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Started by upstream project "BIOFORMATS-test-repo" build number 352 originally caused by: Started by upstream project "Trigger" build number 378 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins643779343815644479.sh + '[' metaxpress = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_56023_merge_ci -v /uod/idr/repos/curated/metaxpress:/data -v /uod/idr-scratch/merge-ci/curated/metaxpress:/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 test-automated: [testng] File leak detector installed [testng] 00:39:07,576 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:39:07,578 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - No custom configurators were discovered as a service. [testng] 00:39:07,578 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:39:07,580 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:39:07,580 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:39:07,580 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:39:07,581 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:39:07,581 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:39:07,581 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:39:07,582 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:39:07,582 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:39:07,582 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:39:07,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:39:07,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:39:07,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:39:07,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:39:07,855 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:39:07,855 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:39:07,855 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:39:07,855 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:39:07,856 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@63355449 - End of configuration. [testng] 00:39:07,856 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48ae9b55 - Registering current configuration as safe fallback point [testng] 00:39:07,857 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 276 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-02-21 00:39:07,866] [main] java.version = 1.8.0_342 [testng] 00:39:07,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:39:07,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:07,918 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-02-21_00-39-07.log] [testng] 00:39:07,920 |-INFO in ch.qos.logback.core.sift.SiftProcessor@765d7657 - End of configuration. [testng] [2025-02-21 00:39:07,921] [main] testng.directory = /data [testng] [2025-02-21 00:39:07,922] [main] testng.configDirectory = /config [testng] [2025-02-21 00:39:07,934] [main] testng.multiplier = 1.0 [testng] [2025-02-21 00:39:07,934] [main] testng.in-memory = false [testng] [2025-02-21 00:39:07,935] [main] testng.allow-missing = false [testng] [2025-02-21 00:39:07,935] [main] user.language = en [testng] [2025-02-21 00:39:07,935] [main] user.country = ${user.country} [testng] [2025-02-21 00:39:07,935] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-02-21 00:46:02,454] [main] ---------------------------------------- [testng] [2025-02-21 00:46:02,454] [main] Total files: 1231 [testng] [2025-02-21 00:46:02,454] [main] Scan time: 414.519 s (336 ms/file) [testng] [2025-02-21 00:46:02,455] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 10 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-02-21 00:50:13,158] [pool-1-thread-1] Initializing /data/public/idr0008/Plate10_Actinome1/Act1_Plate10-SP-A8.HTD: [testng] 00:50:13,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:50:13,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:13,160 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-02-21_00-50-13.log] [testng] 00:50:13,160 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5223e9d7 - End of configuration. [testng] [2025-02-21 00:50:42,000] [pool-1-thread-10] Initializing /data/public/idr0006/plate 11001_Plate_136/TimePoint_1/plate 11001.HTD: [testng] 00:50:42,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:50:42,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:42,002 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-02-21_00-50-42.log] [testng] 00:50:42,003 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b41ce4e - End of configuration. [testng] [2025-02-21 00:51:31,620] [pool-1-thread-9] Initializing /data/public/idr0005/Primary_001/2011-04-19-plate-1.HTD: [testng] 00:51:31,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:51:31,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:31,622 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-02-21_00-51-31.log] [testng] 00:51:31,622 |-INFO in ch.qos.logback.core.sift.SiftProcessor@287fedc4 - End of configuration. [testng] [2025-02-21 00:51:39,598] [pool-1-thread-8] Initializing /data/public/idr0081/BSF018292-1A/BSF018292-1A.HTD: [testng] 00:51:39,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:51:39,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:39,600 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-02-21_00-51-39.log] [testng] 00:51:39,600 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26252ac - End of configuration. [testng] [2025-02-21 00:51:51,929] [pool-1-thread-7] Initializing /data/samples/thumb-test/2011-04-19-plate-1.HTD: [testng] 00:51:51,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:51:51,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:51,931 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-02-21_00-51-51.log] [testng] 00:51:51,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76ff6fe4 - End of configuration. [testng] [2025-02-21 00:52:02,444] [pool-1-thread-6] Initializing /data/samples/single-site-test/single-site.HTD: [testng] 00:52:02,444 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:52:02,444 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:02,445 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-02-21_00-52-02.log] [testng] 00:52:02,445 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68f7b6a8 - End of configuration. [testng] [2025-02-21 00:52:03,989] [pool-1-thread-5] Initializing /data/qa-4207/NSC.HTD: [testng] 00:52:03,990 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:52:03,990 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:03,990 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-02-21_00-52-03.log] [testng] 00:52:03,991 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1607fd64 - End of configuration. [testng] [2025-02-21 00:52:05,050] [pool-1-thread-4] Initializing /data/samples/multi-channel-test/multi-channel.HTD: [testng] 00:52:05,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:52:05,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:05,051 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-02-21_00-52-05.log] [testng] 00:52:05,051 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64a10a0b - End of configuration. [testng] [2025-02-21 00:52:05,727] [pool-1-thread-3] Initializing /data/samples/multi-z/2011-04-19-plate-1.HTD: [testng] 00:52:05,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:52:05,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:05,727 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-02-21_00-52-05.log] [testng] 00:52:05,728 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ef9aba2 - End of configuration. [testng] [2025-02-21 00:52:17,672] [pool-1-thread-2] Initializing /data/samples/multi-channel-missing-corner/multi-channel.HTD: [testng] 00:52:17,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:52:17,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:17,673 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-02-21_00-52-17.log] [testng] 00:52:17,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38d6a370 - End of configuration. time="2025-02-21T01:00:38Z" level=error msg="error waiting for container: unexpected EOF" Build step 'Execute shell' marked build as failure Finished: FAILURE