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Started by upstream project "BIOFORMATS-test-repo" build number 109 originally caused by: Started by upstream project "Trigger" build number 122 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins3477452906550847370.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_16991_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 13:02:36,542 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 13:02:36,544 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 13:02:36,544 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:02:36,545 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:02:36,546 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 13:02:36,546 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 13:02:36,546 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 13:02:36,546 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:02:36,547 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:02:36,547 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 13:02:36,548 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 13:02:36,548 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 13:02:36,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 13:02:36,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 13:02:36,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 13:02:36,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 13:02:36,755 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 13:02:36,755 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 13:02:36,755 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 13:02:36,755 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 13:02:36,755 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 13:02:36,756 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 13:02:36,756 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 209 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-02 13:02:36,765] [main] java.version = 11.0.16 [testng] 13:02:36,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 13:02:36,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:02:36,813 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-02_13-02-36.log] [testng] 13:02:36,814 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-02 13:02:36,816] [main] testng.directory = /data [testng] [2024-07-02 13:02:36,817] [main] testng.configDirectory = /config [testng] [2024-07-02 13:02:36,827] [main] testng.multiplier = 1.0 [testng] [2024-07-02 13:02:36,828] [main] testng.in-memory = false [testng] [2024-07-02 13:02:36,828] [main] testng.allow-missing = false [testng] [2024-07-02 13:02:36,828] [main] user.language = en [testng] [2024-07-02 13:02:36,828] [main] user.country = ${user.country} [testng] [2024-07-02 13:02:36,828] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-02 13:06:45,283] [main] ---------------------------------------- [testng] [2024-07-02 13:06:45,283] [main] Total files: 2169 [testng] [2024-07-02 13:06:45,283] [main] Scan time: 248.454 s (114 ms/file) [testng] [2024-07-02 13:06:45,284] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-02 13:25:05,731] [pool-1-thread-1] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 13:25:05,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 13:25:05,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:25:05,734 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-02_13-25-05.log] [testng] 13:25:05,735 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e2f09c8 - End of configuration. [testng] [2024-07-02 13:25:22,129] [pool-1-thread-12] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 13:25:22,129 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 13:25:22,129 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:25:22,131 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-02_13-25-22.log] [testng] 13:25:22,132 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1439dae0 - End of configuration. [testng] [2024-07-02 13:25:22,375] [pool-1-thread-11] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 13:25:22,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 13:25:22,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:25:22,377 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-02_13-25-22.log] [testng] 13:25:22,377 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1993727d - End of configuration. [testng] [2024-07-02 13:26:22,860] [pool-1-thread-10] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 13:26:22,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 13:26:22,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:26:22,861 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-02_13-26-22.log] [testng] 13:26:22,862 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78bb8b94 - End of configuration. [testng] [2024-07-02 13:26:22,991] [pool-1-thread-9] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 13:26:22,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 13:26:22,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:26:22,992 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-02_13-26-22.log] [testng] 13:26:22,992 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b3e3b92 - End of configuration. [testng] [2024-07-02 13:26:29,858] [pool-1-thread-8] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 13:26:29,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 13:26:29,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:26:29,859 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-02_13-26-29.log] [testng] 13:26:29,859 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6639b482 - End of configuration. [testng] [2024-07-02 13:27:31,014] [pool-1-thread-7] Initializing /data/gideon/experiment_descriptor.xml: [testng] 13:27:31,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 13:27:31,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:27:31,016 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-02_13-27-31.log] [testng] 13:27:31,016 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28ed2723 - End of configuration. [testng] [2024-07-02 13:28:01,654] [pool-1-thread-6] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 13:28:01,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 13:28:01,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:28:01,657 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-02_13-28-01.log] [testng] 13:28:01,657 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e9ef95d - End of configuration. [testng] [2024-07-02 13:29:24,158] [pool-1-thread-5] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 13:29:24,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 13:29:24,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:29:24,160 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-02_13-29-24.log] [testng] 13:29:24,161 |-INFO in ch.qos.logback.core.sift.SiftProcessor@361b85d - End of configuration. [testng] [2024-07-02 13:32:04,672] [pool-1-thread-4] Initializing /data/nadine/experiment_descriptor.xml: [testng] 13:32:04,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 13:32:04,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:32:04,673 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-02_13-32-04.log] [testng] 13:32:04,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3eef234b - End of configuration. [testng] [2024-07-02 13:32:05,166] [pool-1-thread-3] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 13:32:05,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 13:32:05,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:32:05,166 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-02_13-32-05.log] [testng] 13:32:05,167 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c1c149c - End of configuration. [testng] [2024-07-02 13:33:12,309] [pool-1-thread-2] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 13:33:12,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 13:33:12,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:33:12,310 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-02_13-33-12.log] [testng] 13:33:12,310 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5269e55e - End of configuration. [testng] [2024-07-02 13:33:18,063] [pool-1-thread-10] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] [2024-07-02 13:33:18,389] [pool-1-thread-4] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] [2024-07-02 13:33:22,018] [pool-1-thread-10] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] [2024-07-02 13:36:17,512] [pool-1-thread-2] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2024-07-02 13:37:59,460] [pool-1-thread-9] Initializing /data/ruben/scanr_no_labels/Peter/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: 40 minutes 0 seconds Finished: SUCCESS