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Started by upstream project "BIOFORMATS-test-repo" build number 263 originally caused by: Started by user devspace 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/jenkins2866497992247114280.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41582_merge_ci -v /uod/idr/repos/curated/biorad-gel:/data -v /uod/idr-scratch/merge-ci/curated/biorad-gel:/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 19:38:09,134 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 19:38:09,135 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 19:38:09,135 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 19:38:09,136 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 19:38:09,136 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 19:38:09,137 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 19:38:09,137 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 19:38:09,137 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 19:38:09,138 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 19:38:09,138 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 19:38:09,138 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 19:38:09,139 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 19:38:09,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 19:38:09,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 19:38:09,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 19:38:09,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 19:38:09,326 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 19:38:09,326 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 19:38:09,326 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 19:38:09,326 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 19:38:09,326 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 19:38:09,327 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 19:38:09,327 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 189 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-21 19:38:09,336] [main] java.version = 21 [testng] 19:38:09,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 19:38:09,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 19:38:09,379 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-21_19-38-09.log] [testng] 19:38:09,380 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-11-21 19:38:09,382] [main] testng.directory = /data [testng] [2024-11-21 19:38:09,382] [main] testng.configDirectory = /config [testng] [2024-11-21 19:38:09,390] [main] testng.multiplier = 1.0 [testng] [2024-11-21 19:38:09,391] [main] testng.in-memory = false [testng] [2024-11-21 19:38:09,391] [main] testng.allow-missing = false [testng] [2024-11-21 19:38:09,391] [main] user.language = en [testng] [2024-11-21 19:38:09,391] [main] user.country = ${user.country} [testng] [2024-11-21 19:38:09,391] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-21 19:38:15,302] [main] ---------------------------------------- [testng] [2024-11-21 19:38:15,302] [main] Total files: 32 [testng] [2024-11-21 19:38:15,302] [main] Scan time: 5.911 s (184 ms/file) [testng] [2024-11-21 19:38:15,303] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-21 19:39:02,234] [pool-1-thread-1] Initializing /data/qa-16880/c-src v7.1sc: [testng] 19:39:02,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 19:39:02,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 19:39:02,236 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-21_19-39-02.log] [testng] 19:39:02,237 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42ea671f - End of configuration. [testng] [2024-11-21 19:39:02,991] [pool-1-thread-12] Initializing /data/david/Opened in imageJ.tiff: [testng] 19:39:02,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 19:39:02,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 19:39:02,992 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-21_19-39-02.log] [testng] 19:39:02,992 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70f3d793 - End of configuration. [testng] [2024-11-21 19:39:05,671] [pool-1-thread-11] Initializing /data/qa-29459/bad.1sc: [testng] 19:39:05,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 19:39:05,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 19:39:05,672 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-21_19-39-05.log] [testng] 19:39:05,673 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c378640 - End of configuration. [testng] [2024-11-21 19:39:06,424] [pool-1-thread-10] Initializing /data/keith/test2.1sc: [testng] 19:39:06,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 19:39:06,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 19:39:06,425 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-21_19-39-06.log] [testng] 19:39:06,425 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e750512 - End of configuration. [testng] [2024-11-21 19:39:07,153] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] 19:39:07,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 19:39:07,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 19:39:07,154 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-21_19-39-07.log] [testng] 19:39:07,154 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d2ca6a7 - End of configuration. [testng] [2024-11-21 19:39:07,919] [pool-1-thread-8] Initializing /data/geert/good example1.1sc: [testng] 19:39:07,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 19:39:07,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 19:39:07,920 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-21_19-39-07.log] [testng] 19:39:07,921 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f99cd35 - End of configuration. [testng] [2024-11-21 19:39:08,703] [pool-1-thread-7] Initializing /data/keith/pg020410saur3.1sc: [testng] 19:39:08,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 19:39:08,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 19:39:08,704 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-21_19-39-08.log] [testng] 19:39:08,704 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d4e10d9 - End of configuration. [testng] [2024-11-21 19:39:09,570] [pool-1-thread-6] Initializing /data/qa-29469/good.1sc: [testng] 19:39:09,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 19:39:09,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 19:39:09,571 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-21_19-39-09.log] [testng] 19:39:09,571 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f40231a - End of configuration. [testng] [2024-11-21 19:39:10,551] [pool-1-thread-5] Initializing /data/keith/test.1sc: [testng] 19:39:10,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 19:39:10,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 19:39:10,552 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-21_19-39-10.log] [testng] 19:39:10,552 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46e78431 - End of configuration. [testng] [2024-11-21 19:39:11,487] [pool-1-thread-4] Initializing /data/qa-29469/bad2.1sc: [testng] 19:39:11,487 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 19:39:11,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 19:39:11,488 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-21_19-39-11.log] [testng] 19:39:11,488 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e73a547 - End of configuration. [testng] [2024-11-21 19:39:12,370] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 19:39:12,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 19:39:12,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 19:39:12,371 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-21_19-39-12.log] [testng] 19:39:12,372 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e9df493 - End of configuration. [testng] [2024-11-21 19:39:15,435] [pool-1-thread-2] Initializing /data/geert/bad example1.1sc.jpg: [testng] 19:39:15,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 19:39:15,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 19:39:15,436 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-21_19-39-15.log] [testng] 19:39:15,436 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11adfcdc - End of configuration. [testng] [2024-11-21 19:39:23,456] [pool-1-thread-7] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-11-21 19:39:23,798] [pool-1-thread-5] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-11-21 19:39:24,664] [pool-1-thread-10] Initializing /data/qa-29469/bad3.1sc: [testng] [2024-11-21 19:39:25,365] [pool-1-thread-1] Initializing /data/samples/imagesEight.1sc: [testng] [2024-11-21 19:39:26,038] [pool-1-thread-11] Initializing /data/samples/Criterion.1sc: [testng] [2024-11-21 19:39:26,919] [pool-1-thread-6] Initializing /data/adrian/test_img.1sc: [testng] [2024-11-21 19:39:27,922] [pool-1-thread-4] Initializing /data/geert/bad example1.1sc: [testng] [2024-11-21 19:39:28,882] [pool-1-thread-8] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-11-21 19:39:32,296] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] [2024-11-21 19:39:35,756] [pool-1-thread-9] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] [2024-11-21 19:39:41,961] [pool-1-thread-1] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] [2024-11-21 19:39:44,756] [pool-1-thread-11] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] [2024-11-21 19:39:47,592] [pool-1-thread-10] Initializing /data/keith/PF020328saur v3.1sc: [testng] [2024-11-21 19:39:48,315] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] [2024-11-21 19:39:50,857] [pool-1-thread-6] Initializing /data/geert/bad example1.jpg: [testng] [2024-11-21 19:39:51,111] [pool-1-thread-12] Initializing /data/qa-29459/bad.jpg: [testng] [2024-11-21 19:39:51,344] [pool-1-thread-3] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [2024-11-21 19:39:52,010] [pool-1-thread-5] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-11-21 19:39:52,803] [pool-1-thread-7] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-11-21 19:39:53,587] [pool-1-thread-9] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1696, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 2 minutes 4 seconds Finished: SUCCESS