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Started by upstream project "BIOFORMATS-test-repo" build number 215 originally caused by: Started by upstream project "Trigger" build number 242 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins14065578342907670447.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_34173_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] 05:22:26,778 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 05:22:26,779 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 05:22:26,779 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:22:26,780 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:22:26,781 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 05:22:26,781 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 05:22:26,781 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 05:22:26,781 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:22:26,782 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:22:26,782 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 05:22:26,783 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 05:22:26,783 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 05:22:26,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 05:22:26,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 05:22:26,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 05:22:26,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 05:22:26,970 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 05:22:26,970 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 05:22:26,970 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 05:22:26,971 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 05:22:26,971 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 05:22:26,972 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 05:22:26,972 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 190 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-09 05:22:26,980] [main] java.version = 17.0.2 [testng] 05:22:26,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:22:26,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:22:27,023 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-09_05-22-26.log] [testng] 05:22:27,025 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-09 05:22:27,027] [main] testng.directory = /data [testng] [2024-10-09 05:22:27,027] [main] testng.configDirectory = /config [testng] [2024-10-09 05:22:27,035] [main] testng.multiplier = 1.0 [testng] [2024-10-09 05:22:27,036] [main] testng.in-memory = false [testng] [2024-10-09 05:22:27,036] [main] testng.allow-missing = false [testng] [2024-10-09 05:22:27,036] [main] user.language = en [testng] [2024-10-09 05:22:27,036] [main] user.country = ${user.country} [testng] [2024-10-09 05:22:27,036] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-09 05:22:31,361] [main] ---------------------------------------- [testng] [2024-10-09 05:22:31,361] [main] Total files: 32 [testng] [2024-10-09 05:22:31,362] [main] Scan time: 4.324 s (135 ms/file) [testng] [2024-10-09 05:22:31,362] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-09 05:22:54,172] [pool-1-thread-1] Initializing /data/samples/Criterion.1sc: [testng] 05:22:54,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:22:54,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:22:54,174 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-09_05-22-54.log] [testng] 05:22:54,175 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a62f043 - End of configuration. [testng] [2024-10-09 05:22:54,602] [pool-1-thread-12] Initializing /data/qa-29459/bad.jpg: [testng] 05:22:54,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:22:54,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:22:54,603 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-09_05-22-54.log] [testng] 05:22:54,604 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1193bec3 - End of configuration. [testng] [2024-10-09 05:22:54,739] [pool-1-thread-11] Initializing /data/david/Opened in imageJ.tiff: [testng] 05:22:54,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:22:54,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:22:54,740 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-09_05-22-54.log] [testng] 05:22:54,741 |-INFO in ch.qos.logback.core.sift.SiftProcessor@123bbfca - End of configuration. [testng] [2024-10-09 05:22:56,145] [pool-1-thread-10] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 05:22:56,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:22:56,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:22:56,146 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-09_05-22-56.log] [testng] 05:22:56,146 |-INFO in ch.qos.logback.core.sift.SiftProcessor@edbdead - End of configuration. [testng] [2024-10-09 05:22:57,621] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] 05:22:57,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:22:57,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:22:57,621 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-09_05-22-57.log] [testng] 05:22:57,622 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19b532 - End of configuration. [testng] [2024-10-09 05:22:59,047] [pool-1-thread-8] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] 05:22:59,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:22:59,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:22:59,048 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-09_05-22-59.log] [testng] 05:22:59,049 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3591a901 - End of configuration. [testng] [2024-10-09 05:22:59,520] [pool-1-thread-7] Initializing /data/samples/imagesEight.1sc: [testng] 05:22:59,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:22:59,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:22:59,522 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-09_05-22-59.log] [testng] 05:22:59,522 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a6713e - End of configuration. [testng] [2024-10-09 05:22:59,909] [pool-1-thread-6] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] 05:22:59,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:22:59,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:22:59,910 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-09_05-22-59.log] [testng] 05:22:59,910 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e421d6b - End of configuration. [testng] [2024-10-09 05:23:01,367] [pool-1-thread-5] Initializing /data/keith/test2.1sc: [testng] 05:23:01,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:23:01,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:23:01,368 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-09_05-23-01.log] [testng] 05:23:01,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7112b02a - End of configuration. [testng] [2024-10-09 05:23:01,711] [pool-1-thread-4] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] 05:23:01,711 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:23:01,711 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:23:01,712 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-09_05-23-01.log] [testng] 05:23:01,712 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a838257 - End of configuration. [testng] [2024-10-09 05:23:02,089] [pool-1-thread-3] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] 05:23:02,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:23:02,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:23:02,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-09_05-23-02.log] [testng] 05:23:02,090 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76296af6 - End of configuration. [testng] [2024-10-09 05:23:03,545] [pool-1-thread-2] Initializing /data/geert/bad example1.1sc: [testng] 05:23:03,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:23:03,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:23:03,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-09_05-23-03.log] [testng] 05:23:03,546 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20c9ab9f - End of configuration. [testng] [2024-10-09 05:23:08,522] [pool-1-thread-7] Initializing /data/qa-29469/good.1sc: [testng] [2024-10-09 05:23:09,026] [pool-1-thread-5] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-10-09 05:23:09,509] [pool-1-thread-12] Initializing /data/qa-29459/bad.1sc: [testng] [2024-10-09 05:23:09,954] [pool-1-thread-4] Initializing /data/qa-29469/bad3.1sc: [testng] [2024-10-09 05:23:10,387] [pool-1-thread-2] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2024-10-09 05:23:10,570] [pool-1-thread-8] Initializing /data/adrian/test_img.1sc: [testng] [2024-10-09 05:23:10,992] [pool-1-thread-1] Initializing /data/keith/pg020410saur3.1sc: [testng] [2024-10-09 05:23:15,155] [pool-1-thread-1] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [2024-10-09 05:23:15,766] [pool-1-thread-12] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [2024-10-09 05:23:16,397] [pool-1-thread-4] Initializing /data/keith/test.1sc: [testng] [2024-10-09 05:23:16,901] [pool-1-thread-7] Initializing /data/keith/PF020328saur v3.1sc: [testng] [2024-10-09 05:23:17,305] [pool-1-thread-8] Initializing /data/qa-16880/c-src v7.1sc: [testng] [2024-10-09 05:23:17,784] [pool-1-thread-5] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-10-09 05:23:17,924] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-10-09 05:23:18,382] [pool-1-thread-11] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-10-09 05:23:18,838] [pool-1-thread-9] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-10-09 05:23:20,358] [pool-1-thread-6] Initializing /data/geert/good example1.1sc: [testng] [2024-10-09 05:23:20,812] [pool-1-thread-10] Initializing /data/geert/bad example1.jpg: [testng] [2024-10-09 05:23:20,991] [pool-1-thread-2] Initializing /data/qa-29469/bad2.1sc: [testng] [2024-10-09 05:23:23,761] [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 9 seconds Finished: SUCCESS