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Started by upstream project "BIOFORMATS-test-repo" build number 236 originally caused by: Started by upstream project "Trigger" build number 261 originally caused by: Started by timer 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/jenkins10033818356668234962.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37146_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] 02:59:34,213 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:59:34,215 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 02:59:34,215 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:59:34,216 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:59:34,217 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:59:34,218 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:59:34,218 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:59:34,218 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:59:34,219 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:59:34,220 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:59:34,220 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:59:34,221 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:59:34,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:59:34,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:59:34,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:59:34,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:59:34,447 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:59:34,447 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:59:34,447 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:59:34,447 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:59:34,448 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 02:59:34,448 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 02:59:34,448 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 229 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-27 02:59:34,459] [main] java.version = 17.0.2 [testng] 02:59:34,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:59:34,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:34,511 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-27_02-59-34.log] [testng] 02:59:34,513 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-27 02:59:34,515] [main] testng.directory = /data [testng] [2024-10-27 02:59:34,516] [main] testng.configDirectory = /config [testng] [2024-10-27 02:59:34,528] [main] testng.multiplier = 1.0 [testng] [2024-10-27 02:59:34,530] [main] testng.in-memory = false [testng] [2024-10-27 02:59:34,530] [main] testng.allow-missing = false [testng] [2024-10-27 02:59:34,530] [main] user.language = en [testng] [2024-10-27 02:59:34,530] [main] user.country = ${user.country} [testng] [2024-10-27 02:59:34,530] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-27 03:05:46,455] [main] ---------------------------------------- [testng] [2024-10-27 03:05:46,456] [main] Total files: 2169 [testng] [2024-10-27 03:05:46,456] [main] Scan time: 371.925 s (171 ms/file) [testng] [2024-10-27 03:05:46,456] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-27 03:25:06,245] [pool-1-thread-1] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 03:25:06,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:25:06,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:25:06,247 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-27_03-25-06.log] [testng] 03:25:06,248 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d3e96b0 - End of configuration. [testng] [2024-10-27 03:25:06,951] [pool-1-thread-12] Initializing /data/gideon/experiment_descriptor.xml: [testng] 03:25:06,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:25:06,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:25:06,953 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-27_03-25-06.log] [testng] 03:25:06,953 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55896030 - End of configuration. [testng] [2024-10-27 03:25:24,502] [pool-1-thread-11] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 03:25:24,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:25:24,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:25:24,505 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-27_03-25-24.log] [testng] 03:25:24,505 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c14e80 - End of configuration. [testng] [2024-10-27 03:25:54,549] [pool-1-thread-10] Initializing /data/nadine/experiment_descriptor.xml: [testng] 03:25:54,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:25:54,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:25:54,551 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-27_03-25-54.log] [testng] 03:25:54,552 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e1ae0bc - End of configuration. [testng] [2024-10-27 03:25:55,489] [pool-1-thread-9] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 03:25:55,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:25:55,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:25:55,490 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-27_03-25-55.log] [testng] 03:25:55,491 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62389fb6 - End of configuration. [testng] [2024-10-27 03:26:03,311] [pool-1-thread-8] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 03:26:03,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:26:03,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:26:03,312 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-27_03-26-03.log] [testng] 03:26:03,312 |-INFO in ch.qos.logback.core.sift.SiftProcessor@189bf79d - End of configuration. [testng] [2024-10-27 03:26:04,279] [pool-1-thread-7] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 03:26:04,279 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:26:04,279 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:26:04,280 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-27_03-26-04.log] [testng] 03:26:04,280 |-INFO in ch.qos.logback.core.sift.SiftProcessor@686787ad - End of configuration. [testng] [2024-10-27 03:27:05,546] [pool-1-thread-6] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 03:27:05,546 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:27:05,546 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:27:05,548 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-27_03-27-05.log] [testng] 03:27:05,548 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35e0638d - End of configuration. [testng] [2024-10-27 03:28:51,118] [pool-1-thread-5] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 03:28:51,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:28:51,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:28:51,120 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-27_03-28-51.log] [testng] 03:28:51,120 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12e898bc - End of configuration. [testng] [2024-10-27 03:28:53,215] [pool-1-thread-4] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 03:28:53,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:28:53,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:28:53,216 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-27_03-28-53.log] [testng] 03:28:53,217 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35dffa3d - End of configuration. [testng] [2024-10-27 03:29:05,553] [pool-1-thread-3] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 03:29:05,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:29:05,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:29:05,554 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-27_03-29-05.log] [testng] 03:29:05,555 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7aa4b958 - End of configuration. [testng] [2024-10-27 03:30:53,401] [pool-1-thread-2] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 03:30:53,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:30:53,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:30:53,403 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-27_03-30-53.log] [testng] 03:30:53,404 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a002f1 - End of configuration. [testng] [2024-10-27 03:31:58,336] [pool-1-thread-1] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] [2024-10-27 03:34:00,083] [pool-1-thread-8] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] [2024-10-27 03:35:13,925] [pool-1-thread-10] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] [2024-10-27 03:37:30,861] [pool-1-thread-5] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] [2024-10-27 03:44:59,760] [pool-1-thread-5] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 04:40:58,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:40:58,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:40:58,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-27_04-40-58.log] [testng] 04:40:58,963 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cb844c5 - End of configuration. [testng] 04:41:22,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:41:22,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:41:22,033 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-27_04-41-22.log] [testng] 04:41:22,033 |-INFO in ch.qos.logback.core.sift.SiftProcessor@705e5e69 - End of configuration. [testng] 04:41:46,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:41:46,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:41:46,158 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-27_04-41-46.log] [testng] 04:41:46,158 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49fdf463 - End of configuration. [testng] 04:42:25,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:42:25,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:42:25,861 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-27_04-42-25.log] [testng] 04:42:25,862 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b73b194 - End of configuration. [testng] 04:48:08,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:48:08,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:48:08,071 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-27_04-48-08.log] [testng] 04:48:08,071 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d449860 - 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: 108 minutes 37 seconds Finished: SUCCESS