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Started by upstream project "BIOFORMATS-test-repo" build number 202 originally caused by: Started by upstream project "Trigger" build number 228 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins10723708504991292636.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_32086_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 test-automated: [testng] File leak detector installed [testng] 08:14:44,413 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 08:14:44,414 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 08:14:44,414 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:14:44,415 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:14:44,415 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 08:14:44,416 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 08:14:44,416 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 08:14:44,416 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:14:44,416 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:14:44,417 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 08:14:44,417 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 08:14:44,417 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 08:14:44,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 08:14:44,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 08:14:44,669 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 08:14:44,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 08:14:44,677 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 08:14:44,678 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 08:14:44,678 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 08:14:44,678 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 08:14:44,678 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 08:14:44,679 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 08:14:44,679 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 263 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-27 08:14:44,689] [main] java.version = 1.8.0_342 [testng] 08:14:44,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:14:44,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:14:44,737 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-27_08-14-44.log] [testng] 08:14:44,738 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-09-27 08:14:44,740] [main] testng.directory = /data [testng] [2024-09-27 08:14:44,740] [main] testng.configDirectory = /config [testng] [2024-09-27 08:14:44,753] [main] testng.multiplier = 1.0 [testng] [2024-09-27 08:14:44,753] [main] testng.in-memory = false [testng] [2024-09-27 08:14:44,753] [main] testng.allow-missing = false [testng] [2024-09-27 08:14:44,753] [main] user.language = en [testng] [2024-09-27 08:14:44,753] [main] user.country = ${user.country} [testng] [2024-09-27 08:14:44,753] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-09-27 08:19:17,852] [main] ---------------------------------------- [testng] [2024-09-27 08:19:17,852] [main] Total files: 2169 [testng] [2024-09-27 08:19:17,853] [main] Scan time: 273.098 s (125 ms/file) [testng] [2024-09-27 08:19:17,853] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-27 08:42:31,094] [pool-1-thread-1] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 08:42:31,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 08:42:31,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:31,096 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-27_08-42-31.log] [testng] 08:42:31,097 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5421f09 - End of configuration. [testng] [2024-09-27 08:42:38,469] [pool-1-thread-12] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 08:42:38,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 08:42:38,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:38,470 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-27_08-42-38.log] [testng] 08:42:38,471 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7efc14ae - End of configuration. [testng] [2024-09-27 08:44:05,419] [pool-1-thread-11] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 08:44:05,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 08:44:05,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:44:05,421 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-27_08-44-05.log] [testng] 08:44:05,421 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3fef3b1b - End of configuration. [testng] [2024-09-27 08:44:06,666] [pool-1-thread-10] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 08:44:06,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 08:44:06,667 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:44:06,667 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-27_08-44-06.log] [testng] 08:44:06,668 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5aa2a752 - End of configuration. [testng] [2024-09-27 08:44:09,405] [pool-1-thread-9] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 08:44:09,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 08:44:09,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:44:09,406 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-27_08-44-09.log] [testng] 08:44:09,407 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fc83168 - End of configuration. [testng] [2024-09-27 08:45:49,048] [pool-1-thread-8] Initializing /data/nadine/experiment_descriptor.xml: [testng] 08:45:49,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 08:45:49,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:45:49,051 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-27_08-45-49.log] [testng] 08:45:49,051 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bcf7986 - End of configuration. [testng] [2024-09-27 08:45:49,968] [pool-1-thread-7] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 08:45:49,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 08:45:49,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:45:49,969 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-27_08-45-49.log] [testng] 08:45:49,969 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30a5ec16 - End of configuration. [testng] [2024-09-27 08:46:05,107] [pool-1-thread-6] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 08:46:05,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 08:46:05,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:46:05,108 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-27_08-46-05.log] [testng] 08:46:05,108 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e4ccf54 - End of configuration. [testng] [2024-09-27 08:47:38,344] [pool-1-thread-5] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 08:47:38,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 08:47:38,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:47:38,346 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-27_08-47-38.log] [testng] 08:47:38,346 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59936245 - End of configuration. [testng] [2024-09-27 08:48:12,893] [pool-1-thread-4] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 08:48:12,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 08:48:12,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:48:12,894 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-27_08-48-12.log] [testng] 08:48:12,894 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2bed14c4 - End of configuration. [testng] [2024-09-27 08:48:48,925] [pool-1-thread-3] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 08:48:48,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 08:48:48,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:48:48,926 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-27_08-48-48.log] [testng] 08:48:48,926 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2dd3fd98 - End of configuration. [testng] [2024-09-27 08:48:49,813] [pool-1-thread-2] Initializing /data/gideon/experiment_descriptor.xml: [testng] 08:48:49,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 08:48:49,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:48:49,813 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-27_08-48-49.log] [testng] 08:48:49,814 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f3ccfc3 - End of configuration. [testng] [2024-09-27 08:49:55,801] [pool-1-thread-3] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2024-09-27 08:52:40,548] [pool-1-thread-11] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] [2024-09-27 08:53:02,824] [pool-1-thread-8] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] [2024-09-27 08:55:25,989] [pool-1-thread-10] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] [2024-09-27 09:01:33,943] [pool-1-thread-11] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 10:03:48,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:03:48,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:03:48,758 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-27_10-03-48.log] [testng] 10:03:48,758 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e16af33 - End of configuration. [testng] 10:04:02,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:04:02,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:04:02,842 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-27_10-04-02.log] [testng] 10:04:02,842 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48ff6e81 - End of configuration. [testng] 10:05:56,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:05:56,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:05:56,046 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-27_10-05-56.log] [testng] 10:05:56,046 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3984c734 - End of configuration. [testng] 10:06:47,212 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:06:47,212 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:47,212 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-27_10-06-47.log] [testng] 10:06:47,213 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f65c8bf - End of configuration. [testng] 10:11:52,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 10:11:52,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:11:52,814 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-27_10-11-52.log] [testng] 10:11:52,815 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dc38bc - 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: 117 minutes 13 seconds Finished: SUCCESS