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Started by upstream project "BIOFORMATS-test-repo" build number 213 originally caused by: Started by upstream project "Trigger" build number 240 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins17803642161498924441.sh + '[' cv7000 = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_33828_merge_ci -v /uod/idr/repos/curated/cv7000:/data -v /uod/idr-scratch/merge-ci/curated/cv7000:/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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 06:39:19,590 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 06:39:19,592 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 06:39:19,592 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:39:19,594 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:39:19,594 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 06:39:19,595 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 06:39:19,595 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 06:39:19,595 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:39:19,596 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:39:19,597 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 06:39:19,598 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 06:39:19,598 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 06:39:19,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 06:39:19,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 06:39:19,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 06:39:19,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 06:39:19,833 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 06:39:19,834 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 06:39:19,834 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 06:39:19,835 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 06:39:19,835 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 06:39:19,836 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 06:39:19,836 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 240 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-08 06:39:19,850] [main] java.version = 11.0.16 [testng] 06:39:19,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:39:19,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:39:19,914 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-08_06-39-19.log] [testng] 06:39:19,915 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-08 06:39:19,918] [main] testng.directory = /data [testng] [2024-10-08 06:39:19,918] [main] testng.configDirectory = /config [testng] [2024-10-08 06:39:19,929] [main] testng.multiplier = 1.0 [testng] [2024-10-08 06:39:19,930] [main] testng.in-memory = false [testng] [2024-10-08 06:39:19,930] [main] testng.allow-missing = false [testng] [2024-10-08 06:39:19,930] [main] user.language = en [testng] [2024-10-08 06:39:19,930] [main] user.country = ${user.country} [testng] [2024-10-08 06:39:19,930] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-08 06:46:20,368] [main] ---------------------------------------- [testng] [2024-10-08 06:46:20,368] [main] Total files: 31992 [testng] [2024-10-08 06:46:20,368] [main] Scan time: 420.437 s (13 ms/file) [testng] [2024-10-08 06:46:20,368] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 12 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-08 06:47:33,644] [pool-1-thread-1] Initializing /data/samples/multiple-actions-per-channel/test-plate.wpi: [testng] 06:47:33,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 06:47:33,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:47:33,647 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-08_06-47-33.log] [testng] 06:47:33,647 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ef77dc - End of configuration. [testng] [2024-10-08 06:47:34,621] [pool-1-thread-12] Initializing /data/public/idr0088/110000251230/110000251230.wpi: [testng] 06:47:34,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 06:47:34,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:47:34,623 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-08_06-47-34.log] [testng] 06:47:34,623 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e1647c2 - End of configuration. [testng] [2024-10-08 06:47:35,055] [pool-1-thread-11] Initializing /data/glencoe/DW 0001_20161111_100649/AssayPlate_Corning_#3683/AssayPlate_Corning_#3683.wpi: [testng] 06:47:35,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 06:47:35,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:47:35,055 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-08_06-47-35.log] [testng] 06:47:35,056 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23f35480 - End of configuration. [testng] [2024-10-08 06:47:36,008] [pool-1-thread-10] Initializing /data/samples/extra-dirs/AssayPlate_Corning_#3683.wpi: [testng] 06:47:36,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 06:47:36,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:47:36,009 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-08_06-47-36.log] [testng] 06:47:36,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d8eedd4 - End of configuration. [testng] [2024-10-08 06:47:36,488] [pool-1-thread-9] Initializing /data/glencoe/DW 0003_20161111_111619/AssayPlate_Corning_#3683/AssayPlate_Corning_#3683.wpi: [testng] 06:47:36,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 06:47:36,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:47:36,490 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-08_06-47-36.log] [testng] 06:47:36,490 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69a7f45 - End of configuration. [testng] [2024-10-08 06:47:37,102] [pool-1-thread-8] Initializing /data/glencoe/DW 0002_20161111_105720/AssayPlate_Corning_#3683/AssayPlate_Corning_#3683.wpi: [testng] 06:47:37,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 06:47:37,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:47:37,103 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-08_06-47-37.log] [testng] 06:47:37,104 |-INFO in ch.qos.logback.core.sift.SiftProcessor@413d11d8 - End of configuration. [testng] [2024-10-08 06:47:37,825] [pool-1-thread-7] Initializing /data/samples/sparse-channels/sparse.wpi: [testng] 06:47:37,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 06:47:37,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:47:37,826 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-08_06-47-37.log] [testng] 06:47:37,826 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76dc5e33 - End of configuration. [testng] [2024-10-08 06:47:38,548] [pool-1-thread-6] Initializing /data/samples/multi-action-z/test-plate.wpi: [testng] 06:47:38,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:47:38,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:47:38,549 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-08_06-47-38.log] [testng] 06:47:38,550 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59bf40d2 - End of configuration. [testng] [2024-10-08 06:47:39,924] [pool-1-thread-5] Initializing /data/public/idr0093/020/020.wpi: [testng] 06:47:39,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 06:47:39,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:47:39,926 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-08_06-47-39.log] [testng] 06:47:39,926 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2092f9d3 - End of configuration. [testng] [2024-10-08 06:47:42,207] [pool-1-thread-4] Initializing /data/nih/180521-OMERO-Multi-Test_20180521_134927/Test-plate-1/Test-plate-1.wpi: [testng] 06:47:42,207 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 06:47:42,207 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:47:42,208 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-08_06-47-42.log] [testng] 06:47:42,209 |-INFO in ch.qos.logback.core.sift.SiftProcessor@276567cf - End of configuration. [testng] [2024-10-08 06:47:44,276] [pool-1-thread-3] Initializing /data/samples/separate-image-directory/AssayPlate_Corning_#3683.wpi: [testng] 06:47:44,277 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 06:47:44,277 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:47:44,278 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-08_06-47-44.log] [testng] 06:47:44,279 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7dc88c3b - End of configuration. [testng] [2024-10-08 06:47:45,113] [pool-1-thread-2] Initializing /data/samples/channel-subset/AssayPlate_Corning_#3683.wpi: [testng] 06:47:45,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 06:47:45,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:47:45,114 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-08_06-47-45.log] [testng] 06:47:45,114 |-INFO in ch.qos.logback.core.sift.SiftProcessor@701c9edc - End of configuration. time="2024-10-08T06:01:38Z" level=error msg="error waiting for container: unexpected EOF" Build step 'Execute shell' marked build as failure Finished: FAILURE