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Started by upstream project "BIOFORMATS-test-repo" build number 6 originally caused by: Started by upstream project "Trigger" build number 9 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins13527665025120783588.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_916_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] 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] 11:05:53,750 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:05:53,752 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 11:05:53,752 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:05:53,753 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:05:53,753 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:05:53,753 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:05:53,754 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:05:53,754 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:05:53,754 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:05:53,755 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:05:53,756 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:05:53,756 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:05:53,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:05:53,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:05:53,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:05:53,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:05:53,978 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:05:53,978 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:05:53,978 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:05:53,979 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:05:53,979 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 11:05:53,979 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 11:05:53,980 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 225 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-20 11:05:53,989] [main] java.version = 17.0.2 [testng] 11:05:53,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:05:53,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:05:54,032 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-20_11-05-54.log] [testng] 11:05:54,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-03-20 11:05:54,036] [main] testng.directory = /data [testng] [2024-03-20 11:05:54,036] [main] testng.configDirectory = /config [testng] [2024-03-20 11:05:54,045] [main] testng.multiplier = 1.0 [testng] [2024-03-20 11:05:54,046] [main] testng.in-memory = false [testng] [2024-03-20 11:05:54,046] [main] testng.allow-missing = false [testng] [2024-03-20 11:05:54,046] [main] user.language = en [testng] [2024-03-20 11:05:54,046] [main] user.country = ${user.country} [testng] [2024-03-20 11:05:54,046] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-20 11:10:28,601] [main] ---------------------------------------- [testng] [2024-03-20 11:10:28,601] [main] Total files: 2169 [testng] [2024-03-20 11:10:28,601] [main] Scan time: 274.555 s (126 ms/file) [testng] [2024-03-20 11:10:28,601] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-20 11:33:03,480] [pool-1-thread-1] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 11:33:03,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:33:03,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:33:03,482 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-20_11-33-03.log] [testng] 11:33:03,483 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59ddcd7f - End of configuration. [testng] [2024-03-20 11:33:06,242] [pool-1-thread-12] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 11:33:06,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:33:06,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:33:06,244 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-20_11-33-06.log] [testng] 11:33:06,244 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60c810a7 - End of configuration. [testng] [2024-03-20 11:35:10,182] [pool-1-thread-11] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 11:35:10,183 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:35:10,183 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:35:10,185 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-20_11-35-10.log] [testng] 11:35:10,185 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6819a754 - End of configuration. [testng] [2024-03-20 11:35:19,176] [pool-1-thread-10] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 11:35:19,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:35:19,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:35:19,178 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-20_11-35-19.log] [testng] 11:35:19,179 |-INFO in ch.qos.logback.core.sift.SiftProcessor@113d9b07 - End of configuration. [testng] [2024-03-20 11:35:42,864] [pool-1-thread-9] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 11:35:42,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:35:42,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:35:42,866 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-20_11-35-42.log] [testng] 11:35:42,866 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4161d894 - End of configuration. [testng] [2024-03-20 11:35:43,188] [pool-1-thread-8] Initializing /data/nadine/experiment_descriptor.xml: [testng] 11:35:43,188 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:35:43,188 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:35:43,189 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-20_11-35-43.log] [testng] 11:35:43,189 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30a776f0 - End of configuration. [testng] [2024-03-20 11:35:43,726] [pool-1-thread-7] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 11:35:43,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:35:43,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:35:43,727 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-20_11-35-43.log] [testng] 11:35:43,728 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14ee6c8e - End of configuration. [testng] [2024-03-20 11:37:57,665] [pool-1-thread-6] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 11:37:57,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:37:57,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:37:57,667 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-20_11-37-57.log] [testng] 11:37:57,668 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f219143 - End of configuration. [testng] [2024-03-20 11:39:02,976] [pool-1-thread-5] Initializing /data/gideon/experiment_descriptor.xml: [testng] 11:39:02,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:39:02,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:39:02,978 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-20_11-39-02.log] [testng] 11:39:02,978 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37cc862c - End of configuration. [testng] [2024-03-20 11:39:35,420] [pool-1-thread-4] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 11:39:35,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:39:35,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:39:35,421 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-20_11-39-35.log] [testng] 11:39:35,422 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f26caf2 - End of configuration. [testng] [2024-03-20 11:40:02,616] [pool-1-thread-3] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 11:40:02,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:40:02,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:02,618 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-20_11-40-02.log] [testng] 11:40:02,618 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40110b20 - End of configuration. [testng] [2024-03-20 11:40:03,039] [pool-1-thread-2] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 11:40:03,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:40:03,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:03,039 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-20_11-40-03.log] [testng] 11:40:03,040 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59552d6c - End of configuration. [testng] [2024-03-20 11:43:09,982] [pool-1-thread-3] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] [2024-03-20 11:43:27,318] [pool-1-thread-8] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] [2024-03-20 11:43:35,763] [pool-1-thread-9] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] [2024-03-20 11:44:51,028] [pool-1-thread-9] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] [2024-03-20 11:45:47,156] [pool-1-thread-1] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 65 minutes 59 seconds Finished: SUCCESS