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Started by upstream project "BIOFORMATS-test-repo" build number 225 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins14479747319060874661.sh + '[' perkinelmer-operetta = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35470_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 11:55:22,839 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:55:22,840 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 11:55:22,840 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:55:22,841 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:55:22,842 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:55:22,842 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:55:22,842 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:55:22,842 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:55:22,843 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:55:22,843 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:55:22,844 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:55:22,844 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:55:23,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:55:23,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:55:23,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:55:23,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:55:23,037 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:55:23,037 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:55:23,037 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:55:23,037 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:55:23,037 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 11:55:23,038 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 11:55:23,038 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 195 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-17 11:55:23,047] [main] java.version = 21 [testng] 11:55:23,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:55:23,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:55:23,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-17_11-55-23.log] [testng] 11:55:23,095 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-17 11:55:23,096] [main] testng.directory = /data [testng] [2024-10-17 11:55:23,097] [main] testng.configDirectory = /config [testng] [2024-10-17 11:55:23,106] [main] testng.multiplier = 1.0 [testng] [2024-10-17 11:55:23,106] [main] testng.in-memory = false [testng] [2024-10-17 11:55:23,106] [main] testng.allow-missing = false [testng] [2024-10-17 11:55:23,106] [main] user.language = en [testng] [2024-10-17 11:55:23,106] [main] user.country = ${user.country} [testng] [2024-10-17 11:55:23,106] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-17 13:01:48,536] [main] ---------------------------------------- [testng] [2024-10-17 13:01:48,536] [main] Total files: 14663 [testng] [2024-10-17 13:01:48,536] [main] Scan time: 3985.43 s (271 ms/file) [testng] [2024-10-17 13:01:48,537] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 16 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-17 14:49:06,828] [pool-1-thread-1] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml: [testng] 14:49:06,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 14:49:06,829 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:49:06,830 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-17_14-49-06.log] [testng] 14:49:06,830 |-INFO in ch.qos.logback.core.sift.SiftProcessor@629bb087 - End of configuration. [testng] [2024-10-17 14:50:58,719] [pool-1-thread-12] Initializing /data/samples/no-first-series/Index.idx.xml: [testng] 14:50:58,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 14:50:58,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:50:58,720 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-17_14-50-58.log] [testng] 14:50:58,721 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fbfd071 - End of configuration. [testng] [2024-10-17 14:51:01,559] [pool-1-thread-11] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] 14:51:01,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 14:51:01,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:51:01,560 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-17_14-51-01.log] [testng] 14:51:01,561 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6856aa68 - End of configuration. [testng] [2024-10-17 14:51:30,180] [pool-1-thread-10] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png: [testng] 14:51:30,180 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 14:51:30,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:51:30,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-17_14-51-30.log] [testng] 14:51:30,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a5f04ab - End of configuration. [testng] [2024-10-17 14:51:30,452] [pool-1-thread-9] Initializing /data/public/omer/006P_M3/006P_M3_overview.png: [testng] 14:51:30,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 14:51:30,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:51:30,453 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-17_14-51-30.log] [testng] 14:51:30,453 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79de64e1 - End of configuration. [testng] [2024-10-17 14:51:30,733] [pool-1-thread-8] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml: [testng] 14:51:30,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 14:51:30,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:51:30,734 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-17_14-51-30.log] [testng] 14:51:30,734 |-INFO in ch.qos.logback.core.sift.SiftProcessor@371a5252 - End of configuration. [testng] [2024-10-17 14:51:36,662] [pool-1-thread-7] Initializing /data/public/zenodo-7841360/Hoechst__2023-03-07T10_17_54-Measurement 2/Images/Index.idx.xml: [testng] 14:51:36,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 14:51:36,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:51:36,662 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-17_14-51-36.log] [testng] 14:51:36,663 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d70a299 - End of configuration. [testng] [2024-10-17 14:51:41,416] [pool-1-thread-6] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml: [testng] 14:51:41,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 14:51:41,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:51:41,417 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-17_14-51-41.log] [testng] 14:51:41,418 |-INFO in ch.qos.logback.core.sift.SiftProcessor@411b8130 - End of configuration. [testng] [2024-10-17 14:52:04,309] [pool-1-thread-5] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml: [testng] 14:52:04,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 14:52:04,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:52:04,310 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-17_14-52-04.log] [testng] 14:52:04,311 |-INFO in ch.qos.logback.core.sift.SiftProcessor@474d4e42 - End of configuration. [testng] [2024-10-17 14:52:09,947] [pool-1-thread-4] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml: [testng] 14:52:09,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 14:52:09,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:52:09,948 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-17_14-52-09.log] [testng] 14:52:09,948 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7da0858c - End of configuration. [testng] [2024-10-17 14:52:16,345] [pool-1-thread-3] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml: [testng] 14:52:16,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 14:52:16,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:52:16,346 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-17_14-52-16.log] [testng] 14:52:16,347 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72ca7894 - End of configuration. [testng] [2024-10-17 14:52:22,376] [pool-1-thread-2] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml: [testng] 14:52:22,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 14:52:22,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:52:22,378 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-17_14-52-22.log] [testng] 14:52:22,378 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78792ff0 - End of configuration. [testng] [2024-10-17 14:52:32,794] [pool-1-thread-10] Initializing /data/samples/32-bit-file/Index.idx.xml: [testng] [2024-10-17 14:52:39,934] [pool-1-thread-9] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] [2024-10-17 14:54:05,512] [pool-1-thread-7] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml: [testng] [2024-10-17 14:57:44,353] [pool-1-thread-12] Initializing /data/samples/smaller-xy/Index.idx.xml: Build was aborted Calling Pipeline was cancelled Finished: ABORTED