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Started by upstream project "BIOFORMATS-test-repo" build number 209 originally caused by: Started by upstream project "Trigger" build number 235 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins4923414343493342341.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_33242_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 test-automated: [testng] File leak detector installed [testng] 03:40:23,857 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:40:23,859 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 03:40:23,859 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:40:23,860 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:40:23,860 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:40:23,860 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:40:23,860 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:40:23,860 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:40:23,861 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:40:23,861 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:40:23,861 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:40:23,861 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:40:24,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:40:24,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:40:24,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:40:24,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:40:24,117 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:40:24,118 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:40:24,118 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:40:24,118 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:40:24,118 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 03:40:24,119 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 03:40:24,119 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 258 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-04 03:40:24,128] [main] java.version = 1.8.0_342 [testng] 03:40:24,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:40:24,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:24,175 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-04_03-40-24.log] [testng] 03:40:24,176 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-10-04 03:40:24,178] [main] testng.directory = /data [testng] [2024-10-04 03:40:24,178] [main] testng.configDirectory = /config [testng] [2024-10-04 03:40:24,190] [main] testng.multiplier = 1.0 [testng] [2024-10-04 03:40:24,191] [main] testng.in-memory = false [testng] [2024-10-04 03:40:24,191] [main] testng.allow-missing = false [testng] [2024-10-04 03:40:24,191] [main] user.language = en [testng] [2024-10-04 03:40:24,191] [main] user.country = ${user.country} [testng] [2024-10-04 03:40:24,191] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-04 03:40:26,412] [main] ---------------------------------------- [testng] [2024-10-04 03:40:26,413] [main] Total files: 32 [testng] [2024-10-04 03:40:26,413] [main] Scan time: 2.221 s (69 ms/file) [testng] [2024-10-04 03:40:26,413] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-04 03:40:44,733] [pool-1-thread-1] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 03:40:44,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:40:44,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:44,736 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-04_03-40-44.log] [testng] 03:40:44,736 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4eaa82d1 - End of configuration. [testng] [2024-10-04 03:40:45,744] [pool-1-thread-12] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] 03:40:45,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:40:45,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:45,746 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-04_03-40-45.log] [testng] 03:40:45,746 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57ad7026 - End of configuration. [testng] [2024-10-04 03:40:46,731] [pool-1-thread-10] Initializing /data/keith/PF020328saur v3.1sc: [testng] 03:40:46,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:40:46,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:46,732 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-04_03-40-46.log] [testng] 03:40:46,732 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4aa7efb2 - End of configuration. [testng] [2024-10-04 03:40:47,007] [pool-1-thread-9] Initializing /data/samples/Criterion.1sc: [testng] 03:40:47,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:40:47,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:47,008 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-04_03-40-47.log] [testng] 03:40:47,008 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27eea862 - End of configuration. [testng] [2024-10-04 03:40:47,353] [pool-1-thread-11] Initializing /data/qa-29459/bad.jpg: [testng] 03:40:47,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:40:47,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:47,353 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-04_03-40-47.log] [testng] 03:40:47,354 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f457e49 - End of configuration. [testng] [2024-10-04 03:40:47,438] [pool-1-thread-8] Initializing /data/geert/bad example1.1sc.jpg: [testng] 03:40:47,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:40:47,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:47,439 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-04_03-40-47.log] [testng] 03:40:47,439 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c8bef3b - End of configuration. [testng] [2024-10-04 03:40:47,558] [pool-1-thread-7] Initializing /data/geert/bad example1.1sc: [testng] 03:40:47,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:40:47,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:47,559 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-04_03-40-47.log] [testng] 03:40:47,559 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41782280 - End of configuration. [testng] [2024-10-04 03:40:47,851] [pool-1-thread-6] Initializing /data/qa-29469/bad2.1sc: [testng] 03:40:47,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:40:47,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:47,852 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-04_03-40-47.log] [testng] 03:40:47,853 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6280dfdb - End of configuration. [testng] [2024-10-04 03:40:48,153] [pool-1-thread-4] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] 03:40:48,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:40:48,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:48,154 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-04_03-40-48.log] [testng] 03:40:48,154 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1872e58e - End of configuration. [testng] [2024-10-04 03:40:48,446] [pool-1-thread-5] Initializing /data/david/Opened in imageJ.tiff: [testng] 03:40:48,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:40:48,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:48,447 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-04_03-40-48.log] [testng] 03:40:48,447 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44ffd35e - End of configuration. [testng] [2024-10-04 03:40:49,417] [pool-1-thread-2] Initializing /data/adrian/test_img.1sc: [testng] 03:40:49,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:40:49,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:49,419 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-04_03-40-49.log] [testng] 03:40:49,419 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5724a0b1 - End of configuration. [testng] [2024-10-04 03:40:49,729] [pool-1-thread-3] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] 03:40:49,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:40:49,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:49,731 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-04_03-40-49.log] [testng] 03:40:49,731 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79a6b269 - End of configuration. [testng] [2024-10-04 03:40:53,401] [pool-1-thread-11] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-10-04 03:40:54,619] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] [2024-10-04 03:40:55,877] [pool-1-thread-10] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-10-04 03:40:56,263] [pool-1-thread-6] Initializing /data/qa-29459/bad.1sc: [testng] [2024-10-04 03:40:56,637] [pool-1-thread-9] Initializing /data/geert/bad example1.jpg: [testng] [2024-10-04 03:40:56,806] [pool-1-thread-8] Initializing /data/keith/pg020410saur3.1sc: [testng] [2024-10-04 03:40:57,112] [pool-1-thread-7] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-10-04 03:40:57,524] [pool-1-thread-2] Initializing /data/samples/imagesEight.1sc: [testng] [2024-10-04 03:40:57,877] [pool-1-thread-4] Initializing /data/qa-29469/bad3.1sc: [testng] [2024-10-04 03:41:01,240] [pool-1-thread-8] Initializing /data/geert/good example1.1sc: [testng] [2024-10-04 03:41:01,712] [pool-1-thread-6] Initializing /data/qa-16880/c-src v7.1sc: [testng] [2024-10-04 03:41:02,151] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] [2024-10-04 03:41:03,509] [pool-1-thread-4] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-10-04 03:41:03,632] [pool-1-thread-5] Initializing /data/keith/test.1sc: [testng] [2024-10-04 03:41:03,976] [pool-1-thread-1] Initializing /data/qa-29469/good.1sc: [testng] [2024-10-04 03:41:04,339] [pool-1-thread-10] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [2024-10-04 03:41:04,705] [pool-1-thread-7] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-10-04 03:41:05,088] [pool-1-thread-12] Initializing /data/keith/test2.1sc: [testng] [2024-10-04 03:41:05,487] [pool-1-thread-9] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] [2024-10-04 03:41:09,485] [pool-1-thread-12] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1696, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 52 seconds Finished: SUCCESS