Started by upstream project "BIOFORMATS-test-repo" build number 254 originally caused by: Started by upstream project "Trigger" build number 278 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins15901765230635503737.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_40106_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] 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] 03:20:48,586 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:20:48,587 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 03:20:48,587 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:20:48,589 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:20:48,589 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:20:48,589 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:20:48,590 |-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] 03:20:48,590 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:20:48,590 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:20:48,591 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:20:48,591 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:20:48,591 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:20:48,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:20:48,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:20:48,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:20:48,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:20:48,804 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:20:48,804 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:20:48,804 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:20:48,804 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:20:48,804 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 03:20:48,805 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 03:20:48,805 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 215 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-13 03:20:48,814] [main] java.version = 17.0.2 [testng] 03:20:48,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:20:48,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:20:48,857 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-13_03-20-48.log] [testng] 03:20:48,859 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-13 03:20:48,861] [main] testng.directory = /data [testng] [2024-11-13 03:20:48,861] [main] testng.configDirectory = /config [testng] [2024-11-13 03:20:48,870] [main] testng.multiplier = 1.0 [testng] [2024-11-13 03:20:48,871] [main] testng.in-memory = false [testng] [2024-11-13 03:20:48,871] [main] testng.allow-missing = false [testng] [2024-11-13 03:20:48,871] [main] user.language = en [testng] [2024-11-13 03:20:48,871] [main] user.country = ${user.country} [testng] [2024-11-13 03:20:48,871] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-13 03:20:51,294] [main] ---------------------------------------- [testng] [2024-11-13 03:20:51,295] [main] Total files: 32 [testng] [2024-11-13 03:20:51,295] [main] Scan time: 2.423 s (75 ms/file) [testng] [2024-11-13 03:20:51,295] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-13 03:21:17,639] [pool-1-thread-1] Initializing /data/samples/Criterion.1sc: [testng] 03:21:17,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:21:17,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:21:17,640 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-13_03-21-17.log] [testng] 03:21:17,641 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cd9ec15 - End of configuration. [testng] [2024-11-13 03:21:18,224] [pool-1-thread-12] Initializing /data/qa-29459/bad.jpg: [testng] 03:21:18,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:21:18,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:21:18,226 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-13_03-21-18.log] [testng] 03:21:18,227 |-INFO in ch.qos.logback.core.sift.SiftProcessor@188eb254 - End of configuration. [testng] [2024-11-13 03:21:18,439] [pool-1-thread-11] Initializing /data/david/Opened in imageJ.tiff: [testng] 03:21:18,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:21:18,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:21:18,440 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-13_03-21-18.log] [testng] 03:21:18,440 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f6c9d07 - End of configuration. [testng] [2024-11-13 03:21:20,456] [pool-1-thread-10] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 03:21:20,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:21:20,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:21:20,457 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-13_03-21-20.log] [testng] 03:21:20,457 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e11e27b - End of configuration. [testng] [2024-11-13 03:21:22,256] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] 03:21:22,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:21:22,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:21:22,257 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-13_03-21-22.log] [testng] 03:21:22,258 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c5d4bfb - End of configuration. [testng] [2024-11-13 03:21:24,005] [pool-1-thread-8] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] 03:21:24,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:21:24,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:21:24,006 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-13_03-21-24.log] [testng] 03:21:24,006 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cccfb05 - End of configuration. [testng] [2024-11-13 03:21:24,557] [pool-1-thread-7] Initializing /data/samples/imagesEight.1sc: [testng] 03:21:24,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:21:24,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:21:24,558 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-13_03-21-24.log] [testng] 03:21:24,559 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40302b1 - End of configuration. [testng] [2024-11-13 03:21:25,089] [pool-1-thread-6] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] 03:21:25,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:21:25,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:21:25,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-13_03-21-25.log] [testng] 03:21:25,090 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e34d543 - End of configuration. [testng] [2024-11-13 03:21:26,935] [pool-1-thread-5] Initializing /data/keith/test2.1sc: [testng] 03:21:26,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:21:26,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:21:26,936 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-13_03-21-26.log] [testng] 03:21:26,937 |-INFO in ch.qos.logback.core.sift.SiftProcessor@505034f0 - End of configuration. [testng] [2024-11-13 03:21:27,481] [pool-1-thread-4] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] 03:21:27,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:21:27,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:21:27,482 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-13_03-21-27.log] [testng] 03:21:27,483 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60bac8d9 - End of configuration. [testng] [2024-11-13 03:21:28,031] [pool-1-thread-3] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] 03:21:28,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:21:28,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:21:28,032 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-13_03-21-28.log] [testng] 03:21:28,032 |-INFO in ch.qos.logback.core.sift.SiftProcessor@184fd4b0 - End of configuration. [testng] [2024-11-13 03:21:30,121] [pool-1-thread-2] Initializing /data/geert/bad example1.1sc: [testng] 03:21:30,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:21:30,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:21:30,122 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-13_03-21-30.log] [testng] 03:21:30,123 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ddee535 - End of configuration. [testng] [2024-11-13 03:21:35,916] [pool-1-thread-12] Initializing /data/qa-29469/good.1sc: [testng] [2024-11-13 03:21:36,457] [pool-1-thread-7] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-11-13 03:21:37,079] [pool-1-thread-5] Initializing /data/qa-29459/bad.1sc: [testng] [2024-11-13 03:21:37,637] [pool-1-thread-4] Initializing /data/qa-29469/bad3.1sc: [testng] [2024-11-13 03:21:38,110] [pool-1-thread-1] Initializing /data/keith/pg020410saur3.1sc: [testng] [2024-11-13 03:21:38,604] [pool-1-thread-2] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2024-11-13 03:21:38,783] [pool-1-thread-8] Initializing /data/adrian/test_img.1sc: [testng] [2024-11-13 03:21:43,471] [pool-1-thread-1] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [2024-11-13 03:21:44,120] [pool-1-thread-12] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [2024-11-13 03:21:44,710] [pool-1-thread-5] Initializing /data/keith/test.1sc: [testng] [2024-11-13 03:21:45,302] [pool-1-thread-4] Initializing /data/keith/PF020328saur v3.1sc: [testng] [2024-11-13 03:21:45,827] [pool-1-thread-7] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-11-13 03:21:46,378] [pool-1-thread-8] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-11-13 03:21:46,863] [pool-1-thread-11] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-11-13 03:21:48,753] [pool-1-thread-9] Initializing /data/geert/good example1.1sc: [testng] [2024-11-13 03:21:49,319] [pool-1-thread-3] Initializing /data/geert/bad example1.jpg: [testng] [2024-11-13 03:21:49,469] [pool-1-thread-6] Initializing /data/qa-29469/bad2.1sc: [testng] [2024-11-13 03:21:49,950] [pool-1-thread-10] Initializing /data/qa-16880/c-src v7.1sc: [testng] [2024-11-13 03:21:50,427] [pool-1-thread-2] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-11-13 03:21:53,314] [pool-1-thread-1] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1696, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 1 minute 20 seconds Finished: SUCCESS