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Started by upstream project "BIOFORMATS-test-repo" build number 261 originally caused by: Started by upstream project "Trigger" build number 285 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/jenkins4587524124934442540.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41254_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] 04:27:24,179 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 04:27:24,181 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 04:27:24,181 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:27:24,181 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:27:24,182 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:27:24,182 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:27:24,183 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 04:27:24,183 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:27:24,183 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:27:24,184 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:27:24,184 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:27:24,185 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:27:24,342 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:27:24,342 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:27:24,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:27:24,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:27:24,369 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:27:24,369 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:27:24,369 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:27:24,369 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:27:24,370 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 04:27:24,371 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 04:27:24,371 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 188 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-20 04:27:24,379] [main] java.version = 17.0.2 [testng] 04:27:24,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:27:24,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:27:24,421 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-20_04-27-24.log] [testng] 04:27:24,423 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-20 04:27:24,425] [main] testng.directory = /data [testng] [2024-11-20 04:27:24,425] [main] testng.configDirectory = /config [testng] [2024-11-20 04:27:24,433] [main] testng.multiplier = 1.0 [testng] [2024-11-20 04:27:24,434] [main] testng.in-memory = false [testng] [2024-11-20 04:27:24,434] [main] testng.allow-missing = false [testng] [2024-11-20 04:27:24,434] [main] user.language = en [testng] [2024-11-20 04:27:24,434] [main] user.country = ${user.country} [testng] [2024-11-20 04:27:24,434] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-20 04:27:29,101] [main] ---------------------------------------- [testng] [2024-11-20 04:27:29,101] [main] Total files: 32 [testng] [2024-11-20 04:27:29,101] [main] Scan time: 4.667 s (145 ms/file) [testng] [2024-11-20 04:27:29,101] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-20 04:28:07,823] [pool-1-thread-1] Initializing /data/samples/Criterion.1sc: [testng] 04:28:07,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:28:07,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:07,824 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-20_04-28-07.log] [testng] 04:28:07,825 |-INFO in ch.qos.logback.core.sift.SiftProcessor@235dbb7c - End of configuration. [testng] [2024-11-20 04:28:08,675] [pool-1-thread-12] Initializing /data/qa-29459/bad.jpg: [testng] 04:28:08,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:28:08,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:08,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-20_04-28-08.log] [testng] 04:28:08,677 |-INFO in ch.qos.logback.core.sift.SiftProcessor@602468e6 - End of configuration. [testng] [2024-11-20 04:28:08,959] [pool-1-thread-11] Initializing /data/david/Opened in imageJ.tiff: [testng] 04:28:08,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:28:08,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:08,960 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-20_04-28-08.log] [testng] 04:28:08,961 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c1165fa - End of configuration. [testng] [2024-11-20 04:28:11,661] [pool-1-thread-10] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 04:28:11,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:28:11,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:11,662 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-20_04-28-11.log] [testng] 04:28:11,662 |-INFO in ch.qos.logback.core.sift.SiftProcessor@223b823c - End of configuration. [testng] [2024-11-20 04:28:14,149] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] 04:28:14,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:28:14,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:14,149 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-20_04-28-14.log] [testng] 04:28:14,150 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e1080e5 - End of configuration. [testng] [2024-11-20 04:28:16,637] [pool-1-thread-8] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] 04:28:16,637 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:28:16,637 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:16,638 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-20_04-28-16.log] [testng] 04:28:16,638 |-INFO in ch.qos.logback.core.sift.SiftProcessor@184fd4b0 - End of configuration. [testng] [2024-11-20 04:28:17,368] [pool-1-thread-7] Initializing /data/samples/imagesEight.1sc: [testng] 04:28:17,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:28:17,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:17,369 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-20_04-28-17.log] [testng] 04:28:17,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ddee535 - End of configuration. [testng] [2024-11-20 04:28:18,126] [pool-1-thread-6] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] 04:28:18,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:28:18,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:18,127 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-20_04-28-18.log] [testng] 04:28:18,131 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60a01aef - End of configuration. [testng] [2024-11-20 04:28:20,858] [pool-1-thread-5] Initializing /data/keith/test2.1sc: [testng] 04:28:20,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:28:20,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:20,859 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-20_04-28-20.log] [testng] 04:28:20,860 |-INFO in ch.qos.logback.core.sift.SiftProcessor@656cab21 - End of configuration. [testng] [2024-11-20 04:28:21,633] [pool-1-thread-4] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] 04:28:21,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:28:21,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:21,633 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-20_04-28-21.log] [testng] 04:28:21,634 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1961b56a - End of configuration. [testng] [2024-11-20 04:28:22,527] [pool-1-thread-3] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] 04:28:22,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:28:22,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:22,528 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-20_04-28-22.log] [testng] 04:28:22,528 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72a76891 - End of configuration. [testng] [2024-11-20 04:28:25,459] [pool-1-thread-2] Initializing /data/geert/bad example1.1sc: [testng] 04:28:25,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:28:25,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:25,460 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-20_04-28-25.log] [testng] 04:28:25,461 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ee4d402 - End of configuration. [testng] [2024-11-20 04:28:33,567] [pool-1-thread-7] Initializing /data/qa-29469/good.1sc: [testng] [2024-11-20 04:28:34,406] [pool-1-thread-5] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-11-20 04:28:35,193] [pool-1-thread-4] Initializing /data/qa-29459/bad.1sc: [testng] [2024-11-20 04:28:35,957] [pool-1-thread-12] Initializing /data/qa-29469/bad3.1sc: [testng] [2024-11-20 04:28:36,676] [pool-1-thread-1] Initializing /data/keith/pg020410saur3.1sc: [testng] [2024-11-20 04:28:37,406] [pool-1-thread-2] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2024-11-20 04:28:37,657] [pool-1-thread-8] Initializing /data/adrian/test_img.1sc: [testng] [2024-11-20 04:28:44,646] [pool-1-thread-1] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [2024-11-20 04:28:45,598] [pool-1-thread-12] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [2024-11-20 04:28:46,538] [pool-1-thread-7] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-11-20 04:28:47,528] [pool-1-thread-8] Initializing /data/keith/test.1sc: [testng] [2024-11-20 04:28:48,402] [pool-1-thread-4] Initializing /data/keith/PF020328saur v3.1sc: [testng] [2024-11-20 04:28:49,107] [pool-1-thread-5] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-11-20 04:28:49,352] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-11-20 04:28:50,129] [pool-1-thread-3] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-11-20 04:28:52,878] [pool-1-thread-9] Initializing /data/geert/good example1.1sc: [testng] [2024-11-20 04:28:53,614] [pool-1-thread-10] Initializing /data/geert/bad example1.jpg: [testng] [2024-11-20 04:28:53,868] [pool-1-thread-6] Initializing /data/qa-29469/bad2.1sc: [testng] [2024-11-20 04:28:54,520] [pool-1-thread-11] Initializing /data/qa-16880/c-src v7.1sc: [testng] [2024-11-20 04:28:59,348] [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 56 seconds Finished: SUCCESS