_02-15-15.log] [testng] 02:15:15,310 |-INFO in ch.qos.logback.core.sift.SiftProcessor@404dde5 - End of configuration. [testng] [2024-03-17 02:15:15,921] [pool-1-thread-8] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif: [testng] 02:15:15,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:15:15,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:15,922 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-17_02-15-15.log] [testng] 02:15:15,923 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4db03a09 - End of configuration. [testng] [2024-03-17 02:15:16,433] [pool-1-thread-7] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif: [testng] 02:15:16,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:15:16,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:16,434 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-17_02-15-16.log] [testng] 02:15:16,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3904cf8e - End of configuration. [testng] [2024-03-17 02:15:17,056] [pool-1-thread-6] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif: [testng] 02:15:17,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:15:17,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:17,057 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-17_02-15-17.log] [testng] 02:15:17,058 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cd1cbcc - End of configuration. [testng] [2024-03-17 02:15:17,604] [pool-1-thread-5] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif: [testng] 02:15:17,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:15:17,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:17,605 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-17_02-15-17.log] [testng] 02:15:17,606 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5382ff34 - End of configuration. [testng] [2024-03-17 02:15:18,207] [pool-1-thread-4] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif: [testng] 02:15:18,207 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:15:18,207 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:18,207 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-17_02-15-18.log] [testng] 02:15:18,208 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e509863 - End of configuration. [testng] [2024-03-17 02:15:18,760] [pool-1-thread-3] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif: [testng] 02:15:18,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:15:18,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:18,761 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-17_02-15-18.log] [testng] 02:15:18,761 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b486f6 - End of configuration. [testng] [2024-03-17 02:15:19,306] [pool-1-thread-2] Initializing /data/samples/dimension-mismatch/1/acqp: [testng] 02:15:19,306 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:15:19,306 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:19,307 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-17_02-15-19.log] [testng] 02:15:19,307 |-INFO in ch.qos.logback.core.sift.SiftProcessor@160f7ff4 - End of configuration. [testng] [2024-03-17 02:15:25,323] [pool-1-thread-6] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif: [testng] [2024-03-17 02:15:26,034] [pool-1-thread-5] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif: [testng] [2024-03-17 02:15:26,686] [pool-1-thread-3] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif: [testng] [2024-03-17 02:15:27,296] [pool-1-thread-7] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif: [testng] [2024-03-17 02:15:27,934] [pool-1-thread-4] 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: 14 minutes 56 seconds Finished: SUCCESS