Started by upstream project "BIOFORMATS-test-repo" build number 184 originally caused by: Started by upstream project "Trigger" build number 206 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/jenkins6738549094093752956.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_29134_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] 11:37:47,967 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:37:47,969 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 11:37:47,969 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:37:47,970 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:37:47,971 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:37:47,972 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:37:47,972 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:37:47,972 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:37:47,973 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:37:47,974 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:37:47,974 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:37:47,975 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:37:48,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:37:48,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:37:48,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:37:48,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:37:48,249 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:37:48,249 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:37:48,249 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:37:48,249 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:37:48,249 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 11:37:48,250 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 11:37:48,250 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 277 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-11 11:37:48,259] [main] java.version = 17.0.2 [testng] 11:37:48,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:37:48,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:37:48,306 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-11_11-37-48.log] [testng] 11:37:48,307 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-09-11 11:37:48,309] [main] testng.directory = /data [testng] [2024-09-11 11:37:48,310] [main] testng.configDirectory = /config [testng] [2024-09-11 11:37:48,318] [main] testng.multiplier = 1.0 [testng] [2024-09-11 11:37:48,319] [main] testng.in-memory = false [testng] [2024-09-11 11:37:48,319] [main] testng.allow-missing = false [testng] [2024-09-11 11:37:48,319] [main] user.language = en [testng] [2024-09-11 11:37:48,319] [main] user.country = ${user.country} [testng] [2024-09-11 11:37:48,320] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-11 11:42:55,344] [main] ---------------------------------------- [testng] [2024-09-11 11:42:55,345] [main] Total files: 2169 [testng] [2024-09-11 11:42:55,345] [main] Scan time: 307.024 s (141 ms/file) [testng] [2024-09-11 11:42:55,345] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-11 11:58:53,508] [pool-1-thread-1] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 11:58:53,508 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:58:53,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:58:53,510 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-11_11-58-53.log] [testng] 11:58:53,510 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b9c9386 - End of configuration. [testng] [2024-09-11 11:58:57,094] [pool-1-thread-12] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 11:58:57,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:58:57,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:58:57,095 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-11_11-58-57.log] [testng] 11:58:57,096 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37bebaee - End of configuration. [testng] [2024-09-11 11:59:32,399] [pool-1-thread-11] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 11:59:32,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:59:32,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:59:32,401 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-11_11-59-32.log] [testng] 11:59:32,401 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41a97571 - End of configuration. [testng] [2024-09-11 12:00:52,681] [pool-1-thread-10] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 12:00:52,682 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:00:52,682 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:00:52,683 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-11_12-00-52.log] [testng] 12:00:52,683 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62389fb6 - End of configuration. [testng] [2024-09-11 12:01:03,570] [pool-1-thread-9] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 12:01:03,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:01:03,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:01:03,571 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-11_12-01-03.log] [testng] 12:01:03,571 |-INFO in ch.qos.logback.core.sift.SiftProcessor@189bf79d - End of configuration. [testng] [2024-09-11 12:01:05,903] [pool-1-thread-8] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 12:01:05,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:01:05,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:01:05,905 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-11_12-01-05.log] [testng] 12:01:05,905 |-INFO in ch.qos.logback.core.sift.SiftProcessor@686787ad - End of configuration. [testng] [2024-09-11 12:01:35,815] [pool-1-thread-7] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 12:01:35,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:01:35,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:01:35,818 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-11_12-01-35.log] [testng] 12:01:35,819 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35e0638d - End of configuration. [testng] [2024-09-11 12:01:38,644] [pool-1-thread-6] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 12:01:38,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:01:38,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:01:38,645 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-11_12-01-38.log] [testng] 12:01:38,645 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12e898bc - End of configuration. [testng] [2024-09-11 12:01:38,811] [pool-1-thread-5] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 12:01:38,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:01:38,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:01:38,812 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-11_12-01-38.log] [testng] 12:01:38,812 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35dffa3d - End of configuration. [testng] [2024-09-11 12:03:36,706] [pool-1-thread-4] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 12:03:36,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:03:36,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:03:36,708 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-11_12-03-36.log] [testng] 12:03:36,709 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7aa4b958 - End of configuration. [testng] [2024-09-11 12:03:37,105] [pool-1-thread-3] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 12:03:37,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:03:37,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:03:37,106 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-11_12-03-37.log] [testng] 12:03:37,106 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a002f1 - End of configuration. [testng] [2024-09-11 12:04:31,401] [pool-1-thread-2] Initializing /data/nadine/experiment_descriptor.xml: [testng] 12:04:31,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:04:31,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:04:31,401 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-11_12-04-31.log] [testng] 12:04:31,402 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fcb720b - End of configuration. [testng] [2024-09-11 12:04:35,088] [pool-1-thread-4] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] [2024-09-11 12:06:05,171] [pool-1-thread-6] Initializing /data/gideon/experiment_descriptor.xml: [testng] [2024-09-11 12:06:36,222] [pool-1-thread-2] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] [2024-09-11 12:06:55,209] [pool-1-thread-1] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] [2024-09-11 12:09:01,869] [pool-1-thread-7] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 39 minutes 25 seconds Finished: SUCCESS