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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@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins13950504637113940271.sh + '[' perkinelmer-operetta = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_33803_merge_ci -v /uod/idr/repos/curated/perkinelmer-operetta:/data -v /uod/idr-scratch/merge-ci/curated/perkinelmer-operetta:/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] 06:24:40,602 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 06:24:40,604 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 06:24:40,604 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:24:40,605 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:24:40,605 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 06:24:40,606 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 06:24:40,606 |-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] 06:24:40,606 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:24:40,607 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:24:40,607 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 06:24:40,607 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 06:24:40,608 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 06:24:40,778 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 06:24:40,778 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 06:24:40,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 06:24:40,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 06:24:40,807 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 06:24:40,807 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 06:24:40,808 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 06:24:40,808 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 06:24:40,808 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 06:24:40,809 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 06:24:40,809 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 202 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-08 06:24:40,819] [main] java.version = 11.0.16 [testng] 06:24:40,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:24:40,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:24:40,873 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-08_06-24-40.log] [testng] 06:24:40,874 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-08 06:24:40,876] [main] testng.directory = /data [testng] [2024-10-08 06:24:40,876] [main] testng.configDirectory = /config [testng] [2024-10-08 06:24:40,888] [main] testng.multiplier = 1.0 [testng] [2024-10-08 06:24:40,890] [main] testng.in-memory = false [testng] [2024-10-08 06:24:40,890] [main] testng.allow-missing = false [testng] [2024-10-08 06:24:40,890] [main] user.language = en [testng] [2024-10-08 06:24:40,890] [main] user.country = ${user.country} [testng] [2024-10-08 06:24:40,890] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-08 06:28:47,106] [main] ---------------------------------------- [testng] [2024-10-08 06:28:47,106] [main] Total files: 14663 [testng] [2024-10-08 06:28:47,106] [main] Scan time: 246.216 s (16 ms/file) [testng] [2024-10-08 06:28:47,106] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 16 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-08 06:30:59,973] [pool-1-thread-1] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml: [testng] 06:30:59,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 06:30:59,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:30:59,975 |-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_06-30-59.log] [testng] 06:30:59,975 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71b07fe7 - End of configuration. [testng] [2024-10-08 06:31:00,168] [pool-1-thread-12] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] 06:31:00,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 06:31:00,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:00,170 |-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_06-31-00.log] [testng] 06:31:00,170 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a7d2f01 - End of configuration. [testng] [2024-10-08 06:31:00,509] [pool-1-thread-11] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml: [testng] 06:31:00,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 06:31:00,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:00,510 |-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_06-31-00.log] [testng] 06:31:00,511 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6364ee6 - End of configuration. [testng] [2024-10-08 06:31:01,694] [pool-1-thread-10] Initializing /data/samples/no-first-series/Index.idx.xml: [testng] 06:31:01,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 06:31:01,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:01,695 |-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_06-31-01.log] [testng] 06:31:01,695 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2087252b - End of configuration. [testng] [2024-10-08 06:31:01,739] [pool-1-thread-9] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml: [testng] 06:31:01,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 06:31:01,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:01,740 |-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_06-31-01.log] [testng] 06:31:01,740 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72a92125 - End of configuration. [testng] [2024-10-08 06:31:01,785] [pool-1-thread-8] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml: [testng] 06:31:01,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 06:31:01,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:01,786 |-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_06-31-01.log] [testng] 06:31:01,786 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4aba8d1b - End of configuration. [testng] [2024-10-08 06:31:01,866] [pool-1-thread-7] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png: [testng] 06:31:01,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 06:31:01,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:01,868 |-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_06-31-01.log] [testng] 06:31:01,868 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e48d4fc - End of configuration. [testng] [2024-10-08 06:31:01,879] [pool-1-thread-6] Initializing /data/public/omer/006P_M3/006P_M3_overview.png: [testng] 06:31:01,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:31:01,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:01,880 |-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_06-31-01.log] [testng] 06:31:01,880 |-INFO in ch.qos.logback.core.sift.SiftProcessor@652f4154 - End of configuration. [testng] [2024-10-08 06:31:01,900] [pool-1-thread-5] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml: [testng] 06:31:01,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 06:31:01,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:01,901 |-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_06-31-01.log] [testng] 06:31:01,901 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63c8d9d2 - End of configuration. [testng] [2024-10-08 06:31:02,164] [pool-1-thread-4] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml: [testng] 06:31:02,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 06:31:02,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:02,165 |-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_06-31-02.log] [testng] 06:31:02,166 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66a93049 - End of configuration. [testng] [2024-10-08 06:31:02,234] [pool-1-thread-3] Initializing /data/samples/smaller-xy/Index.idx.xml: [testng] 06:31:02,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 06:31:02,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:02,236 |-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_06-31-02.log] [testng] 06:31:02,236 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32f69690 - End of configuration. [testng] [2024-10-08 06:31:02,304] [pool-1-thread-2] Initializing /data/public/zenodo-7841360/Hoechst__2023-03-07T10_17_54-Measurement 2/Images/Index.idx.xml: [testng] 06:31:02,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 06:31:02,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:02,305 |-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_06-31-02.log] [testng] 06:31:02,305 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d3966ac - End of configuration. [testng] [2024-10-08 06:31:03,813] [pool-1-thread-6] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] [2024-10-08 06:31:04,263] [pool-1-thread-7] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml: [testng] [2024-10-08 06:31:05,311] [pool-1-thread-2] Initializing /data/samples/32-bit-file/Index.idx.xml: [testng] [2024-10-08 06:31:16,833] [pool-1-thread-10] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml: 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