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Started by upstream project "BIOFORMATS-test-repo" build number 229 originally caused by: Started by upstream project "Trigger" build number 254 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins16901053442163876120.sh + '[' specs = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35898_merge_ci -v /uod/idr/repos/curated/specs:/data -v /uod/idr-scratch/merge-ci/curated/specs:/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] 01:27:03,926 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:27:03,928 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 01:27:03,928 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:27:03,929 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:27:03,930 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:27:03,930 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:27:03,930 |-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] 01:27:03,930 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:27:03,931 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:27:03,931 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:27:03,932 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:27:03,932 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:27:04,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:27:04,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:27:04,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:27:04,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:27:04,150 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:27:04,150 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:27:04,150 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:27:04,151 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:27:04,151 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 01:27:04,151 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 01:27:04,152 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 221 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-20 01:27:04,162] [main] java.version = 17.0.2 [testng] 01:27:04,167 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:27:04,167 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:04,221 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-20_01-27-04.log] [testng] 01:27:04,223 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-20 01:27:04,226] [main] testng.directory = /data [testng] [2024-10-20 01:27:04,227] [main] testng.configDirectory = /config [testng] [2024-10-20 01:27:04,237] [main] testng.multiplier = 1.0 [testng] [2024-10-20 01:27:04,238] [main] testng.in-memory = false [testng] [2024-10-20 01:27:04,238] [main] testng.allow-missing = false [testng] [2024-10-20 01:27:04,238] [main] user.language = en [testng] [2024-10-20 01:27:04,238] [main] user.country = ${user.country} [testng] [2024-10-20 01:27:04,238] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-20 01:29:40,765] [main] ---------------------------------------- [testng] [2024-10-20 01:29:40,765] [main] Total files: 226 [testng] [2024-10-20 01:29:40,765] [main] Scan time: 156.527 s (692 ms/file) [testng] [2024-10-20 01:29:40,765] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-20 01:31:06,995] [pool-1-thread-1] Initializing /data/fluoview/SpineAnimation.tif: [testng] 01:31:06,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:31:06,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:06,997 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-20_01-31-06.log] [testng] 01:31:06,997 |-INFO in ch.qos.logback.core.sift.SiftProcessor@125bcbe2 - End of configuration. [testng] [2024-10-20 01:31:07,239] [pool-1-thread-12] Initializing /data/fluoview/Sample_XYZ.TIF: [testng] 01:31:07,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:31:07,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:07,240 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-20_01-31-07.log] [testng] 01:31:07,240 |-INFO in ch.qos.logback.core.sift.SiftProcessor@729b99d8 - End of configuration. [testng] [2024-10-20 01:31:07,497] [pool-1-thread-11] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test2.dm3: [testng] 01:31:07,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:31:07,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:07,498 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-20_01-31-07.log] [testng] 01:31:07,498 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54496c6d - End of configuration. [testng] [2024-10-20 01:31:07,557] [pool-1-thread-10] Initializing /data/iplab/Blend_Dapi.IPL: [testng] 01:31:07,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:31:07,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:07,558 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-20_01-31-07.log] [testng] 01:31:07,558 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c63b372 - End of configuration. [testng] [2024-10-20 01:31:07,596] [pool-1-thread-9] Initializing /data/iplab/Blend_Fitc.IPL: [testng] 01:31:07,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:31:07,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:07,597 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-20_01-31-07.log] [testng] 01:31:07,598 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19db13c8 - End of configuration. [testng] [2024-10-20 01:31:07,637] [pool-1-thread-8] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-2.lsm: [testng] 01:31:07,637 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:31:07,637 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:07,637 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-20_01-31-07.log] [testng] 01:31:07,638 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c425b87 - End of configuration. [testng] [2024-10-20 01:31:07,879] [pool-1-thread-7] Initializing /data/iplab/Color Histology.IPL: [testng] 01:31:07,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:31:07,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:07,880 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-20_01-31-07.log] [testng] 01:31:07,881 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36adcaa0 - End of configuration. [testng] [2024-10-20 01:31:07,918] [pool-1-thread-6] Initializing /data/iplab/Blend_Final.IPL: [testng] 01:31:07,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:31:07,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:07,919 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-20_01-31-07.log] [testng] 01:31:07,919 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71b5cb66 - End of configuration. [testng] [2024-10-20 01:31:07,959] [pool-1-thread-5] Initializing /data/fluoview/Sample_XT.tif: [testng] 01:31:07,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:31:07,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:07,960 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-20_01-31-07.log] [testng] 01:31:07,960 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b2de5d9 - End of configuration. [testng] [2024-10-20 01:31:08,176] [pool-1-thread-4] Initializing /data/iplab/Blend_DIC.IPL: [testng] 01:31:08,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:31:08,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:08,177 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-20_01-31-08.log] [testng] 01:31:08,177 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56c73bfd - End of configuration. [testng] [2024-10-20 01:31:08,221] [pool-1-thread-3] Initializing /data/fluoview/sample_labled_XYTCh.tif: [testng] 01:31:08,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:31:08,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:08,223 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-20_01-31-08.log] [testng] 01:31:08,223 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79426596 - End of configuration. [testng] [2024-10-20 01:31:08,421] [pool-1-thread-2] Initializing /data/iplab/16Bit XRay.IPL: [testng] 01:31:08,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:31:08,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:08,422 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-20_01-31-08.log] [testng] 01:31:08,422 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b59108f - End of configuration. [testng] [2024-10-20 01:31:10,261] [pool-1-thread-2] Initializing /data/iplab/Actin.IPL: [testng] [2024-10-20 01:31:10,286] [pool-1-thread-7] Initializing /data/fluoview/Sample_XYT.TIF: [testng] [2024-10-20 01:31:10,434] [pool-1-thread-6] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile--MultiTrack-1.lsm: [testng] [2024-10-20 01:31:10,610] [pool-1-thread-4] Initializing /data/iplab/3t3 Cell.IPL: [testng] [2024-10-20 01:31:10,636] [pool-1-thread-10] Initializing /data/fluoview/SpineAnimation.avi: [testng] [2024-10-20 01:31:10,714] [pool-1-thread-9] Initializing /data/iplab/Color Image.IPL: [testng] [2024-10-20 01:31:10,736] [pool-1-thread-11] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/test3.dm3: [testng] [2024-10-20 01:31:10,987] [pool-1-thread-3] Initializing /data/fluoview/Sample_TwoCH.TIF: [testng] [2024-10-20 01:31:11,721] [pool-1-thread-12] Initializing /data/iplab/Chromosomes.IPL: [testng] [2024-10-20 01:31:11,756] [pool-1-thread-1] Initializing /data/iplab/Blend_Tritc.IPL: [testng] [2024-10-20 01:31:11,792] [pool-1-thread-5] Initializing /data/iplab/10x Blood and Bacteria.IPL: [testng] [2024-10-20 01:31:11,854] [pool-1-thread-9] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-1.lsm: [testng] [2024-10-20 01:31:12,135] [pool-1-thread-4] Initializing /data/fluoview/sample_labled_XYZTCh.tif: [testng] [2024-10-20 01:31:12,416] [pool-1-thread-2] Initializing /data/fluoview/Sample_ThreeCH.TIF: [testng] [2024-10-20 01:31:12,637] [pool-1-thread-11] Initializing /data/fluoview/sample_labled_XYZCh.tif: [testng] [2024-10-20 01:31:13,251] [pool-1-thread-12] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test.dm3: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1484, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 4 minutes 15 seconds Finished: SUCCESS