Started by upstream project "BIOFORMATS-test-repo" build number 270 originally caused by: Started by user devspace 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/jenkins1415212233646303329.sh + '[' cellh5 = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42619_merge_ci -v /uod/idr/repos/curated/cellh5:/data -v /uod/idr-scratch/merge-ci/curated/cellh5:/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] 11:39:15,335 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:39:15,337 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 11:39:15,337 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:39:15,338 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:39:15,338 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:39:15,338 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:39:15,339 |-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] 11:39:15,339 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:39:15,339 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:39:15,340 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:39:15,340 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:39:15,340 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:39:15,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:39:15,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:39:15,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:39:15,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:39:15,539 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:39:15,539 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:39:15,539 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:39:15,540 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:39:15,540 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 11:39:15,541 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 11:39:15,541 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 202 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-27 11:39:15,550] [main] java.version = 17.0.2 [testng] 11:39:15,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:39:15,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:39:15,595 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-27_11-39-15.log] [testng] 11:39:15,597 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-27 11:39:15,599] [main] testng.directory = /data [testng] [2024-11-27 11:39:15,599] [main] testng.configDirectory = /config [testng] [2024-11-27 11:39:15,608] [main] testng.multiplier = 1.0 [testng] [2024-11-27 11:39:15,608] [main] testng.in-memory = false [testng] [2024-11-27 11:39:15,608] [main] testng.allow-missing = false [testng] [2024-11-27 11:39:15,608] [main] user.language = en [testng] [2024-11-27 11:39:15,609] [main] user.country = ${user.country} [testng] [2024-11-27 11:39:15,609] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-27 11:39:16,212] [main] ---------------------------------------- [testng] [2024-11-27 11:39:16,212] [main] Total files: 11 [testng] [2024-11-27 11:39:16,212] [main] Scan time: 0.603 s (54 ms/file) [testng] [2024-11-27 11:39:16,212] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 10 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-27 11:43:28,065] [pool-1-thread-1] Initializing /data/public/samples/full/0042.ch5: [testng] 11:43:28,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:43:28,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:43:28,067 |-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_11-43-28.log] [testng] 11:43:28,068 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55f7b8be - End of configuration. [testng] [2024-11-27 11:43:28,737] [pool-1-thread-10] Initializing /data/public/idr0013/00001_01.ch5: [testng] 11:43:28,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:43:28,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:43:28,738 |-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_11-43-28.log] [testng] 11:43:28,739 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5506f702 - End of configuration. [testng] [2024-11-27 11:43:29,440] [pool-1-thread-9] Initializing /data/public/samples/full/0040.ch5: [testng] 11:43:29,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:43:29,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:43:29,441 |-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_11-43-29.log] [testng] 11:43:29,441 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64abfcfc - End of configuration. [testng] [2024-11-27 11:43:30,086] [pool-1-thread-8] Initializing /data/public/samples/full/0046.ch5: [testng] 11:43:30,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:43:30,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:43:30,087 |-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_11-43-30.log] [testng] 11:43:30,087 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ab1587b - End of configuration. [testng] [2024-11-27 11:43:30,727] [pool-1-thread-7] Initializing /data/public/samples/full/0039.ch5: [testng] 11:43:30,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:43:30,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:43:30,728 |-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_11-43-30.log] [testng] 11:43:30,728 |-INFO in ch.qos.logback.core.sift.SiftProcessor@edce13d - End of configuration. [testng] [2024-11-27 11:43:31,370] [pool-1-thread-6] Initializing /data/public/samples/full/0041.ch5: [testng] 11:43:31,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:43:31,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:43:31,371 |-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_11-43-31.log] [testng] 11:43:31,371 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b749b7b - End of configuration. [testng] [2024-11-27 11:43:32,029] [pool-1-thread-5] Initializing /data/public/samples/full/0037.ch5: [testng] 11:43:32,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:43:32,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:43:32,030 |-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_11-43-32.log] [testng] 11:43:32,031 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45a07d6d - End of configuration. [testng] [2024-11-27 11:43:32,704] [pool-1-thread-4] Initializing /data/public/samples/full/0013.ch5: [testng] 11:43:32,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:43:32,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:43:32,705 |-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_11-43-32.log] [testng] 11:43:32,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@512dbad3 - End of configuration. [testng] [2024-11-27 11:43:33,352] [pool-1-thread-3] Initializing /data/public/samples/full/0045.ch5: [testng] 11:43:33,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:43:33,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:43:33,353 |-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_11-43-33.log] [testng] 11:43:33,354 |-INFO in ch.qos.logback.core.sift.SiftProcessor@495b473c - End of configuration. [testng] [2024-11-27 11:43:34,011] [pool-1-thread-2] Initializing /data/public/samples/reduced/0038.ch5: [testng] 11:43:34,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:43:34,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:43:34,012 |-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_11-43-34.log] [testng] 11:43:34,013 |-INFO in ch.qos.logback.core.sift.SiftProcessor@301f4895 - End of configuration. Build was aborted Calling Pipeline was cancelled Finished: ABORTED