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Started by upstream project "BIOFORMATS-test-repo" build number 43 originally caused by: Started by upstream project "Trigger" build number 50 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins12233362854087749446.sh + '[' samples = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_6071_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] 01:24:12,003 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:24:12,004 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:24:12,004 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:12,005 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:12,005 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:24:12,006 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:24:12,006 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:24:12,006 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:12,006 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:12,007 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:24:12,007 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:24:12,008 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:24:12,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:24:12,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:24:12,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:24:12,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:24:12,198 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:24:12,198 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:24:12,198 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:24:12,199 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:24:12,199 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:24:12,200 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:24:12,200 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 194 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-24 01:24:12,209] [main] java.version = 17.0.2 [testng] 01:24:12,212 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:24:12,212 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:12,252 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-24_01-24-12.log] [testng] 01:24:12,254 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-04-24 01:24:12,256] [main] testng.directory = /data [testng] [2024-04-24 01:24:12,256] [main] testng.configDirectory = /config [testng] [2024-04-24 01:24:12,264] [main] testng.multiplier = 1.0 [testng] [2024-04-24 01:24:12,265] [main] testng.in-memory = false [testng] [2024-04-24 01:24:12,266] [main] testng.allow-missing = false [testng] [2024-04-24 01:24:12,266] [main] user.language = en [testng] [2024-04-24 01:24:12,266] [main] user.country = ${user.country} [testng] [2024-04-24 01:24:12,266] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-24 01:24:32,036] [main] ---------------------------------------- [testng] [2024-04-24 01:24:32,037] [main] Total files: 164 [testng] [2024-04-24 01:24:32,037] [main] Scan time: 19.77 s (120 ms/file) [testng] [2024-04-24 01:24:32,037] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-24 01:24:41,943] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:24:41,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:24:41,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:41,945 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-24_01-24-41.log] [testng] 01:24:41,946 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74e3a573 - End of configuration. [testng] [2024-04-24 01:24:42,009] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 01:24:42,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:24:42,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,010 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-24_01-24-42.log] [testng] 01:24:42,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55b7c62c - End of configuration. [testng] [2024-04-24 01:24:42,063] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:24:42,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:24:42,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,065 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-24_01-24-42.log] [testng] 01:24:42,065 |-INFO in ch.qos.logback.core.sift.SiftProcessor@166a90ed - End of configuration. [testng] [2024-04-24 01:24:42,085] [pool-1-thread-10] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:24:42,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:24:42,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,087 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-24_01-24-42.log] [testng] 01:24:42,088 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a49a255 - End of configuration. [testng] [2024-04-24 01:24:42,182] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 01:24:42,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:24:42,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,183 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-24_01-24-42.log] [testng] 01:24:42,183 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41802fc1 - End of configuration. [testng] [2024-04-24 01:24:42,197] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:24:42,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:24:42,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,198 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-24_01-24-42.log] [testng] 01:24:42,199 |-INFO in ch.qos.logback.core.sift.SiftProcessor@594515a3 - End of configuration. [testng] [2024-04-24 01:24:42,215] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:24:42,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:24:42,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,217 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-24_01-24-42.log] [testng] 01:24:42,217 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35b457b7 - End of configuration. [testng] [2024-04-24 01:24:42,278] [pool-1-thread-6] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 01:24:42,279 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:24:42,279 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,281 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-24_01-24-42.log] [testng] 01:24:42,282 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56ee7015 - End of configuration. [testng] [2024-04-24 01:24:42,422] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 01:24:42,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:24:42,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,424 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-24_01-24-42.log] [testng] 01:24:42,425 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66688b - End of configuration. [testng] [2024-04-24 01:24:42,439] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] 01:24:42,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:24:42,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,441 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-24_01-24-42.log] [testng] 01:24:42,441 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19469044 - End of configuration. [testng] [2024-04-24 01:24:42,490] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 01:24:42,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:24:42,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,492 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-24_01-24-42.log] [testng] 01:24:42,492 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22ad1bf6 - End of configuration. [testng] [2024-04-24 01:24:42,513] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 01:24:42,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:24:42,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:42,515 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-24_01-24-42.log] [testng] 01:24:42,516 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4520f0e3 - End of configuration. [testng] [2024-04-24 01:24:44,863] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-04-24 01:24:44,871] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-04-24 01:24:44,878] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-04-24 01:24:44,891] [pool-1-thread-1] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-04-24 01:24:44,906] [pool-1-thread-7] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-04-24 01:24:45,135] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-04-24 01:24:45,142] [pool-1-thread-12] Initializing /data/sdub/sdub.pattern: [testng] [2024-04-24 01:24:45,611] [pool-1-thread-3] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-04-24 01:24:45,802] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-04-24 01:24:45,833] [pool-1-thread-2] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-04-24 01:24:46,076] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-04-24 01:24:46,084] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-04-24 01:24:46,319] [pool-1-thread-5] Initializing /data/ome/worm.tiff: [testng] [2024-04-24 01:24:46,380] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-04-24 01:24:46,652] [pool-1-thread-8] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-04-24 01:24:46,944] [pool-1-thread-6] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-04-24 01:24:47,080] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-04-24 01:24:47,161] [pool-1-thread-8] Initializing /data/ome/654Atemp.stk: [testng] [2024-04-24 01:24:47,535] [pool-1-thread-2] Initializing /data/ome/embryo.lsm: [testng] [2024-04-24 01:24:47,572] [pool-1-thread-4] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-04-24 01:24:47,881] [pool-1-thread-12] Initializing /data/ome/C1.lsm: [testng] [2024-04-24 01:24:48,211] [pool-1-thread-11] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-04-24 01:24:49,464] [pool-1-thread-7] Initializing /data/ome/cb_1.r3d: [testng] [2024-04-24 01:24:49,553] [pool-1-thread-3] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-04-24 01:24:49,624] [pool-1-thread-2] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-04-24 01:24:49,663] [pool-1-thread-6] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-04-24 01:24:50,354] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-04-24 01:24:50,447] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-04-24 01:24:50,749] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-04-24 01:24:50,795] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-04-24 01:24:50,878] [pool-1-thread-10] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-04-24 01:24:50,890] [pool-1-thread-5] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-04-24 01:24:51,126] [pool-1-thread-4] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-04-24 01:24:51,161] [pool-1-thread-8] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-04-24 01:24:51,269] [pool-1-thread-2] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-04-24 01:24:51,454] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-04-24 01:24:51,552] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-04-24 01:24:51,560] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-04-24 01:24:51,785] [pool-1-thread-10] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-04-24 01:24:51,856] [pool-1-thread-9] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-04-24 01:24:52,049] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-04-24 01:24:52,105] [pool-1-thread-8] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-04-24 01:24:52,166] [pool-1-thread-4] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-04-24 01:24:52,199] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-04-24 01:24:52,303] [pool-1-thread-7] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-04-24 01:24:52,376] [pool-1-thread-5] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-04-24 01:24:52,453] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJW.bmp: [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 16 seconds Finished: SUCCESS