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Started by upstream project "BIOFORMATS-test-repo" build number 379 originally caused by: Started by upstream project "Trigger" build number 401 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/jenkins13825583664649585427.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_60031_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] 08:36:56,281 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 08:36:56,283 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 08:36:56,283 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:36:56,284 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:36:56,284 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 08:36:56,285 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 08:36:56,285 |-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] 08:36:56,285 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:36:56,285 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:36:56,286 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 08:36:56,286 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 08:36:56,287 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 08:36:56,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 08:36:56,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 08:36:56,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 08:36:56,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 08:36:56,471 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 08:36:56,471 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 08:36:56,471 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 08:36:56,472 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 08:36:56,472 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 08:36:56,473 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 08:36:56,473 |-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] [2025-03-15 08:36:56,481] [main] java.version = 11.0.16 [testng] 08:36:56,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:36:56,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:36:56,525 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-15_08-36-56.log] [testng] 08:36:56,526 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-03-15 08:36:56,528] [main] testng.directory = /data [testng] [2025-03-15 08:36:56,528] [main] testng.configDirectory = /config [testng] [2025-03-15 08:36:56,538] [main] testng.multiplier = 1.0 [testng] [2025-03-15 08:36:56,539] [main] testng.in-memory = false [testng] [2025-03-15 08:36:56,539] [main] testng.allow-missing = false [testng] [2025-03-15 08:36:56,539] [main] user.language = en [testng] [2025-03-15 08:36:56,539] [main] user.country = ${user.country} [testng] [2025-03-15 08:36:56,539] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-15 08:37:03,119] [main] ---------------------------------------- [testng] [2025-03-15 08:37:03,119] [main] Total files: 32 [testng] [2025-03-15 08:37:03,119] [main] Scan time: 6.58 s (205 ms/file) [testng] [2025-03-15 08:37:03,120] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-15 08:38:01,319] [pool-1-thread-1] Initializing /data/keith/PF020328saur v3.1sc: [testng] 08:38:01,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 08:38:01,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:38:01,321 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-15_08-38-01.log] [testng] 08:38:01,322 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e029385 - End of configuration. [testng] [2025-03-15 08:38:02,329] [pool-1-thread-12] Initializing /data/qa-29469/bad3.1sc: [testng] 08:38:02,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 08:38:02,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:38:02,330 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-15_08-38-02.log] [testng] 08:38:02,331 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4daa5cb0 - End of configuration. [testng] [2025-03-15 08:38:03,427] [pool-1-thread-11] Initializing /data/qa-29459/bad.1sc: [testng] 08:38:03,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 08:38:03,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:38:03,428 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-15_08-38-03.log] [testng] 08:38:03,429 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60bfd03a - End of configuration. [testng] [2025-03-15 08:38:04,509] [pool-1-thread-10] Initializing /data/samples/Criterion.1sc: [testng] 08:38:04,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 08:38:04,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:38:04,510 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-15_08-38-04.log] [testng] 08:38:04,510 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24e651fd - End of configuration. [testng] [2025-03-15 08:38:05,764] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] 08:38:05,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 08:38:05,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:38:05,765 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-15_08-38-05.log] [testng] 08:38:05,765 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e698575 - End of configuration. [testng] [2025-03-15 08:38:06,912] [pool-1-thread-8] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] 08:38:06,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 08:38:06,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:38:06,913 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-15_08-38-06.log] [testng] 08:38:06,913 |-INFO in ch.qos.logback.core.sift.SiftProcessor@269d0770 - End of configuration. [testng] [2025-03-15 08:38:08,025] [pool-1-thread-7] Initializing /data/keith/pg020410saur3.1sc: [testng] 08:38:08,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 08:38:08,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:38:08,026 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-15_08-38-08.log] [testng] 08:38:08,026 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bcddaab - End of configuration. [testng] [2025-03-15 08:38:09,144] [pool-1-thread-6] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] 08:38:09,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 08:38:09,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:38:09,145 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-15_08-38-09.log] [testng] 08:38:09,145 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cf71a67 - End of configuration. [testng] [2025-03-15 08:38:10,126] [pool-1-thread-5] Initializing /data/geert/good example1.1sc.jpg: [testng] 08:38:10,127 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 08:38:10,127 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:38:10,127 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-15_08-38-10.log] [testng] 08:38:10,128 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65ca33dd - End of configuration. [testng] [2025-03-15 08:38:10,422] [pool-1-thread-4] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] 08:38:10,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 08:38:10,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:38:10,423 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-15_08-38-10.log] [testng] 08:38:10,423 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77ea705b - End of configuration. [testng] [2025-03-15 08:38:14,503] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 08:38:14,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 08:38:14,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:38:14,504 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-15_08-38-14.log] [testng] 08:38:14,504 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a3788d6 - End of configuration. [testng] [2025-03-15 08:38:18,097] [pool-1-thread-2] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] 08:38:18,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 08:38:18,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:38:18,098 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-15_08-38-18.log] [testng] 08:38:18,098 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e9e0304 - End of configuration. [testng] [2025-03-15 08:38:31,471] [pool-1-thread-1] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] [2025-03-15 08:38:35,521] [pool-1-thread-12] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] [2025-03-15 08:38:36,950] [pool-1-thread-10] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] [2025-03-15 08:38:38,248] [pool-1-thread-5] Initializing /data/qa-29469/good.1sc: [testng] [2025-03-15 08:38:39,651] [pool-1-thread-7] Initializing /data/keith/test.1sc: [testng] [2025-03-15 08:38:40,939] [pool-1-thread-6] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2025-03-15 08:38:42,107] [pool-1-thread-11] Initializing /data/geert/bad example1.1sc: [testng] [2025-03-15 08:38:43,277] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [2025-03-15 08:38:44,536] [pool-1-thread-8] Initializing /data/qa-29469/bad2.1sc: [testng] [2025-03-15 08:38:54,205] [pool-1-thread-7] Initializing /data/geert/good example1.1sc: [testng] [2025-03-15 08:38:55,294] [pool-1-thread-12] Initializing /data/samples/imagesEight.1sc: [testng] [2025-03-15 08:38:56,674] [pool-1-thread-5] Initializing /data/adrian/test_img.1sc: [testng] [2025-03-15 08:38:57,894] [pool-1-thread-11] Initializing /data/keith/test2.1sc: [testng] [2025-03-15 08:38:59,028] [pool-1-thread-6] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] [2025-03-15 08:39:02,595] [pool-1-thread-10] Initializing /data/qa-29459/bad.jpg: [testng] [2025-03-15 08:39:02,977] [pool-1-thread-8] Initializing /data/david/Opened in imageJ.tiff: [testng] [2025-03-15 08:39:06,889] [pool-1-thread-4] Initializing /data/qa-16880/c-src v7.1sc: [testng] [2025-03-15 08:39:08,115] [pool-1-thread-9] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2025-03-15 08:39:08,442] [pool-1-thread-2] Initializing /data/geert/bad example1.jpg: [testng] [2025-03-15 08:39:08,669] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [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 47 seconds Finished: SUCCESS