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Started by upstream project "BIOFORMATS-test-repo" build number 218 originally caused by: Started by upstream project "Trigger" build number 245 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/jenkins3441584778970533377.sh + '[' samples = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_34562_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] 01:51:24,140 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:51:24,142 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 01:51:24,142 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:51:24,144 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:51:24,144 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:51:24,145 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:51:24,145 |-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] 01:51:24,145 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:51:24,146 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:51:24,147 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:51:24,148 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:51:24,148 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:51:24,326 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:51:24,326 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:51:24,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:51:24,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:51:24,355 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:51:24,355 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:51:24,355 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:51:24,355 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:51:24,355 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 01:51:24,356 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 01:51:24,356 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 210 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-12 01:51:24,365] [main] java.version = 11.0.16 [testng] 01:51:24,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:51:24,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:51:24,410 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-12_01-51-24.log] [testng] 01:51:24,412 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-12 01:51:24,414] [main] testng.directory = /data [testng] [2024-10-12 01:51:24,414] [main] testng.configDirectory = /config [testng] [2024-10-12 01:51:24,424] [main] testng.multiplier = 1.0 [testng] [2024-10-12 01:51:24,425] [main] testng.in-memory = false [testng] [2024-10-12 01:51:24,425] [main] testng.allow-missing = false [testng] [2024-10-12 01:51:24,425] [main] user.language = en [testng] [2024-10-12 01:51:24,425] [main] user.country = ${user.country} [testng] [2024-10-12 01:51:24,425] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-12 01:53:32,685] [main] ---------------------------------------- [testng] [2024-10-12 01:53:32,685] [main] Total files: 164 [testng] [2024-10-12 01:53:32,685] [main] Scan time: 128.26 s (782 ms/file) [testng] [2024-10-12 01:53:32,685] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-12 01:56:19,928] [pool-1-thread-1] Initializing /data/openjpeg/Rome.bmp: [testng] 01:56:19,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:56:19,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:19,931 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-12_01-56-19.log] [testng] 01:56:19,931 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58b5a26f - End of configuration. [testng] [2024-10-12 01:56:20,268] [pool-1-thread-12] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:56:20,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:56:20,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:20,269 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-12_01-56-20.log] [testng] 01:56:20,270 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4718282f - End of configuration. [testng] [2024-10-12 01:56:21,916] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 01:56:21,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:56:21,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:21,917 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-12_01-56-21.log] [testng] 01:56:21,917 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3908e818 - End of configuration. [testng] [2024-10-12 01:56:22,025] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] 01:56:22,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:56:22,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:22,026 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-12_01-56-22.log] [testng] 01:56:22,027 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70bb634b - End of configuration. [testng] [2024-10-12 01:56:22,142] [pool-1-thread-9] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 01:56:22,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:56:22,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:22,143 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-12_01-56-22.log] [testng] 01:56:22,144 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cd19254 - End of configuration. [testng] [2024-10-12 01:56:24,130] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:56:24,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:56:24,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:24,131 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-12_01-56-24.log] [testng] 01:56:24,132 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e0513e7 - End of configuration. [testng] [2024-10-12 01:56:24,974] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:56:24,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:56:24,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:24,975 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-12_01-56-24.log] [testng] 01:56:24,976 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ddc88e2 - End of configuration. [testng] [2024-10-12 01:56:27,132] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 01:56:27,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:56:27,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:27,133 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-12_01-56-27.log] [testng] 01:56:27,134 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49e0772a - End of configuration. [testng] [2024-10-12 01:56:27,642] [pool-1-thread-5] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 01:56:27,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:56:27,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:27,644 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-12_01-56-27.log] [testng] 01:56:27,645 |-INFO in ch.qos.logback.core.sift.SiftProcessor@192bf027 - End of configuration. [testng] [2024-10-12 01:56:30,480] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] 01:56:30,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:56:30,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:30,481 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-12_01-56-30.log] [testng] 01:56:30,482 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6226c8c4 - End of configuration. [testng] [2024-10-12 01:56:31,664] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 01:56:31,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:56:31,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:31,665 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-12_01-56-31.log] [testng] 01:56:31,665 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ed0e726 - End of configuration. [testng] [2024-10-12 01:56:32,239] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 01:56:32,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:56:32,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:32,240 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-12_01-56-32.log] [testng] 01:56:32,240 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e9e38e5 - End of configuration. [testng] [2024-10-12 01:56:38,497] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-10-12 01:56:42,342] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2024-10-12 01:56:45,214] [pool-1-thread-10] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-10-12 01:57:34,813] [pool-1-thread-11] Initializing /data/ome/cb_1.r3d: [testng] [2024-10-12 01:57:35,592] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-10-12 01:57:36,584] [pool-1-thread-2] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-10-12 01:57:38,538] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-10-12 01:57:38,922] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-10-12 01:57:39,064] [pool-1-thread-7] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-10-12 01:57:40,314] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-10-12 01:57:41,429] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-10-12 01:57:42,414] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-10-12 01:57:42,804] [pool-1-thread-3] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-10-12 01:57:43,875] [pool-1-thread-8] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-10-12 01:57:44,896] [pool-1-thread-1] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-10-12 01:57:46,846] [pool-1-thread-2] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-10-12 01:57:47,235] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-10-12 01:57:47,403] [pool-1-thread-12] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-10-12 01:57:51,395] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-10-12 01:57:52,703] [pool-1-thread-2] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-10-12 01:57:54,201] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-10-12 01:57:54,786] [pool-1-thread-8] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-10-12 01:57:56,590] [pool-1-thread-11] Initializing /data/ome/654Atemp.stk: [testng] [2024-10-12 01:57:59,331] [pool-1-thread-4] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-10-12 01:57:59,895] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-10-12 01:57:59,981] [pool-1-thread-3] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-10-12 01:58:01,366] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-10-12 01:58:02,689] [pool-1-thread-7] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-10-12 01:58:04,135] [pool-1-thread-2] Initializing /data/ome/worm.tiff: [testng] [2024-10-12 01:58:06,485] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-10-12 01:58:06,806] [pool-1-thread-6] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-10-12 01:58:06,999] [pool-1-thread-12] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-10-12 01:58:08,348] [pool-1-thread-4] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-10-12 01:58:09,649] [pool-1-thread-7] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-10-12 01:58:11,214] [pool-1-thread-1] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-10-12 01:58:15,696] [pool-1-thread-6] Initializing /data/ome/C1.lsm: [testng] [2024-10-12 01:58:16,693] [pool-1-thread-11] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-10-12 01:58:16,805] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-10-12 01:58:17,403] [pool-1-thread-7] Initializing /data/sdub/sdub.pattern: [testng] [2024-10-12 01:58:29,815] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-10-12 01:58:30,090] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-10-12 01:58:32,331] [pool-1-thread-4] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-10-12 01:58:32,522] [pool-1-thread-12] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-10-12 01:58:33,497] [pool-1-thread-2] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-10-12 01:58:34,813] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-10-12 01:58:36,813] [pool-1-thread-6] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-10-12 01:58:38,651] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 9 minutes 53 seconds Finished: SUCCESS