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Started by upstream project "BIOFORMATS-test-repo" build number 307 originally caused by: Started by upstream project "Trigger" build number 329 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins6750780137749544091.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_48679_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] 03:15:49,109 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:15:49,111 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 03:15:49,111 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:15:49,112 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:15:49,112 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:15:49,112 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:15:49,112 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:15:49,112 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:15:49,113 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:15:49,113 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:15:49,113 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:15:49,113 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:15:49,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:15:49,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:15:49,373 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:15:49,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:15:49,383 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:15:49,383 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:15:49,383 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:15:49,384 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:15:49,384 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 03:15:49,385 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 03:15:49,385 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 272 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-03 03:15:49,397] [main] java.version = 1.8.0_342 [testng] 03:15:49,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:15:49,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:15:49,447 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-03_03-15-49.log] [testng] 03:15:49,449 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2025-01-03 03:15:49,451] [main] testng.directory = /data [testng] [2025-01-03 03:15:49,451] [main] testng.configDirectory = /config [testng] [2025-01-03 03:15:49,463] [main] testng.multiplier = 1.0 [testng] [2025-01-03 03:15:49,464] [main] testng.in-memory = false [testng] [2025-01-03 03:15:49,464] [main] testng.allow-missing = false [testng] [2025-01-03 03:15:49,464] [main] user.language = en [testng] [2025-01-03 03:15:49,464] [main] user.country = ${user.country} [testng] [2025-01-03 03:15:49,464] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-01-03 03:20:23,030] [main] ---------------------------------------- [testng] [2025-01-03 03:20:23,031] [main] Total files: 2169 [testng] [2025-01-03 03:20:23,031] [main] Scan time: 273.566 s (126 ms/file) [testng] [2025-01-03 03:20:23,031] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-03 03:40:46,459] [pool-1-thread-1] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 03:40:46,460 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:40:46,460 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:46,461 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-03_03-40-46.log] [testng] 03:40:46,461 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d1dde58 - End of configuration. [testng] [2025-01-03 03:40:59,666] [pool-1-thread-12] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 03:40:59,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:40:59,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:59,668 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-03_03-40-59.log] [testng] 03:40:59,668 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41190063 - End of configuration. [testng] [2025-01-03 03:41:00,506] [pool-1-thread-11] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 03:41:00,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:41:00,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:41:00,507 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-03_03-41-00.log] [testng] 03:41:00,507 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b09ddd6 - End of configuration. [testng] [2025-01-03 03:41:41,316] [pool-1-thread-10] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 03:41:41,316 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:41:41,316 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:41:41,317 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-03_03-41-41.log] [testng] 03:41:41,317 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e605137 - End of configuration. [testng] [2025-01-03 03:41:43,879] [pool-1-thread-9] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 03:41:43,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:41:43,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:41:43,880 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-03_03-41-43.log] [testng] 03:41:43,880 |-INFO in ch.qos.logback.core.sift.SiftProcessor@669d5575 - End of configuration. [testng] [2025-01-03 03:43:42,822] [pool-1-thread-8] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 03:43:42,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:43:42,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:43:42,823 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-03_03-43-42.log] [testng] 03:43:42,823 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37fc0829 - End of configuration. [testng] [2025-01-03 03:46:15,617] [pool-1-thread-7] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 03:46:15,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:46:15,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:46:15,618 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-03_03-46-15.log] [testng] 03:46:15,619 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d504eaf - End of configuration. [testng] [2025-01-03 03:46:24,305] [pool-1-thread-6] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 03:46:24,305 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:46:24,305 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:46:24,306 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-03_03-46-24.log] [testng] 03:46:24,306 |-INFO in ch.qos.logback.core.sift.SiftProcessor@110a96b - End of configuration. [testng] [2025-01-03 03:49:17,336] [pool-1-thread-5] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 03:49:17,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:49:17,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:17,337 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-03_03-49-17.log] [testng] 03:49:17,337 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68435c30 - End of configuration. [testng] [2025-01-03 03:49:19,381] [pool-1-thread-4] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 03:49:19,381 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:49:19,381 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:19,382 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-03_03-49-19.log] [testng] 03:49:19,382 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ae8261f - End of configuration. [testng] [2025-01-03 03:51:09,585] [pool-1-thread-3] Initializing /data/gideon/experiment_descriptor.xml: [testng] 03:51:09,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:51:09,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:09,586 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-03_03-51-09.log] [testng] 03:51:09,586 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50347991 - End of configuration. [testng] [2025-01-03 03:51:41,556] [pool-1-thread-2] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 03:51:41,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:51:41,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:41,557 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-03_03-51-41.log] [testng] 03:51:41,557 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47a98946 - End of configuration. [testng] [2025-01-03 03:52:15,311] [pool-1-thread-12] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] [2025-01-03 03:54:06,702] [pool-1-thread-5] Initializing /data/nadine/experiment_descriptor.xml: [testng] [2025-01-03 03:54:50,340] [pool-1-thread-5] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] [2025-01-03 03:56:08,961] [pool-1-thread-10] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] [2025-01-03 04:00:08,410] [pool-1-thread-7] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 05:08:39,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:08:39,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:39,028 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-03_05-08-39.log] [testng] 05:08:39,029 |-INFO in ch.qos.logback.core.sift.SiftProcessor@481fc98e - End of configuration. [testng] 05:08:57,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:08:57,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:57,512 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-03_05-08-57.log] [testng] 05:08:57,512 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d35487e - End of configuration. [testng] 05:10:45,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:10:45,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:10:45,340 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-03_05-10-45.log] [testng] 05:10:45,341 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cfbd51b - End of configuration. [testng] 05:10:45,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:10:45,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:10:45,979 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-03_05-10-45.log] [testng] 05:10:45,979 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43f55050 - End of configuration. [testng] 05:17:10,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:17:10,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:17:10,967 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-03_05-17-10.log] [testng] 05:17:10,967 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c6e3c25 - 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: 121 minutes 24 seconds Finished: SUCCESS