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Started by upstream project "BIOFORMATS-test-repo" build number 368 originally caused by: Started by upstream project "Trigger" build number 394 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/jenkins11301557863885083753.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_58739_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] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.8.9-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml [resolver:resolve] Resolving artifacts [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.8.9-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml compile-tests: [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.8.9-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml [resolver:resolve] Resolving artifacts [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.8.9-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml [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] 12:40:47,769 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 12:40:47,771 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 12:40:47,771 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:40:47,772 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:40:47,772 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:40:47,773 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:40:47,773 |-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] 12:40:47,773 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:40:47,774 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:40:47,774 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:40:47,774 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:40:47,775 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:40:47,935 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:40:47,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:40:47,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:40:47,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:40:47,963 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:40:47,963 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:40:47,963 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:40:47,964 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:40:47,964 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 12:40:47,964 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 12:40:47,964 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 190 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-09 12:40:47,973] [main] java.version = 11.0.16 [testng] 12:40:47,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:40:47,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:40:48,017 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-09_12-40-47.log] [testng] 12:40:48,018 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-03-09 12:40:48,021] [main] testng.directory = /data [testng] [2025-03-09 12:40:48,021] [main] testng.configDirectory = /config [testng] [2025-03-09 12:40:48,030] [main] testng.multiplier = 1.0 [testng] [2025-03-09 12:40:48,031] [main] testng.in-memory = false [testng] [2025-03-09 12:40:48,032] [main] testng.allow-missing = false [testng] [2025-03-09 12:40:48,032] [main] user.language = en [testng] [2025-03-09 12:40:48,032] [main] user.country = ${user.country} [testng] [2025-03-09 12:40:48,032] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-09 12:40:52,386] [main] ---------------------------------------- [testng] [2025-03-09 12:40:52,386] [main] Total files: 32 [testng] [2025-03-09 12:40:52,386] [main] Scan time: 4.354 s (136 ms/file) [testng] [2025-03-09 12:40:52,386] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-09 12:41:54,132] [pool-1-thread-1] Initializing /data/keith/PF020328saur v3.1sc: [testng] 12:41:54,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:41:54,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:41:54,135 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-09_12-41-54.log] [testng] 12:41:54,135 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12faa868 - End of configuration. [testng] [2025-03-09 12:41:55,315] [pool-1-thread-12] Initializing /data/qa-29469/bad3.1sc: [testng] 12:41:55,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:41:55,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:41:55,316 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-09_12-41-55.log] [testng] 12:41:55,316 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e698575 - End of configuration. [testng] [2025-03-09 12:41:56,437] [pool-1-thread-11] Initializing /data/qa-29459/bad.1sc: [testng] 12:41:56,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:41:56,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:41:56,438 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-09_12-41-56.log] [testng] 12:41:56,439 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ac0a8cf - End of configuration. [testng] [2025-03-09 12:41:57,510] [pool-1-thread-10] Initializing /data/samples/Criterion.1sc: [testng] 12:41:57,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:41:57,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:41:57,511 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-09_12-41-57.log] [testng] 12:41:57,511 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fa2c105 - End of configuration. [testng] [2025-03-09 12:41:58,554] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] 12:41:58,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:41:58,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:41:58,555 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-09_12-41-58.log] [testng] 12:41:58,555 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75bf3eb3 - End of configuration. [testng] [2025-03-09 12:41:59,744] [pool-1-thread-8] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] 12:41:59,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:41:59,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:41:59,745 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-09_12-41-59.log] [testng] 12:41:59,745 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24183548 - End of configuration. [testng] [2025-03-09 12:42:00,913] [pool-1-thread-7] Initializing /data/keith/pg020410saur3.1sc: [testng] 12:42:00,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:42:00,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:42:00,914 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-09_12-42-00.log] [testng] 12:42:00,914 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d2b1214 - End of configuration. [testng] [2025-03-09 12:42:01,991] [pool-1-thread-6] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] 12:42:01,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:42:01,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:42:01,992 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-09_12-42-01.log] [testng] 12:42:01,992 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70b21faf - End of configuration. [testng] [2025-03-09 12:42:03,159] [pool-1-thread-5] Initializing /data/geert/good example1.1sc.jpg: [testng] 12:42:03,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:42:03,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:42:03,160 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-09_12-42-03.log] [testng] 12:42:03,160 |-INFO in ch.qos.logback.core.sift.SiftProcessor@118a9a4b - End of configuration. [testng] [2025-03-09 12:42:03,583] [pool-1-thread-4] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] 12:42:03,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:42:03,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:42:03,584 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-09_12-42-03.log] [testng] 12:42:03,584 |-INFO in ch.qos.logback.core.sift.SiftProcessor@121df256 - End of configuration. [testng] [2025-03-09 12:42:08,033] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 12:42:08,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:42:08,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:42:08,034 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-09_12-42-08.log] [testng] 12:42:08,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75459243 - End of configuration. [testng] [2025-03-09 12:42:13,043] [pool-1-thread-2] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] 12:42:13,043 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:42:13,043 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:42:13,044 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-09_12-42-13.log] [testng] 12:42:13,044 |-INFO in ch.qos.logback.core.sift.SiftProcessor@796e5942 - End of configuration. [testng] [2025-03-09 12:42:23,190] [pool-1-thread-1] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] [2025-03-09 12:42:25,260] [pool-1-thread-12] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] [2025-03-09 12:42:25,926] [pool-1-thread-7] Initializing /data/qa-29469/good.1sc: [testng] [2025-03-09 12:42:26,567] [pool-1-thread-5] Initializing /data/keith/test.1sc: [testng] [2025-03-09 12:42:27,469] [pool-1-thread-6] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2025-03-09 12:42:28,787] [pool-1-thread-11] Initializing /data/geert/bad example1.1sc: [testng] [2025-03-09 12:42:30,179] [pool-1-thread-8] Initializing /data/qa-29469/bad2.1sc: [testng] [2025-03-09 12:42:31,507] [pool-1-thread-9] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] [2025-03-09 12:42:32,760] [pool-1-thread-10] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [2025-03-09 12:42:45,262] [pool-1-thread-5] Initializing /data/geert/good example1.1sc: [testng] [2025-03-09 12:42:46,726] [pool-1-thread-9] Initializing /data/samples/imagesEight.1sc: [testng] [2025-03-09 12:42:48,367] [pool-1-thread-7] Initializing /data/qa-16880/c-src v7.1sc: [testng] [2025-03-09 12:42:50,017] [pool-1-thread-10] Initializing /data/adrian/test_img.1sc: [testng] [2025-03-09 12:42:51,485] [pool-1-thread-11] Initializing /data/keith/test2.1sc: [testng] [2025-03-09 12:42:52,809] [pool-1-thread-6] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] [2025-03-09 12:42:56,993] [pool-1-thread-12] Initializing /data/qa-29459/bad.jpg: [testng] [2025-03-09 12:42:57,391] [pool-1-thread-8] Initializing /data/david/Opened in imageJ.tiff: [testng] [2025-03-09 12:43:03,430] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] [2025-03-09 12:43:09,093] [pool-1-thread-4] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2025-03-09 12:43:09,782] [pool-1-thread-2] Initializing /data/geert/bad example1.jpg: [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 57 seconds Finished: SUCCESS