Started by upstream project "BIOFORMATS-test-repo" build number 318 originally caused by: Started by upstream project "Trigger" build number 341 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins17286691900118942148.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_50502_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 12:55:14,598 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 12:55:14,599 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 12:55:14,599 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:55:14,600 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:55:14,600 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:55:14,601 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:55:14,601 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 12:55:14,601 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:55:14,601 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:55:14,602 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:55:14,602 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:55:14,603 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:55:14,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:55:14,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:55:14,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:55:14,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:55:14,787 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:55:14,787 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:55:14,787 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:55:14,788 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:55:14,788 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 12:55:14,789 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 12:55:14,789 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 188 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-14 12:55:14,797] [main] java.version = 11.0.16 [testng] 12:55:14,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:55:14,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:55:14,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-14_12-55-14.log] [testng] 12:55:14,841 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-01-14 12:55:14,843] [main] testng.directory = /data [testng] [2025-01-14 12:55:14,843] [main] testng.configDirectory = /config [testng] [2025-01-14 12:55:14,852] [main] testng.multiplier = 1.0 [testng] [2025-01-14 12:55:14,853] [main] testng.in-memory = false [testng] [2025-01-14 12:55:14,854] [main] testng.allow-missing = false [testng] [2025-01-14 12:55:14,854] [main] user.language = en [testng] [2025-01-14 12:55:14,854] [main] user.country = ${user.country} [testng] [2025-01-14 12:55:14,854] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-14 12:55:18,372] [main] ---------------------------------------- [testng] [2025-01-14 12:55:18,372] [main] Total files: 32 [testng] [2025-01-14 12:55:18,372] [main] Scan time: 3.518 s (109 ms/file) [testng] [2025-01-14 12:55:18,372] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-14 12:55:43,992] [pool-1-thread-1] Initializing /data/keith/PF020328saur v3.1sc: [testng] 12:55:43,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:55:43,993 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:55:43,994 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-14_12-55-43.log] [testng] 12:55:43,995 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14c4ba5d - End of configuration. [testng] [2025-01-14 12:55:44,485] [pool-1-thread-12] Initializing /data/qa-29469/bad3.1sc: [testng] 12:55:44,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:55:44,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:55:44,486 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-14_12-55-44.log] [testng] 12:55:44,486 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27edf96a - End of configuration. [testng] [2025-01-14 12:55:44,985] [pool-1-thread-11] Initializing /data/qa-29459/bad.1sc: [testng] 12:55:44,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:55:44,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:55:44,986 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-14_12-55-44.log] [testng] 12:55:44,986 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c859443 - End of configuration. [testng] [2025-01-14 12:55:45,591] [pool-1-thread-10] Initializing /data/samples/Criterion.1sc: [testng] 12:55:45,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:55:45,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:55:45,592 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-14_12-55-45.log] [testng] 12:55:45,592 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22443920 - End of configuration. [testng] [2025-01-14 12:55:46,218] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] 12:55:46,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:55:46,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:55:46,219 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-14_12-55-46.log] [testng] 12:55:46,219 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79ecc7c4 - End of configuration. [testng] [2025-01-14 12:55:46,770] [pool-1-thread-8] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] 12:55:46,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:55:46,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:55:46,771 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-14_12-55-46.log] [testng] 12:55:46,771 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37e23c95 - End of configuration. [testng] [2025-01-14 12:55:47,299] [pool-1-thread-7] Initializing /data/keith/pg020410saur3.1sc: [testng] 12:55:47,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:55:47,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:55:47,300 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-14_12-55-47.log] [testng] 12:55:47,300 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a25037d - End of configuration. [testng] [2025-01-14 12:55:47,770] [pool-1-thread-6] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] 12:55:47,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:55:47,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:55:47,771 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-14_12-55-47.log] [testng] 12:55:47,771 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18a60b9a - End of configuration. [testng] [2025-01-14 12:55:48,272] [pool-1-thread-5] Initializing /data/geert/good example1.1sc.jpg: [testng] 12:55:48,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:55:48,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:55:48,273 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-14_12-55-48.log] [testng] 12:55:48,273 |-INFO in ch.qos.logback.core.sift.SiftProcessor@796e5942 - End of configuration. [testng] [2025-01-14 12:55:48,438] [pool-1-thread-4] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] 12:55:48,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:55:48,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:55:48,439 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-14_12-55-48.log] [testng] 12:55:48,439 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50036c63 - End of configuration. [testng] [2025-01-14 12:55:50,142] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 12:55:50,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:55:50,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:55:50,142 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-14_12-55-50.log] [testng] 12:55:50,143 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21472e47 - End of configuration. [testng] [2025-01-14 12:55:51,920] [pool-1-thread-2] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] 12:55:51,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:55:51,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:55:51,921 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-14_12-55-51.log] [testng] 12:55:51,921 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66093f1d - End of configuration. [testng] [2025-01-14 12:55:59,191] [pool-1-thread-5] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] [2025-01-14 12:56:00,973] [pool-1-thread-6] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] [2025-01-14 12:56:01,495] [pool-1-thread-1] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] [2025-01-14 12:56:01,995] [pool-1-thread-7] Initializing /data/qa-29469/good.1sc: [testng] [2025-01-14 12:56:02,488] [pool-1-thread-11] Initializing /data/keith/test.1sc: [testng] [2025-01-14 12:56:02,982] [pool-1-thread-12] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2025-01-14 12:56:03,564] [pool-1-thread-10] Initializing /data/geert/bad example1.1sc: [testng] [2025-01-14 12:56:04,165] [pool-1-thread-8] Initializing /data/qa-29469/bad2.1sc: [testng] [2025-01-14 12:56:05,023] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [2025-01-14 12:56:08,990] [pool-1-thread-11] Initializing /data/geert/good example1.1sc: [testng] [2025-01-14 12:56:09,608] [pool-1-thread-7] Initializing /data/samples/imagesEight.1sc: [testng] [2025-01-14 12:56:10,144] [pool-1-thread-10] Initializing /data/qa-29459/bad.jpg: [testng] [2025-01-14 12:56:10,342] [pool-1-thread-6] Initializing /data/david/Opened in imageJ.tiff: [testng] [2025-01-14 12:56:12,671] [pool-1-thread-1] Initializing /data/keith/test2.1sc: [testng] [2025-01-14 12:56:13,155] [pool-1-thread-12] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] [2025-01-14 12:56:14,920] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] [2025-01-14 12:56:17,264] [pool-1-thread-4] Initializing /data/qa-16880/c-src v7.1sc: [testng] [2025-01-14 12:56:17,796] [pool-1-thread-3] Initializing /data/adrian/test_img.1sc: [testng] [2025-01-14 12:56:18,292] [pool-1-thread-8] Initializing /data/geert/bad example1.jpg: [testng] [2025-01-14 12:56:20,460] [pool-1-thread-9] Initializing /data/geert/bad example1.1sc.jpg: [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