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Started by upstream project "BIOFORMATS-test-repo" build number 287 originally caused by: Started by upstream project "Trigger" build number 306 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins14904955317263012950.sh + '[' specs = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_45284_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] 00:30:49,292 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:30:49,294 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:30:49,294 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:30:49,295 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:30:49,295 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:30:49,295 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:30:49,295 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:30:49,296 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:30:49,296 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:30:49,296 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:30:49,297 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:30:49,297 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:30:49,460 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:30:49,460 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:30:49,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:30:49,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:30:49,495 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:30:49,495 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:30:49,495 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:30:49,496 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:30:49,496 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:30:49,497 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:30:49,497 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 201 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-11 00:30:49,507] [main] java.version = 17.0.2 [testng] 00:30:49,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:30:49,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:49,556 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-11_00-30-49.log] [testng] 00:30:49,557 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-11 00:30:49,559] [main] testng.directory = /data [testng] [2024-12-11 00:30:49,559] [main] testng.configDirectory = /config [testng] [2024-12-11 00:30:49,568] [main] testng.multiplier = 1.0 [testng] [2024-12-11 00:30:49,569] [main] testng.in-memory = false [testng] [2024-12-11 00:30:49,569] [main] testng.allow-missing = false [testng] [2024-12-11 00:30:49,569] [main] user.language = en [testng] [2024-12-11 00:30:49,569] [main] user.country = ${user.country} [testng] [2024-12-11 00:30:49,569] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-11 00:37:16,540] [main] ---------------------------------------- [testng] [2024-12-11 00:37:16,540] [main] Total files: 226 [testng] [2024-12-11 00:37:16,540] [main] Scan time: 386.971 s (1712 ms/file) [testng] [2024-12-11 00:37:16,540] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-11 00:43:29,196] [pool-1-thread-1] Initializing /data/fluoview/SpineAnimation.tif: [testng] 00:43:29,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:43:29,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:29,198 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-11_00-43-29.log] [testng] 00:43:29,199 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12f21637 - End of configuration. [testng] [2024-12-11 00:43:30,021] [pool-1-thread-12] Initializing /data/fluoview/Sample_XYZ.TIF: [testng] 00:43:30,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:43:30,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:30,022 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-11_00-43-30.log] [testng] 00:43:30,023 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75fc7c2 - End of configuration. [testng] [2024-12-11 00:43:30,999] [pool-1-thread-11] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test2.dm3: [testng] 00:43:30,999 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:43:30,999 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:31,000 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-11_00-43-31.log] [testng] 00:43:31,000 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e415ae3 - End of configuration. [testng] [2024-12-11 00:43:31,209] [pool-1-thread-10] Initializing /data/iplab/Blend_Dapi.IPL: [testng] 00:43:31,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:43:31,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:31,210 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-11_00-43-31.log] [testng] 00:43:31,210 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e1302c3 - End of configuration. [testng] [2024-12-11 00:43:31,329] [pool-1-thread-9] Initializing /data/iplab/Blend_Fitc.IPL: [testng] 00:43:31,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:43:31,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:31,330 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-11_00-43-31.log] [testng] 00:43:31,331 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ed9c18d - End of configuration. [testng] [2024-12-11 00:43:31,464] [pool-1-thread-8] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-2.lsm: [testng] 00:43:31,464 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:43:31,464 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:31,465 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-11_00-43-31.log] [testng] 00:43:31,465 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32bc5080 - End of configuration. [testng] [2024-12-11 00:43:32,299] [pool-1-thread-7] Initializing /data/iplab/Color Histology.IPL: [testng] 00:43:32,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:43:32,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:32,300 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-11_00-43-32.log] [testng] 00:43:32,301 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67a4a550 - End of configuration. [testng] [2024-12-11 00:43:32,516] [pool-1-thread-6] Initializing /data/iplab/Blend_Final.IPL: [testng] 00:43:32,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:43:32,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:32,517 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-11_00-43-32.log] [testng] 00:43:32,518 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e5b4dca - End of configuration. [testng] [2024-12-11 00:43:32,740] [pool-1-thread-5] Initializing /data/fluoview/Sample_XT.tif: [testng] 00:43:32,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:43:32,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:32,741 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-11_00-43-32.log] [testng] 00:43:32,742 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ee5ff5d - End of configuration. [testng] [2024-12-11 00:43:34,083] [pool-1-thread-4] Initializing /data/iplab/Blend_DIC.IPL: [testng] 00:43:34,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:43:34,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:34,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-11_00-43-34.log] [testng] 00:43:34,084 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18855e3f - End of configuration. [testng] [2024-12-11 00:43:34,247] [pool-1-thread-3] Initializing /data/fluoview/sample_labled_XYTCh.tif: [testng] 00:43:34,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:43:34,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:34,248 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-11_00-43-34.log] [testng] 00:43:34,248 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79caa6f3 - End of configuration. [testng] [2024-12-11 00:43:35,271] [pool-1-thread-2] Initializing /data/iplab/16Bit XRay.IPL: [testng] 00:43:35,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:43:35,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:35,272 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-11_00-43-35.log] [testng] 00:43:35,273 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63b27e45 - End of configuration. [testng] [2024-12-11 00:43:39,396] [pool-1-thread-7] Initializing /data/iplab/Actin.IPL: [testng] [2024-12-11 00:43:39,599] [pool-1-thread-11] Initializing /data/fluoview/Sample_XYT.TIF: [testng] [2024-12-11 00:43:40,425] [pool-1-thread-2] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile--MultiTrack-1.lsm: [testng] [2024-12-11 00:43:41,188] [pool-1-thread-6] Initializing /data/iplab/3t3 Cell.IPL: [testng] [2024-12-11 00:43:41,379] [pool-1-thread-10] Initializing /data/fluoview/SpineAnimation.avi: [testng] [2024-12-11 00:43:41,637] [pool-1-thread-4] Initializing /data/iplab/Color Image.IPL: [testng] [2024-12-11 00:43:41,744] [pool-1-thread-9] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/test3.dm3: [testng] [2024-12-11 00:43:44,149] [pool-1-thread-4] Initializing /data/fluoview/Sample_TwoCH.TIF: [testng] [2024-12-11 00:43:44,860] [pool-1-thread-6] Initializing /data/iplab/Chromosomes.IPL: [testng] [2024-12-11 00:43:44,980] [pool-1-thread-7] Initializing /data/iplab/10x Blood and Bacteria.IPL: [testng] [2024-12-11 00:43:45,129] [pool-1-thread-9] Initializing /data/iplab/Blend_Tritc.IPL: [testng] [2024-12-11 00:43:45,511] [pool-1-thread-1] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-1.lsm: [testng] [2024-12-11 00:43:46,571] [pool-1-thread-3] Initializing /data/fluoview/Sample_ThreeCH.TIF: [testng] [2024-12-11 00:43:47,731] [pool-1-thread-12] Initializing /data/fluoview/sample_labled_XYZTCh.tif: [testng] [2024-12-11 00:43:48,638] [pool-1-thread-5] Initializing /data/fluoview/sample_labled_XYZCh.tif: [testng] [2024-12-11 00:43:49,914] [pool-1-thread-10] 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: 13 minutes 18 seconds Finished: SUCCESS