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Started by upstream project "BIOFORMATS-test-repo" build number 194 originally caused by: Started by user devspace 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/jenkins5403303359735741312.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_30774_merge_ci -v /uod/idr/repos/curated/scanr:/data -v /uod/idr-scratch/merge-ci/curated/scanr:/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 14:07:14,334 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 14:07:14,336 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 14:07:14,336 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:07:14,337 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:07:14,337 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 14:07:14,337 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 14:07:14,338 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 14:07:14,338 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:07:14,338 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:07:14,339 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 14:07:14,339 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 14:07:14,339 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 14:07:14,494 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 14:07:14,494 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 14:07:14,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 14:07:14,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 14:07:14,524 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 14:07:14,524 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 14:07:14,525 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 14:07:14,525 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 14:07:14,525 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 14:07:14,526 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 14:07:14,526 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 188 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-19 14:07:14,535] [main] java.version = 21 [testng] 14:07:14,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 14:07:14,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:07:14,578 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-19_14-07-14.log] [testng] 14:07:14,580 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-09-19 14:07:14,581] [main] testng.directory = /data [testng] [2024-09-19 14:07:14,581] [main] testng.configDirectory = /config [testng] [2024-09-19 14:07:14,590] [main] testng.multiplier = 1.0 [testng] [2024-09-19 14:07:14,591] [main] testng.in-memory = false [testng] [2024-09-19 14:07:14,591] [main] testng.allow-missing = false [testng] [2024-09-19 14:07:14,591] [main] user.language = en [testng] [2024-09-19 14:07:14,592] [main] user.country = ${user.country} [testng] [2024-09-19 14:07:14,592] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-19 14:13:15,215] [main] ---------------------------------------- [testng] [2024-09-19 14:13:15,216] [main] Total files: 2169 [testng] [2024-09-19 14:13:15,216] [main] Scan time: 360.623 s (166 ms/file) [testng] [2024-09-19 14:13:15,217] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-19 14:38:09,357] [pool-1-thread-1] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 14:38:09,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 14:38:09,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:38:09,360 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-19_14-38-09.log] [testng] 14:38:09,360 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23f7dbee - End of configuration. [testng] [2024-09-19 14:39:08,547] [pool-1-thread-12] Initializing /data/gideon/experiment_descriptor.xml: [testng] 14:39:08,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 14:39:08,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:39:08,549 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-19_14-39-08.log] [testng] 14:39:08,549 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6cbcfc18 - End of configuration. [testng] [2024-09-19 14:39:38,363] [pool-1-thread-11] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 14:39:38,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 14:39:38,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:39:38,364 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-19_14-39-38.log] [testng] 14:39:38,365 |-INFO in ch.qos.logback.core.sift.SiftProcessor@110f8673 - End of configuration. [testng] [2024-09-19 14:40:19,852] [pool-1-thread-10] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 14:40:19,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 14:40:19,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:40:19,853 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-19_14-40-19.log] [testng] 14:40:19,853 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ee831c3 - End of configuration. [testng] [2024-09-19 14:40:23,149] [pool-1-thread-9] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 14:40:23,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 14:40:23,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:40:23,150 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-19_14-40-23.log] [testng] 14:40:23,150 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d170371 - End of configuration. [testng] [2024-09-19 14:40:41,502] [pool-1-thread-8] Initializing /data/nadine/experiment_descriptor.xml: [testng] 14:40:41,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 14:40:41,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:40:41,504 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-19_14-40-41.log] [testng] 14:40:41,504 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14de67f8 - End of configuration. [testng] [2024-09-19 14:40:42,884] [pool-1-thread-7] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 14:40:42,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 14:40:42,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:40:42,885 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-19_14-40-42.log] [testng] 14:40:42,886 |-INFO in ch.qos.logback.core.sift.SiftProcessor@498bbb23 - End of configuration. [testng] [2024-09-19 14:43:29,744] [pool-1-thread-6] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 14:43:29,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 14:43:29,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:43:29,746 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-19_14-43-29.log] [testng] 14:43:29,747 |-INFO in ch.qos.logback.core.sift.SiftProcessor@326caeaf - End of configuration. [testng] [2024-09-19 14:46:33,779] [pool-1-thread-5] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 14:46:33,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 14:46:33,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:46:33,781 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-19_14-46-33.log] [testng] 14:46:33,781 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22487505 - End of configuration. [testng] [2024-09-19 14:49:06,692] [pool-1-thread-4] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 14:49:06,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 14:49:06,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:49:06,696 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-19_14-49-06.log] [testng] 14:49:06,697 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a3c1a9a - End of configuration. [testng] [2024-09-19 14:49:07,958] [pool-1-thread-3] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 14:49:07,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 14:49:07,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:49:07,959 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-19_14-49-07.log] [testng] 14:49:07,959 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74d0d93 - End of configuration. [testng] [2024-09-19 14:49:19,392] [pool-1-thread-2] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 14:49:19,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 14:49:19,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:49:19,395 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-19_14-49-19.log] [testng] 14:49:19,395 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f9e96a0 - End of configuration. [testng] [2024-09-19 14:51:08,642] [pool-1-thread-4] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] [2024-09-19 14:53:33,927] [pool-1-thread-8] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] [2024-09-19 14:56:30,142] [pool-1-thread-10] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] [2024-09-19 15:05:24,742] [pool-1-thread-10] Initializing /data/christian/example/experiment_descriptor.xml: [testng] [2024-09-19 15:05:49,009] [pool-1-thread-10] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 16:13:34,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 16:13:34,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:13:34,568 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-19_16-13-34.log] [testng] 16:13:34,569 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b47237 - End of configuration. [testng] 16:15:06,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 16:15:06,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:15:06,878 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-19_16-15-06.log] [testng] 16:15:06,879 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b425b5 - End of configuration. [testng] 16:16:19,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 16:16:19,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:16:19,701 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-19_16-16-19.log] [testng] 16:16:19,702 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65294ab0 - End of configuration. [testng] 16:16:19,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 16:16:19,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:16:19,703 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-19_16-16-19.log] [testng] 16:16:19,703 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a029340 - End of configuration. [testng] 16:24:34,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 16:24:34,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:24:34,360 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-19_16-24-34.log] [testng] 16:24:34,360 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8d70fd - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 137 minutes 22 seconds Finished: SUCCESS