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Started by upstream project "BIOFORMATS-test-repo" build number 269 originally caused by: Started by upstream project "Trigger" build number 292 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10 [BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins5313385079501535074.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42558_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] 04:06:48,251 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 04:06:48,253 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 04:06:48,253 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:06:48,254 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:06:48,254 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:06:48,255 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:06:48,255 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 04:06:48,255 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:06:48,256 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:06:48,256 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:06:48,257 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:06:48,257 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:06:48,429 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:06:48,429 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:06:48,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:06:48,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:06:48,460 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:06:48,461 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:06:48,461 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:06:48,461 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:06:48,461 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 04:06:48,462 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 04:06:48,463 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 207 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-27 04:06:48,472] [main] java.version = 17.0.2 [testng] 04:06:48,475 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:06:48,475 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:06:48,518 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-27_04-06-48.log] [testng] 04:06:48,519 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-27 04:06:48,521] [main] testng.directory = /data [testng] [2024-11-27 04:06:48,521] [main] testng.configDirectory = /config [testng] [2024-11-27 04:06:48,530] [main] testng.multiplier = 1.0 [testng] [2024-11-27 04:06:48,531] [main] testng.in-memory = false [testng] [2024-11-27 04:06:48,531] [main] testng.allow-missing = false [testng] [2024-11-27 04:06:48,532] [main] user.language = en [testng] [2024-11-27 04:06:48,532] [main] user.country = ${user.country} [testng] [2024-11-27 04:06:48,532] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-27 04:11:37,791] [main] ---------------------------------------- [testng] [2024-11-27 04:11:37,791] [main] Total files: 2169 [testng] [2024-11-27 04:11:37,792] [main] Scan time: 289.259 s (133 ms/file) [testng] [2024-11-27 04:11:37,792] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-27 04:28:18,963] [pool-1-thread-1] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 04:28:18,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:28:18,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:18,964 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-27_04-28-18.log] [testng] 04:28:18,965 |-INFO in ch.qos.logback.core.sift.SiftProcessor@403b1a1b - End of configuration. [testng] [2024-11-27 04:28:20,103] [pool-1-thread-12] Initializing /data/gideon/experiment_descriptor.xml: [testng] 04:28:20,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:28:20,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:20,104 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-27_04-28-20.log] [testng] 04:28:20,105 |-INFO in ch.qos.logback.core.sift.SiftProcessor@217af219 - End of configuration. [testng] [2024-11-27 04:29:18,837] [pool-1-thread-11] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 04:29:18,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:29:18,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:29:18,838 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-27_04-29-18.log] [testng] 04:29:18,839 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41ac9d44 - End of configuration. [testng] [2024-11-27 04:30:09,875] [pool-1-thread-10] Initializing /data/nadine/experiment_descriptor.xml: [testng] 04:30:09,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:30:09,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:30:09,877 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-27_04-30-09.log] [testng] 04:30:09,877 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bf4aabd - End of configuration. [testng] [2024-11-27 04:30:11,403] [pool-1-thread-9] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 04:30:11,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:30:11,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:30:11,404 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-27_04-30-11.log] [testng] 04:30:11,404 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dbe3b09 - End of configuration. [testng] [2024-11-27 04:30:27,528] [pool-1-thread-8] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 04:30:27,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:30:27,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:30:27,529 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-27_04-30-27.log] [testng] 04:30:27,530 |-INFO in ch.qos.logback.core.sift.SiftProcessor@361b4519 - End of configuration. [testng] [2024-11-27 04:30:29,112] [pool-1-thread-7] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 04:30:29,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:30:29,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:30:29,112 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-27_04-30-29.log] [testng] 04:30:29,113 |-INFO in ch.qos.logback.core.sift.SiftProcessor@625d44db - End of configuration. [testng] [2024-11-27 04:32:23,727] [pool-1-thread-6] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 04:32:23,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:32:23,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:23,728 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-27_04-32-23.log] [testng] 04:32:23,728 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42344517 - End of configuration. [testng] [2024-11-27 04:38:40,991] [pool-1-thread-5] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 04:38:40,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:38:40,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:38:40,993 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-27_04-38-40.log] [testng] 04:38:40,993 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66b107cd - End of configuration. [testng] [2024-11-27 04:38:44,364] [pool-1-thread-4] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 04:38:44,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:38:44,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:38:44,365 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-27_04-38-44.log] [testng] 04:38:44,365 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f886058 - End of configuration. [testng] [2024-11-27 04:39:04,513] [pool-1-thread-3] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 04:39:04,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:39:04,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:39:04,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-27_04-39-04.log] [testng] 04:39:04,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c6e3370 - End of configuration. [testng] [2024-11-27 04:42:45,883] [pool-1-thread-2] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 04:42:45,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:42:45,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:42:45,884 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-27_04-42-45.log] [testng] 04:42:45,884 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8364c3c - End of configuration. [testng] [2024-11-27 04:44:06,833] [pool-1-thread-1] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] [2024-11-27 04:46:58,627] [pool-1-thread-8] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] [2024-11-27 04:48:08,586] [pool-1-thread-10] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] [2024-11-27 04:52:36,005] [pool-1-thread-5] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] [2024-11-27 05:05:15,780] [pool-1-thread-5] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 06:25:18,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 06:25:18,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:25:18,056 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-27_06-25-18.log] [testng] 06:25:18,056 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17276764 - End of configuration. [testng] 06:36:52,493 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 06:36:52,493 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:36:52,496 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-27_06-36-52.log] [testng] 06:36:52,497 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b3fa42a - End of configuration. [testng] 06:37:31,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 06:37:31,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:37:31,584 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-27_06-37-31.log] [testng] 06:37:31,584 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2904321f - End of configuration. [testng] 06:38:59,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:38:59,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:38:59,696 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-27_06-38-59.log] [testng] 06:38:59,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e35949b - End of configuration. [testng] 06:39:54,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 06:39:54,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:39:54,881 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-27_06-39-54.log] [testng] 06:39:54,881 |-INFO in ch.qos.logback.core.sift.SiftProcessor@359c93bd - End of configuration. [testng] 06:47:18,711 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:47:18,711 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:47:18,712 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-27_06-47-18.log] [testng] 06:47:18,712 |-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: 160 minutes 35 seconds Finished: SUCCESS