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Started by upstream project "BIOFORMATS-test-repo" build number 251 originally caused by: Started by upstream project "Trigger" build number 275 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/jenkins11770624980365080634.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_39597_merge_ci -v /uod/idr/repos/curated/imaris:/data -v /uod/idr-scratch/merge-ci/curated/imaris:/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] 04:01:43,943 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 04:01:43,945 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 04:01:43,945 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:01:43,946 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:01:43,946 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:01:43,947 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:01:43,947 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 04:01:43,947 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:01:43,947 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:01:43,948 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:01:43,948 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:01:43,948 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:01:44,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:01:44,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:01:44,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:01:44,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:01:44,137 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:01:44,137 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:01:44,138 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:01:44,138 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:01:44,138 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 04:01:44,139 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 04:01:44,139 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 192 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-10 04:01:44,148] [main] java.version = 17.0.2 [testng] 04:01:44,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:01:44,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:01:44,192 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-10_04-01-44.log] [testng] 04:01:44,193 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-10 04:01:44,195] [main] testng.directory = /data [testng] [2024-11-10 04:01:44,196] [main] testng.configDirectory = /config [testng] [2024-11-10 04:01:44,204] [main] testng.multiplier = 1.0 [testng] [2024-11-10 04:01:44,205] [main] testng.in-memory = false [testng] [2024-11-10 04:01:44,205] [main] testng.allow-missing = false [testng] [2024-11-10 04:01:44,205] [main] user.language = en [testng] [2024-11-10 04:01:44,205] [main] user.country = ${user.country} [testng] [2024-11-10 04:01:44,205] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-10 04:02:26,590] [main] ---------------------------------------- [testng] [2024-11-10 04:02:26,590] [main] Total files: 68 [testng] [2024-11-10 04:02:26,590] [main] Scan time: 42.385 s (623 ms/file) [testng] [2024-11-10 04:02:26,590] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 60 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-10 04:03:15,979] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_1T_confocal_IMS3.ims: [testng] 04:03:15,980 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:03:15,980 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:03:15,981 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-10_04-03-15.log] [testng] 04:03:15,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@209e5dcc - End of configuration. [testng] [2024-11-10 04:03:16,492] [pool-1-thread-12] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_deconvolved.ims: [testng] 04:03:16,492 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:03:16,492 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:03:16,493 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-10_04-03-16.log] [testng] 04:03:16,493 |-INFO in ch.qos.logback.core.sift.SiftProcessor@184c6a8e - End of configuration. [testng] [2024-11-10 04:03:16,934] [pool-1-thread-11] Initializing /data/public/davemason/TransFactors_2C_SRRF_IMS3.ims: [testng] 04:03:16,934 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:03:16,934 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:03:16,935 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-10_04-03-16.log] [testng] 04:03:16,935 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50d2ec52 - End of configuration. [testng] [2024-11-10 04:03:17,450] [pool-1-thread-10] Initializing /data/oliver/Stack2_u16Bit.ims: [testng] 04:03:17,450 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:03:17,450 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:03:17,451 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-10_04-03-17.log] [testng] 04:03:17,451 |-INFO in ch.qos.logback.core.sift.SiftProcessor@589c63ce - End of configuration. [testng] [2024-11-10 04:03:17,931] [pool-1-thread-9] Initializing /data/jason/imaris_5_5_demoimages/retina.ims: [testng] 04:03:17,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:03:17,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:03:17,932 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-10_04-03-17.log] [testng] 04:03:17,933 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11320dcd - End of configuration. [testng] [2024-11-10 04:03:18,402] [pool-1-thread-8] Initializing /data/jcb/fig 6B GFP-AP-2d.ims: [testng] 04:03:18,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:03:18,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:03:18,403 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-10_04-03-18.log] [testng] 04:03:18,403 |-INFO in ch.qos.logback.core.sift.SiftProcessor@487595e2 - End of configuration. [testng] [2024-11-10 04:03:18,829] [pool-1-thread-7] Initializing /data/public/eliana/retina_large.ims: [testng] 04:03:18,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:03:18,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:03:18,831 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-10_04-03-18.log] [testng] 04:03:18,831 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a7bbf4e - End of configuration. [testng] [2024-11-10 04:03:19,290] [pool-1-thread-6] Initializing /data/niko/imaris-testfile_5x5x5.ims: [testng] 04:03:19,290 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:03:19,290 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:03:19,291 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-10_04-03-19.log] [testng] 04:03:19,291 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18a2fb10 - End of configuration. [testng] [2024-11-10 04:03:19,755] [pool-1-thread-5] Initializing /data/qa-17839/Fusion_2048_2048_50_1_Acquire.ims: [testng] 04:03:19,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:03:19,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:03:19,756 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-10_04-03-19.log] [testng] 04:03:19,757 |-INFO in ch.qos.logback.core.sift.SiftProcessor@617a6337 - End of configuration. [testng] [2024-11-10 04:03:20,258] [pool-1-thread-4] Initializing /data/generated/10-31_E_t0004.ims: [testng] 04:03:20,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:03:20,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:03:20,259 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-10_04-03-20.log] [testng] 04:03:20,259 |-INFO in ch.qos.logback.core.sift.SiftProcessor@595ac850 - End of configuration. [testng] [2024-11-10 04:03:20,433] [pool-1-thread-3] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal.ims: [testng] 04:03:20,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:03:20,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:03:20,434 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-10_04-03-20.log] [testng] 04:03:20,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ef860ff - End of configuration. [testng] [2024-11-10 04:03:20,913] [pool-1-thread-2] Initializing /data/generated/10-31_E_t0005.ims: [testng] 04:03:20,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:03:20,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:03:20,914 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-10_04-03-20.log] [testng] 04:03:20,915 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d1801fe - End of configuration. BUILD SUCCESSFUL Total time: 3 minutes 56 seconds Finished: SUCCESS