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Started by upstream project "BIOFORMATS-test-repo" build number 271 originally caused by: Started by upstream project "Trigger" build number 293 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins14413133577301306017.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42765_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 05:07:09,286 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 05:07:09,287 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 05:07:09,287 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:07:09,288 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:07:09,288 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 05:07:09,289 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 05:07:09,289 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 05:07:09,289 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:07:09,289 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:07:09,290 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 05:07:09,291 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 05:07:09,291 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 05:07:09,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 05:07:09,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 05:07:09,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 05:07:09,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 05:07:09,487 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 05:07:09,487 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 05:07:09,487 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 05:07:09,487 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 05:07:09,488 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 05:07:09,488 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 05:07:09,488 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 199 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-28 05:07:09,497] [main] java.version = 21 [testng] 05:07:09,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:07:09,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:09,551 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-28_05-07-09.log] [testng] 05:07:09,552 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-11-28 05:07:09,554] [main] testng.directory = /data [testng] [2024-11-28 05:07:09,554] [main] testng.configDirectory = /config [testng] [2024-11-28 05:07:09,562] [main] testng.multiplier = 1.0 [testng] [2024-11-28 05:07:09,563] [main] testng.in-memory = false [testng] [2024-11-28 05:07:09,563] [main] testng.allow-missing = false [testng] [2024-11-28 05:07:09,563] [main] user.language = en [testng] [2024-11-28 05:07:09,563] [main] user.country = ${user.country} [testng] [2024-11-28 05:07:09,563] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-28 05:07:14,518] [main] ---------------------------------------- [testng] [2024-11-28 05:07:14,518] [main] Total files: 32 [testng] [2024-11-28 05:07:14,518] [main] Scan time: 4.955 s (154 ms/file) [testng] [2024-11-28 05:07:14,519] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-28 05:07:55,201] [pool-1-thread-1] Initializing /data/qa-16880/c-src v7.1sc: [testng] 05:07:55,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:07:55,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:55,203 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-28_05-07-55.log] [testng] 05:07:55,203 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27ac1dd6 - End of configuration. [testng] [2024-11-28 05:07:55,983] [pool-1-thread-12] Initializing /data/david/Opened in imageJ.tiff: [testng] 05:07:55,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:07:55,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:55,984 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-28_05-07-55.log] [testng] 05:07:55,984 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78b85f99 - End of configuration. [testng] [2024-11-28 05:07:58,782] [pool-1-thread-11] Initializing /data/qa-29459/bad.1sc: [testng] 05:07:58,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:07:58,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:58,783 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-28_05-07-58.log] [testng] 05:07:58,783 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ef33d0d - End of configuration. [testng] [2024-11-28 05:07:59,550] [pool-1-thread-10] Initializing /data/keith/test2.1sc: [testng] 05:07:59,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:07:59,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:59,551 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-28_05-07-59.log] [testng] 05:07:59,551 |-INFO in ch.qos.logback.core.sift.SiftProcessor@177b6011 - End of configuration. [testng] [2024-11-28 05:08:00,312] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] 05:08:00,312 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:08:00,312 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:00,313 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-28_05-08-00.log] [testng] 05:08:00,313 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25553984 - End of configuration. [testng] [2024-11-28 05:08:01,125] [pool-1-thread-8] Initializing /data/geert/good example1.1sc: [testng] 05:08:01,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:08:01,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:01,126 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-28_05-08-01.log] [testng] 05:08:01,127 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cd3686b - End of configuration. [testng] [2024-11-28 05:08:01,896] [pool-1-thread-7] Initializing /data/keith/pg020410saur3.1sc: [testng] 05:08:01,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:08:01,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:01,896 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-28_05-08-01.log] [testng] 05:08:01,897 |-INFO in ch.qos.logback.core.sift.SiftProcessor@327d1670 - End of configuration. [testng] [2024-11-28 05:08:02,603] [pool-1-thread-6] Initializing /data/qa-29469/good.1sc: [testng] 05:08:02,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:08:02,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:02,603 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-28_05-08-02.log] [testng] 05:08:02,604 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f818e47 - End of configuration. [testng] [2024-11-28 05:08:03,458] [pool-1-thread-5] Initializing /data/keith/test.1sc: [testng] 05:08:03,458 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:08:03,458 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:03,459 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-28_05-08-03.log] [testng] 05:08:03,460 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b55ba8c - End of configuration. [testng] [2024-11-28 05:08:04,226] [pool-1-thread-4] Initializing /data/qa-29469/bad2.1sc: [testng] 05:08:04,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:08:04,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:04,227 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-28_05-08-04.log] [testng] 05:08:04,227 |-INFO in ch.qos.logback.core.sift.SiftProcessor@530fbc6c - End of configuration. [testng] [2024-11-28 05:08:05,054] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 05:08:05,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:08:05,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:05,054 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-28_05-08-05.log] [testng] 05:08:05,055 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ea58e5b - End of configuration. [testng] [2024-11-28 05:08:07,767] [pool-1-thread-2] Initializing /data/geert/bad example1.1sc.jpg: [testng] 05:08:07,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:08:07,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:07,768 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-28_05-08-07.log] [testng] 05:08:07,768 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9c49573 - End of configuration. [testng] [2024-11-28 05:08:15,291] [pool-1-thread-7] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-11-28 05:08:15,605] [pool-1-thread-4] Initializing /data/samples/Criterion.1sc: [testng] [2024-11-28 05:08:16,491] [pool-1-thread-2] Initializing /data/adrian/test_img.1sc: [testng] [2024-11-28 05:08:17,397] [pool-1-thread-10] Initializing /data/geert/bad example1.1sc: [testng] [2024-11-28 05:08:18,292] [pool-1-thread-5] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-11-28 05:08:21,497] [pool-1-thread-11] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] [2024-11-28 05:08:24,674] [pool-1-thread-1] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-11-28 05:08:25,645] [pool-1-thread-6] Initializing /data/qa-29469/bad3.1sc: [testng] [2024-11-28 05:08:26,572] [pool-1-thread-8] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] [2024-11-28 05:08:27,510] [pool-1-thread-9] Initializing /data/samples/imagesEight.1sc: [testng] [2024-11-28 05:08:35,522] [pool-1-thread-9] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] [2024-11-28 05:08:38,889] [pool-1-thread-10] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] [2024-11-28 05:08:42,163] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-11-28 05:08:43,101] [pool-1-thread-8] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-11-28 05:08:44,011] [pool-1-thread-1] Initializing /data/keith/PF020328saur v3.1sc: [testng] [2024-11-28 05:08:44,856] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] [2024-11-28 05:08:47,954] [pool-1-thread-6] Initializing /data/geert/bad example1.jpg: [testng] [2024-11-28 05:08:48,279] [pool-1-thread-3] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] [2024-11-28 05:08:49,168] [pool-1-thread-12] Initializing /data/qa-29459/bad.jpg: [testng] [2024-11-28 05:08:49,451] [pool-1-thread-7] Initializing /data/keith/PF020426MRSA v2.1sc: [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 0 seconds Finished: SUCCESS