Started by upstream project "BIOFORMATS-test-repo" build number 239 originally caused by: Started by upstream project "Trigger" build number 264 originally caused by: Started by timer 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/jenkins16551154142120236969.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37638_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] 03:02:46,875 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:02:46,876 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 03:02:46,876 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:02:46,877 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:02:46,878 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:02:46,878 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:02:46,878 |-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] 03:02:46,878 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:02:46,878 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:02:46,879 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:02:46,879 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:02:46,879 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:02:47,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:02:47,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:02:47,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:02:47,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:02:47,059 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:02:47,059 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:02:47,059 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:02:47,060 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:02:47,060 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 03:02:47,060 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 03:02:47,060 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 182 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-30 03:02:47,069] [main] java.version = 17.0.2 [testng] 03:02:47,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:02:47,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:47,110 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-30_03-02-47.log] [testng] 03:02:47,111 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-30 03:02:47,113] [main] testng.directory = /data [testng] [2024-10-30 03:02:47,113] [main] testng.configDirectory = /config [testng] [2024-10-30 03:02:47,121] [main] testng.multiplier = 1.0 [testng] [2024-10-30 03:02:47,122] [main] testng.in-memory = false [testng] [2024-10-30 03:02:47,123] [main] testng.allow-missing = false [testng] [2024-10-30 03:02:47,123] [main] user.language = en [testng] [2024-10-30 03:02:47,123] [main] user.country = ${user.country} [testng] [2024-10-30 03:02:47,123] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-30 03:07:24,130] [main] ---------------------------------------- [testng] [2024-10-30 03:07:24,130] [main] Total files: 2169 [testng] [2024-10-30 03:07:24,130] [main] Scan time: 277.007 s (127 ms/file) [testng] [2024-10-30 03:07:24,130] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-30 03:28:31,526] [pool-1-thread-1] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 03:28:31,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:28:31,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:28:31,528 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-30_03-28-31.log] [testng] 03:28:31,528 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75e86f38 - End of configuration. [testng] [2024-10-30 03:28:32,444] [pool-1-thread-12] Initializing /data/gideon/experiment_descriptor.xml: [testng] 03:28:32,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:28:32,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:28:32,446 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-30_03-28-32.log] [testng] 03:28:32,446 |-INFO in ch.qos.logback.core.sift.SiftProcessor@741703f5 - End of configuration. [testng] [2024-10-30 03:29:09,760] [pool-1-thread-11] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 03:29:09,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:29:09,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:29:09,762 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-30_03-29-09.log] [testng] 03:29:09,763 |-INFO in ch.qos.logback.core.sift.SiftProcessor@607f1474 - End of configuration. [testng] [2024-10-30 03:30:19,100] [pool-1-thread-10] Initializing /data/nadine/experiment_descriptor.xml: [testng] 03:30:19,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:30:19,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:30:19,101 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-30_03-30-19.log] [testng] 03:30:19,102 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7914afa9 - End of configuration. [testng] [2024-10-30 03:30:20,629] [pool-1-thread-9] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 03:30:20,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:30:20,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:30:20,630 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-30_03-30-20.log] [testng] 03:30:20,630 |-INFO in ch.qos.logback.core.sift.SiftProcessor@783b7106 - End of configuration. [testng] [2024-10-30 03:30:34,225] [pool-1-thread-8] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 03:30:34,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:30:34,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:30:34,226 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-30_03-30-34.log] [testng] 03:30:34,227 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c31bd20 - End of configuration. [testng] [2024-10-30 03:30:36,194] [pool-1-thread-7] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 03:30:36,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:30:36,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:30:36,196 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-30_03-30-36.log] [testng] 03:30:36,196 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43ee698f - End of configuration. [testng] [2024-10-30 03:32:02,647] [pool-1-thread-6] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 03:32:02,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:32:02,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:32:02,649 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-30_03-32-02.log] [testng] 03:32:02,650 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22c27c61 - End of configuration. [testng] [2024-10-30 03:35:22,157] [pool-1-thread-5] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 03:35:22,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:35:22,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:22,158 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-30_03-35-22.log] [testng] 03:35:22,159 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c0ac1f7 - End of configuration. [testng] [2024-10-30 03:35:24,708] [pool-1-thread-4] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 03:35:24,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:35:24,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:24,709 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-30_03-35-24.log] [testng] 03:35:24,709 |-INFO in ch.qos.logback.core.sift.SiftProcessor@763c82e3 - End of configuration. [testng] [2024-10-30 03:35:56,850] [pool-1-thread-3] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 03:35:56,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:35:56,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:56,852 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-30_03-35-56.log] [testng] 03:35:56,852 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b13bd2 - End of configuration. [testng] [2024-10-30 03:38:59,251] [pool-1-thread-2] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 03:38:59,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:38:59,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:38:59,253 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-30_03-38-59.log] [testng] 03:38:59,253 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c6dc7be - End of configuration. [testng] [2024-10-30 03:39:53,751] [pool-1-thread-1] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] [2024-10-30 03:43:32,416] [pool-1-thread-8] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] [2024-10-30 03:44:54,829] [pool-1-thread-10] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] [2024-10-30 03:48:56,475] [pool-1-thread-5] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] [2024-10-30 03:53:43,885] [pool-1-thread-9] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 04:54:33,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:54:33,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:54:33,123 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-30_04-54-33.log] [testng] 04:54:33,124 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d994789 - End of configuration. [testng] 04:55:23,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:55:23,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:55:23,174 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-30_04-55-23.log] [testng] 04:55:23,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e423064 - End of configuration. [testng] 04:55:55,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:55:55,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:55:55,782 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-30_04-55-55.log] [testng] 04:55:55,783 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55836c3e - End of configuration. [testng] 04:57:01,531 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:57:01,531 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:57:01,532 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-30_04-57-01.log] [testng] 04:57:01,532 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e213a1c - End of configuration. [testng] 05:03:12,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:03:12,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:03:12,562 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-30_05-03-12.log] [testng] 05:03:12,563 |-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: 120 minutes 30 seconds Finished: SUCCESS