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Started by upstream project "BIOFORMATS-test-repo" build number 206 originally caused by: Started by upstream project "Trigger" build number 232 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/jenkins8869777035797298361.sh + '[' samples = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_32646_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] 01:29:26,963 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:29:26,966 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:29:26,966 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:29:26,968 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:29:26,969 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:29:26,969 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:29:26,970 |-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] 01:29:26,970 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:29:26,970 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:29:26,971 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:29:26,972 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:29:26,972 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:29:27,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:29:27,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:29:27,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:29:27,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:29:27,206 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:29:27,207 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:29:27,207 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:29:27,207 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:29:27,207 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:29:27,208 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:29:27,208 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 238 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-01 01:29:27,219] [main] java.version = 11.0.16 [testng] 01:29:27,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:29:27,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:29:27,274 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-01_01-29-27.log] [testng] 01:29:27,276 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-10-01 01:29:27,278] [main] testng.directory = /data [testng] [2024-10-01 01:29:27,278] [main] testng.configDirectory = /config [testng] [2024-10-01 01:29:27,289] [main] testng.multiplier = 1.0 [testng] [2024-10-01 01:29:27,291] [main] testng.in-memory = false [testng] [2024-10-01 01:29:27,291] [main] testng.allow-missing = false [testng] [2024-10-01 01:29:27,291] [main] user.language = en [testng] [2024-10-01 01:29:27,291] [main] user.country = ${user.country} [testng] [2024-10-01 01:29:27,291] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-01 01:29:50,664] [main] ---------------------------------------- [testng] [2024-10-01 01:29:50,664] [main] Total files: 164 [testng] [2024-10-01 01:29:50,665] [main] Scan time: 23.373 s (142 ms/file) [testng] [2024-10-01 01:29:50,665] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-01 01:30:22,630] [pool-1-thread-1] Initializing /data/openjpeg/Rome.ppm: [testng] 01:30:22,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:30:22,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:30:22,634 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-01_01-30-22.log] [testng] 01:30:22,634 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59bc925f - End of configuration. [testng] [2024-10-01 01:30:22,687] [pool-1-thread-12] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 01:30:22,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:30:22,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:30:22,688 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-01_01-30-22.log] [testng] 01:30:22,689 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47f3d9c0 - End of configuration. [testng] [2024-10-01 01:30:23,251] [pool-1-thread-11] Initializing /data/openjpeg/Rome.jp2: [testng] 01:30:23,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:30:23,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:30:23,252 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-01_01-30-23.log] [testng] 01:30:23,253 |-INFO in ch.qos.logback.core.sift.SiftProcessor@450a18d5 - End of configuration. [testng] [2024-10-01 01:30:23,448] [pool-1-thread-10] Initializing /data/openjpeg/Rome.bmp: [testng] 01:30:23,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:30:23,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:30:23,449 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-01_01-30-23.log] [testng] 01:30:23,449 |-INFO in ch.qos.logback.core.sift.SiftProcessor@274a5a38 - End of configuration. [testng] [2024-10-01 01:30:23,493] [pool-1-thread-9] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] 01:30:23,493 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:30:23,493 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:30:23,494 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-01_01-30-23.log] [testng] 01:30:23,494 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3629b908 - End of configuration. [testng] [2024-10-01 01:30:24,112] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.bmp: [testng] 01:30:24,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:30:24,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:30:24,113 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-01_01-30-24.log] [testng] 01:30:24,114 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45b9f091 - End of configuration. [testng] [2024-10-01 01:30:24,158] [pool-1-thread-7] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] 01:30:24,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:30:24,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:30:24,159 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-01_01-30-24.log] [testng] 01:30:24,160 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29658e9f - End of configuration. [testng] [2024-10-01 01:30:24,826] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.ppm: [testng] 01:30:24,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:30:24,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:30:24,828 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-01_01-30-24.log] [testng] 01:30:24,828 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68d21947 - End of configuration. [testng] [2024-10-01 01:30:24,882] [pool-1-thread-5] Initializing /data/ome/arwen0205_raw00201.pic: [testng] 01:30:24,882 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:30:24,882 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:30:24,883 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-01_01-30-24.log] [testng] 01:30:24,883 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ff2078 - End of configuration. [testng] [2024-10-01 01:30:25,149] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 01:30:25,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:30:25,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:30:25,150 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-01_01-30-25.log] [testng] 01:30:25,150 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a866d9d - End of configuration. [testng] [2024-10-01 01:30:25,212] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 01:30:25,212 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:30:25,212 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:30:25,213 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-01_01-30-25.log] [testng] 01:30:25,213 |-INFO in ch.qos.logback.core.sift.SiftProcessor@628228e1 - End of configuration. [testng] [2024-10-01 01:30:25,331] [pool-1-thread-2] Initializing /data/openjpeg/Facade.bmp: [testng] 01:30:25,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:30:25,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:30:25,333 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-01_01-30-25.log] [testng] 01:30:25,334 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5127b3af - End of configuration. [testng] [2024-10-01 01:30:27,923] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-10-01 01:30:28,452] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2024-10-01 01:30:28,890] [pool-1-thread-4] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-10-01 01:30:29,079] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-10-01 01:30:29,676] [pool-1-thread-3] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-10-01 01:30:30,184] [pool-1-thread-2] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-10-01 01:30:31,203] [pool-1-thread-8] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-10-01 01:30:31,872] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-10-01 01:30:32,080] [pool-1-thread-3] Initializing /data/sdub/sdub.pattern: [testng] [2024-10-01 01:30:37,082] [pool-1-thread-11] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-10-01 01:30:37,853] [pool-1-thread-4] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-10-01 01:30:38,623] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-10-01 01:30:38,690] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-10-01 01:30:39,045] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-10-01 01:30:39,952] [pool-1-thread-9] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-10-01 01:30:40,562] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-10-01 01:30:40,630] [pool-1-thread-10] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-10-01 01:30:41,433] [pool-1-thread-2] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-10-01 01:30:41,861] [pool-1-thread-11] Initializing /data/ome/worm.tiff: [testng] [2024-10-01 01:30:43,018] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-10-01 01:30:43,564] [pool-1-thread-1] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-10-01 01:30:43,834] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-10-01 01:30:44,336] [pool-1-thread-2] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-10-01 01:30:55,770] [pool-1-thread-4] Initializing /data/ome/C1.lsm: [testng] [2024-10-01 01:30:56,188] [pool-1-thread-5] Initializing /data/ome/654Atemp.stk: [testng] [2024-10-01 01:30:56,965] [pool-1-thread-7] Initializing /data/ome/cb_1.r3d: [testng] [2024-10-01 01:30:57,758] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-10-01 01:30:58,911] [pool-1-thread-7] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-10-01 01:30:59,438] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-10-01 01:30:59,974] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-10-01 01:31:00,175] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-10-01 01:31:00,755] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-10-01 01:31:00,872] [pool-1-thread-4] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-10-01 01:31:01,641] [pool-1-thread-1] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-10-01 01:31:02,842] [pool-1-thread-9] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-10-01 01:31:03,252] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-10-01 01:31:03,665] [pool-1-thread-6] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-10-01 01:31:07,620] [pool-1-thread-7] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-10-01 01:31:08,319] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-10-01 01:31:08,740] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-10-01 01:31:09,235] [pool-1-thread-4] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-10-01 01:31:09,643] [pool-1-thread-12] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-10-01 01:31:10,410] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-10-01 01:31:10,660] [pool-1-thread-11] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-10-01 01:31:11,427] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-10-01 01:31:12,421] [pool-1-thread-1] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-10-01 01:31:13,756] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.ppm: [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 13 seconds Finished: SUCCESS