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Started by upstream project "BIOFORMATS-test-repo" build number 380 originally caused by: Started by upstream project "Trigger" build number 402 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins15760958506014529057.sh + '[' samples = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_60092_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] 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] 00:48:49,743 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:48:49,744 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 00:48:49,744 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:48:49,745 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:48:49,746 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:48:49,746 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:48:49,746 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:48:49,746 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:48:49,747 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:48:49,748 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:48:49,748 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:48:49,748 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:48:49,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:48:49,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:48:49,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:48:49,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:48:49,939 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:48:49,939 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:48:49,939 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:48:49,940 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:48:49,940 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 00:48:49,940 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 00:48:49,941 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 194 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-16 00:48:49,949] [main] java.version = 17.0.2 [testng] 00:48:49,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:48:49,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:48:49,992 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-16_00-48-49.log] [testng] 00:48:49,994 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-16 00:48:49,996] [main] testng.directory = /data [testng] [2025-03-16 00:48:49,996] [main] testng.configDirectory = /config [testng] [2025-03-16 00:48:50,005] [main] testng.multiplier = 1.0 [testng] [2025-03-16 00:48:50,005] [main] testng.in-memory = false [testng] [2025-03-16 00:48:50,006] [main] testng.allow-missing = false [testng] [2025-03-16 00:48:50,006] [main] user.language = en [testng] [2025-03-16 00:48:50,006] [main] user.country = ${user.country} [testng] [2025-03-16 00:48:50,006] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-16 00:51:38,331] [main] ---------------------------------------- [testng] [2025-03-16 00:51:38,331] [main] Total files: 165 [testng] [2025-03-16 00:51:38,331] [main] Scan time: 168.325 s (1020 ms/file) [testng] [2025-03-16 00:51:38,332] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 60 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-16 00:57:28,251] [pool-1-thread-1] Initializing /data/ome/anusgfpzs.lsm: [testng] 00:57:28,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:57:28,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:28,253 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-16_00-57-28.log] [testng] 00:57:28,254 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c0ba4de - End of configuration. [testng] [2025-03-16 00:57:31,038] [pool-1-thread-12] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] 00:57:31,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:57:31,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:31,039 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-16_00-57-31.log] [testng] 00:57:31,040 |-INFO in ch.qos.logback.core.sift.SiftProcessor@117c216c - End of configuration. [testng] [2025-03-16 00:57:34,973] [pool-1-thread-11] Initializing /data/openjpeg/Facade.pnm: [testng] 00:57:34,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:57:34,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:34,974 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-16_00-57-34.log] [testng] 00:57:34,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b44256f - End of configuration. [testng] [2025-03-16 00:57:35,377] [pool-1-thread-10] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] 00:57:35,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:57:35,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:35,383 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-16_00-57-35.log] [testng] 00:57:35,383 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c1bf6dd - End of configuration. [testng] [2025-03-16 00:57:40,914] [pool-1-thread-9] Initializing /data/ome/C1midmusnorm.lsm: [testng] 00:57:40,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:57:40,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:40,915 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-16_00-57-40.log] [testng] 00:57:40,916 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a28f71e - End of configuration. [testng] [2025-03-16 00:57:43,344] [pool-1-thread-8] Initializing /data/openjpeg/thumb_facade.jpg: [testng] 00:57:43,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:57:43,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:43,346 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-16_00-57-43.log] [testng] 00:57:43,347 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4991492b - End of configuration. [testng] [2025-03-16 00:57:43,878] [pool-1-thread-7] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] 00:57:43,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:57:43,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:43,879 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-16_00-57-43.log] [testng] 00:57:43,879 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48868ad6 - End of configuration. [testng] [2025-03-16 00:57:44,311] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.ppm: [testng] 00:57:44,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:57:44,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:44,312 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-16_00-57-44.log] [testng] 00:57:44,312 |-INFO in ch.qos.logback.core.sift.SiftProcessor@190dd4a8 - End of configuration. [testng] [2025-03-16 00:57:44,824] [pool-1-thread-5] Initializing /data/ome/C1.lsm: [testng] 00:57:44,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:57:44,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:44,825 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-16_00-57-44.log] [testng] 00:57:44,825 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bfa7bd7 - End of configuration. [testng] [2025-03-16 00:57:47,233] [pool-1-thread-4] Initializing /data/ome/CHOBI_d3d.dv: [testng] 00:57:47,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:57:47,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:47,234 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-16_00-57-47.log] [testng] 00:57:47,234 |-INFO in ch.qos.logback.core.sift.SiftProcessor@424c6bc9 - End of configuration. [testng] [2025-03-16 00:57:47,924] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 00:57:47,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:57:47,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:47,925 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-16_00-57-47.log] [testng] 00:57:47,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36080fc3 - End of configuration. [testng] [2025-03-16 00:57:49,898] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 00:57:49,898 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:57:49,898 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:49,899 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-16_00-57-49.log] [testng] 00:57:49,899 |-INFO in ch.qos.logback.core.sift.SiftProcessor@442f9fdc - End of configuration. [testng] [2025-03-16 00:57:57,478] [pool-1-thread-6] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2025-03-16 00:58:03,571] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2025-03-16 00:58:04,384] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2025-03-16 00:58:05,899] [pool-1-thread-7] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2025-03-16 00:58:07,249] [pool-1-thread-4] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2025-03-16 00:58:16,930] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2025-03-16 00:58:22,079] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2025-03-16 00:58:22,934] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2025-03-16 00:58:27,793] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2025-03-16 00:58:28,295] [pool-1-thread-3] Initializing /data/ome/011B1_Morph.HTD: [testng] [2025-03-16 00:58:32,484] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2025-03-16 00:58:35,296] [pool-1-thread-5] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2025-03-16 00:58:38,178] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2025-03-16 00:58:42,174] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2025-03-16 00:58:48,607] [pool-1-thread-11] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2025-03-16 00:58:50,580] [pool-1-thread-2] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2025-03-16 00:58:54,055] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2025-03-16 00:59:01,673] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2025-03-16 00:59:04,717] [pool-1-thread-1] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2025-03-16 00:59:06,183] [pool-1-thread-5] Initializing /data/ome/654Atemp.stk: [testng] [2025-03-16 00:59:14,188] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2025-03-16 00:59:17,103] [pool-1-thread-7] Initializing /data/sdub/sdub.pattern: [testng] [2025-03-16 00:59:58,622] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2025-03-16 00:59:59,491] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2025-03-16 01:00:01,533] [pool-1-thread-9] Initializing /data/ome/Adultmidsection.lsm: [testng] [2025-03-16 01:00:14,757] [pool-1-thread-12] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2025-03-16 01:00:19,853] [pool-1-thread-2] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2025-03-16 01:00:26,631] [pool-1-thread-10] Initializing /data/ARFTest/ARFTest.arf: [testng] [2025-03-16 01:00:31,225] [pool-1-thread-4] Initializing /data/ome/embryo.lsm: [testng] [2025-03-16 01:00:39,198] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2025-03-16 01:00:47,541] [pool-1-thread-10] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2025-03-16 01:00:53,100] [pool-1-thread-9] Initializing /data/ome/cb_1.r3d: [testng] [2025-03-16 01:00:56,212] [pool-1-thread-12] Initializing /data/openjpeg/Rome.ppm: [testng] [2025-03-16 01:00:57,046] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2025-03-16 01:00:59,145] [pool-1-thread-11] Initializing /data/ome/worm.tiff: [testng] [2025-03-16 01:01:09,119] [pool-1-thread-8] Initializing /data/ome/tiffany.color.tiff: [testng] [2025-03-16 01:01:19,743] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2025-03-16 01:01:24,528] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2025-03-16 01:01:25,388] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2025-03-16 01:01:33,240] [pool-1-thread-12] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2025-03-16 01:01:38,750] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2025-03-16 01:01:39,569] [pool-1-thread-1] Initializing /data/openjpeg/Facade.bmp: [testng] [2025-03-16 01:01:45,005] [pool-1-thread-3] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2025-03-16 01:01:47,031] [pool-1-thread-10] Initializing /data/openjpeg/Rome.jp2: [testng] [2025-03-16 01:01:51,047] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2025-03-16 01:01:53,525] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2025-03-16 01:01:54,379] [pool-1-thread-9] Initializing /data/TAABA/TAABA.pattern: [testng] [2025-03-16 01:03:43,953] [pool-1-thread-1] Initializing /data/openjpeg/Rome.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3180, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 25 minutes 29 seconds Finished: SUCCESS