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Started by upstream project "BIOFORMATS-test-repo" build number 260 originally caused by: Started by upstream project "Trigger" build number 284 originally caused by: Started by timer 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/jenkins8453786858734269412.sh + '[' samples = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_40986_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] 00:33:53,859 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:33:53,861 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 00:33:53,861 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:33:53,862 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:33:53,862 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:33:53,863 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:33:53,863 |-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] 00:33:53,863 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:33:53,863 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:33:53,864 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:33:53,864 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:33:53,865 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:33:54,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:33:54,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:33:54,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:33:54,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:33:54,077 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:33:54,078 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:33:54,078 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:33:54,078 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:33:54,078 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 00:33:54,079 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 00:33:54,079 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 216 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-19 00:33:54,089] [main] java.version = 11.0.16 [testng] 00:33:54,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:33:54,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:54,141 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-19_00-33-54.log] [testng] 00:33:54,144 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-19 00:33:54,147] [main] testng.directory = /data [testng] [2024-11-19 00:33:54,147] [main] testng.configDirectory = /config [testng] [2024-11-19 00:33:54,161] [main] testng.multiplier = 1.0 [testng] [2024-11-19 00:33:54,163] [main] testng.in-memory = false [testng] [2024-11-19 00:33:54,163] [main] testng.allow-missing = false [testng] [2024-11-19 00:33:54,163] [main] user.language = en [testng] [2024-11-19 00:33:54,163] [main] user.country = ${user.country} [testng] [2024-11-19 00:33:54,163] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-19 00:34:15,144] [main] ---------------------------------------- [testng] [2024-11-19 00:34:15,144] [main] Total files: 164 [testng] [2024-11-19 00:34:15,144] [main] Scan time: 20.981 s (127 ms/file) [testng] [2024-11-19 00:34:15,144] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-19 00:34:59,031] [pool-1-thread-1] Initializing /data/openjpeg/Rome.bmp: [testng] 00:34:59,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:34:59,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:59,034 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-19_00-34-59.log] [testng] 00:34:59,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@646189ba - End of configuration. [testng] [2024-11-19 00:34:59,165] [pool-1-thread-12] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:34:59,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:34:59,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:59,167 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-19_00-34-59.log] [testng] 00:34:59,167 |-INFO in ch.qos.logback.core.sift.SiftProcessor@744fc5a8 - End of configuration. [testng] [2024-11-19 00:35:00,138] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 00:35:00,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:35:00,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:00,139 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-19_00-35-00.log] [testng] 00:35:00,140 |-INFO in ch.qos.logback.core.sift.SiftProcessor@558fb959 - End of configuration. [testng] [2024-11-19 00:35:00,292] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] 00:35:00,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:35:00,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:00,293 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-19_00-35-00.log] [testng] 00:35:00,294 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19309ce9 - End of configuration. [testng] [2024-11-19 00:35:00,459] [pool-1-thread-9] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 00:35:00,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:35:00,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:00,460 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-19_00-35-00.log] [testng] 00:35:00,460 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2896de06 - End of configuration. [testng] [2024-11-19 00:35:01,820] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 00:35:01,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:35:01,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:01,821 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-19_00-35-01.log] [testng] 00:35:01,821 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40d289ef - End of configuration. [testng] [2024-11-19 00:35:02,461] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:35:02,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:35:02,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:02,462 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-19_00-35-02.log] [testng] 00:35:02,462 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67b916de - End of configuration. [testng] [2024-11-19 00:35:03,711] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 00:35:03,711 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:35:03,711 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:03,712 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-19_00-35-03.log] [testng] 00:35:03,712 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6585bc6d - End of configuration. [testng] [2024-11-19 00:35:03,914] [pool-1-thread-5] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 00:35:03,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:35:03,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:03,915 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-19_00-35-03.log] [testng] 00:35:03,916 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d58dd44 - End of configuration. [testng] [2024-11-19 00:35:05,368] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] 00:35:05,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:35:05,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:05,369 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-19_00-35-05.log] [testng] 00:35:05,370 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ab4916f - End of configuration. [testng] [2024-11-19 00:35:06,021] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 00:35:06,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:35:06,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:06,023 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-19_00-35-06.log] [testng] 00:35:06,023 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ee51c98 - End of configuration. [testng] [2024-11-19 00:35:06,357] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:35:06,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:35:06,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:06,358 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-19_00-35-06.log] [testng] 00:35:06,359 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3883ccfb - End of configuration. [testng] [2024-11-19 00:35:09,745] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-11-19 00:35:11,332] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2024-11-19 00:35:12,247] [pool-1-thread-3] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-11-19 00:35:34,936] [pool-1-thread-10] Initializing /data/ome/cb_1.r3d: [testng] [2024-11-19 00:35:35,200] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-11-19 00:35:35,672] [pool-1-thread-2] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-11-19 00:35:36,848] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-11-19 00:35:37,428] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-11-19 00:35:37,655] [pool-1-thread-7] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-11-19 00:35:39,170] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-11-19 00:35:39,914] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-11-19 00:35:40,425] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-11-19 00:35:40,515] [pool-1-thread-11] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-11-19 00:35:41,050] [pool-1-thread-6] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-11-19 00:35:42,020] [pool-1-thread-12] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-11-19 00:35:43,382] [pool-1-thread-2] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-11-19 00:35:43,595] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-11-19 00:35:44,081] [pool-1-thread-8] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-11-19 00:35:46,840] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-11-19 00:35:47,599] [pool-1-thread-7] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-11-19 00:35:48,646] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-11-19 00:35:48,836] [pool-1-thread-6] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-11-19 00:35:49,920] [pool-1-thread-1] Initializing /data/ome/654Atemp.stk: [testng] [2024-11-19 00:35:51,487] [pool-1-thread-9] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-11-19 00:35:52,289] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-11-19 00:35:52,422] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-11-19 00:35:52,567] [pool-1-thread-12] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-11-19 00:35:54,629] [pool-1-thread-2] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-11-19 00:35:56,488] [pool-1-thread-7] Initializing /data/ome/worm.tiff: [testng] [2024-11-19 00:35:58,447] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-11-19 00:35:58,847] [pool-1-thread-9] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-11-19 00:35:59,332] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-11-19 00:36:00,182] [pool-1-thread-8] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-11-19 00:36:00,878] [pool-1-thread-5] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-11-19 00:36:01,100] [pool-1-thread-2] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-11-19 00:36:03,356] [pool-1-thread-4] Initializing /data/ome/C1.lsm: [testng] [2024-11-19 00:36:03,985] [pool-1-thread-9] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-11-19 00:36:05,689] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-11-19 00:36:06,180] [pool-1-thread-8] Initializing /data/sdub/sdub.pattern: [testng] [2024-11-19 00:36:12,300] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-11-19 00:36:12,389] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-11-19 00:36:13,352] [pool-1-thread-5] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-11-19 00:36:14,110] [pool-1-thread-9] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-11-19 00:36:15,145] [pool-1-thread-1] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-11-19 00:36:15,455] [pool-1-thread-4] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-11-19 00:36:16,220] [pool-1-thread-7] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-11-19 00:36:18,076] [pool-1-thread-1] 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: 3 minutes 34 seconds Finished: SUCCESS