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Started by upstream project "BIOFORMATS-test-repo" build number 63 originally caused by: Started by upstream project "Trigger" build number 70 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins9275810146555822394.sh + '[' samples = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_9351_merge_ci -v /uod/idr/repos/curated/samples:/data -v /uod/idr-scratch/merge-ci/curated/samples:/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] 01:23:16,966 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:23:16,968 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:23:16,968 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:23:16,969 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:23:16,970 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:23:16,971 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:23:16,971 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:23:16,971 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:23:16,972 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:23:16,973 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:23:16,973 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:23:16,974 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:23:17,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:23:17,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:23:17,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:23:17,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:23:17,270 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:23:17,271 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:23:17,271 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:23:17,271 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:23:17,272 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:23:17,273 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:23:17,273 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 301 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-14 01:23:17,288] [main] java.version = 11.0.16 [testng] 01:23:17,294 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:23:17,294 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:17,368 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-14_01-23-17.log] [testng] 01:23:17,372 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-05-14 01:23:17,376] [main] testng.directory = /data [testng] [2024-05-14 01:23:17,376] [main] testng.configDirectory = /config [testng] [2024-05-14 01:23:17,396] [main] testng.multiplier = 1.0 [testng] [2024-05-14 01:23:17,399] [main] testng.in-memory = false [testng] [2024-05-14 01:23:17,399] [main] testng.allow-missing = false [testng] [2024-05-14 01:23:17,399] [main] user.language = en [testng] [2024-05-14 01:23:17,399] [main] user.country = ${user.country} [testng] [2024-05-14 01:23:17,400] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-14 01:23:39,130] [main] ---------------------------------------- [testng] [2024-05-14 01:23:39,130] [main] Total files: 164 [testng] [2024-05-14 01:23:39,130] [main] Scan time: 21.73 s (132 ms/file) [testng] [2024-05-14 01:23:39,130] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-14 01:23:47,005] [pool-1-thread-1] Initializing /data/ome/C1.lsm: [testng] 01:23:47,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:23:47,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:47,010 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-14_01-23-47.log] [testng] 01:23:47,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c1fecd8 - End of configuration. [testng] [2024-05-14 01:23:47,049] [pool-1-thread-12] Initializing /data/openjpeg/Facade.bmp: [testng] 01:23:47,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:23:47,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:47,050 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-14_01-23-47.log] [testng] 01:23:47,051 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c7afbf8 - End of configuration. [testng] [2024-05-14 01:23:47,071] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:23:47,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:23:47,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:47,072 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-14_01-23-47.log] [testng] 01:23:47,073 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c71afd9 - End of configuration. [testng] [2024-05-14 01:23:47,112] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] 01:23:47,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:23:47,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:47,113 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-14_01-23-47.log] [testng] 01:23:47,113 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7df77b58 - End of configuration. [testng] [2024-05-14 01:23:47,128] [pool-1-thread-9] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] 01:23:47,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:23:47,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:47,129 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-14_01-23-47.log] [testng] 01:23:47,130 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cf371b4 - End of configuration. [testng] [2024-05-14 01:23:47,190] [pool-1-thread-8] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:23:47,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:23:47,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:47,191 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-14_01-23-47.log] [testng] 01:23:47,191 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bece206 - End of configuration. [testng] [2024-05-14 01:23:47,223] [pool-1-thread-7] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 01:23:47,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:23:47,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:47,224 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-14_01-23-47.log] [testng] 01:23:47,225 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50f353dd - End of configuration. [testng] [2024-05-14 01:23:47,416] [pool-1-thread-6] Initializing /data/openjpeg/Rome.ppm: [testng] 01:23:47,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:23:47,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:47,418 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-14_01-23-47.log] [testng] 01:23:47,418 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30d8c25f - End of configuration. [testng] [2024-05-14 01:23:47,431] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:23:47,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:23:47,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:47,432 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-14_01-23-47.log] [testng] 01:23:47,432 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a284a3a - End of configuration. [testng] [2024-05-14 01:23:47,465] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 01:23:47,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:23:47,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:47,467 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-14_01-23-47.log] [testng] 01:23:47,468 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ee457c6 - End of configuration. [testng] [2024-05-14 01:23:47,479] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 01:23:47,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:23:47,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:47,480 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-14_01-23-47.log] [testng] 01:23:47,480 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65d073d9 - End of configuration. [testng] [2024-05-14 01:23:47,526] [pool-1-thread-2] Initializing /data/sdub/sdub.pattern: [testng] 01:23:47,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:23:47,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:47,527 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-14_01-23-47.log] [testng] 01:23:47,527 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a9d53ed - End of configuration. [testng] [2024-05-14 01:23:49,860] [pool-1-thread-10] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-05-14 01:23:49,887] [pool-1-thread-4] Initializing /data/ome/654Atemp.stk: [testng] [2024-05-14 01:23:49,991] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-05-14 01:23:49,997] [pool-1-thread-5] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-05-14 01:23:50,037] [pool-1-thread-1] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-05-14 01:23:50,044] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-05-14 01:23:50,352] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-05-14 01:23:50,783] [pool-1-thread-9] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-05-14 01:23:50,804] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-05-14 01:23:50,812] [pool-1-thread-6] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-05-14 01:23:50,852] [pool-1-thread-1] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-05-14 01:23:50,884] [pool-1-thread-2] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-05-14 01:23:50,906] [pool-1-thread-7] Initializing /data/ome/worm.tiff: [testng] [2024-05-14 01:23:51,201] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-05-14 01:23:51,210] [pool-1-thread-11] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-05-14 01:23:51,472] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-05-14 01:23:51,481] [pool-1-thread-5] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-05-14 01:23:51,518] [pool-1-thread-2] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-05-14 01:23:52,401] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-05-14 01:23:52,517] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-05-14 01:23:52,562] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-05-14 01:23:52,847] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-05-14 01:23:52,955] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-05-14 01:23:53,102] [pool-1-thread-4] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-05-14 01:23:53,180] [pool-1-thread-11] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-05-14 01:23:53,227] [pool-1-thread-5] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-05-14 01:23:53,468] [pool-1-thread-6] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-05-14 01:23:53,563] [pool-1-thread-3] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-05-14 01:23:53,712] [pool-1-thread-5] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-05-14 01:23:53,763] [pool-1-thread-4] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-05-14 01:23:53,996] [pool-1-thread-11] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-05-14 01:23:54,068] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-05-14 01:23:54,152] [pool-1-thread-11] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-05-14 01:23:54,843] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-05-14 01:23:54,931] [pool-1-thread-12] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-05-14 01:23:55,040] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-05-14 01:23:55,098] [pool-1-thread-5] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-05-14 01:23:55,144] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-05-14 01:23:55,224] [pool-1-thread-10] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-05-14 01:23:55,303] [pool-1-thread-8] Initializing /data/ome/cb_1.r3d: [testng] [2024-05-14 01:23:55,520] [pool-1-thread-6] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-05-14 01:23:55,740] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-05-14 01:23:55,903] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-05-14 01:23:56,089] [pool-1-thread-8] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-05-14 01:23:56,149] [pool-1-thread-3] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-05-14 01:23:56,481] [pool-1-thread-1] Initializing /data/ome/embryo.lsm: [testng] [2024-05-14 01:23:56,723] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 2 minutes 18 seconds Finished: SUCCESS