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Started by upstream project "BIOFORMATS-test-repo" build number 83 originally caused by: Started by upstream project "Trigger" build number 93 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins13428484269251092131.sh + '[' samples = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_12631_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] 01:25:02,148 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:25:02,149 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:25:02,149 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:25:02,150 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:25:02,151 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:25:02,151 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:25:02,151 |-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] 01:25:02,151 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:25:02,152 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:25:02,152 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:25:02,153 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:25:02,153 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:25:02,327 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:25:02,327 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:25:02,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:25:02,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:25:02,354 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:25:02,354 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:25:02,355 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:25:02,355 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:25:02,355 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:25:02,356 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:25:02,356 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 204 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-05 01:25:02,365] [main] java.version = 17.0.2 [testng] 01:25:02,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:25:02,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:02,407 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-05_01-25-02.log] [testng] 01:25:02,409 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-05 01:25:02,410] [main] testng.directory = /data [testng] [2024-06-05 01:25:02,411] [main] testng.configDirectory = /config [testng] [2024-06-05 01:25:02,419] [main] testng.multiplier = 1.0 [testng] [2024-06-05 01:25:02,420] [main] testng.in-memory = false [testng] [2024-06-05 01:25:02,420] [main] testng.allow-missing = false [testng] [2024-06-05 01:25:02,420] [main] user.language = en [testng] [2024-06-05 01:25:02,420] [main] user.country = ${user.country} [testng] [2024-06-05 01:25:02,420] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-05 01:25:20,864] [main] ---------------------------------------- [testng] [2024-06-05 01:25:20,865] [main] Total files: 164 [testng] [2024-06-05 01:25:20,865] [main] Scan time: 18.444 s (112 ms/file) [testng] [2024-06-05 01:25:20,865] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-05 01:25:29,091] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:25:29,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:25:29,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:29,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-05_01-25-29.log] [testng] 01:25:29,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e6e2388 - End of configuration. [testng] [2024-06-05 01:25:29,138] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 01:25:29,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:25:29,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:29,140 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-05_01-25-29.log] [testng] 01:25:29,140 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20634cc8 - End of configuration. [testng] [2024-06-05 01:25:29,180] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:25:29,180 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:25:29,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:29,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-05_01-25-29.log] [testng] 01:25:29,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@160567df - End of configuration. [testng] [2024-06-05 01:25:29,197] [pool-1-thread-10] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:25:29,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:25:29,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:29,198 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-05_01-25-29.log] [testng] 01:25:29,199 |-INFO in ch.qos.logback.core.sift.SiftProcessor@408cc8ce - End of configuration. [testng] [2024-06-05 01:25:29,226] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 01:25:29,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:25:29,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:29,228 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-05_01-25-29.log] [testng] 01:25:29,228 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63cd54bd - End of configuration. [testng] [2024-06-05 01:25:29,237] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:25:29,237 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:25:29,237 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:29,238 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-05_01-25-29.log] [testng] 01:25:29,238 |-INFO in ch.qos.logback.core.sift.SiftProcessor@146325c5 - End of configuration. [testng] [2024-06-05 01:25:29,249] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:25:29,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:25:29,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:29,250 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-05_01-25-29.log] [testng] 01:25:29,250 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3eead53f - End of configuration. [testng] [2024-06-05 01:25:29,279] [pool-1-thread-6] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 01:25:29,279 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:25:29,279 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:29,280 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-05_01-25-29.log] [testng] 01:25:29,280 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7038b55 - End of configuration. [testng] [2024-06-05 01:25:29,360] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 01:25:29,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:25:29,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:29,361 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-05_01-25-29.log] [testng] 01:25:29,361 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5cdedf76 - End of configuration. [testng] [2024-06-05 01:25:29,371] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] 01:25:29,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:25:29,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:29,372 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-05_01-25-29.log] [testng] 01:25:29,372 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36762f40 - End of configuration. [testng] [2024-06-05 01:25:29,417] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 01:25:29,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:25:29,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:29,418 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-05_01-25-29.log] [testng] 01:25:29,419 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ad31aab - End of configuration. [testng] [2024-06-05 01:25:29,437] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 01:25:29,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:25:29,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:29,439 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-05_01-25-29.log] [testng] 01:25:29,439 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17493967 - End of configuration. [testng] [2024-06-05 01:25:31,528] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-06-05 01:25:31,536] [pool-1-thread-3] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-06-05 01:25:31,564] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-06-05 01:25:31,571] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-06-05 01:25:31,578] [pool-1-thread-1] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-06-05 01:25:31,589] [pool-1-thread-4] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-06-05 01:25:31,765] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-06-05 01:25:31,771] [pool-1-thread-7] Initializing /data/sdub/sdub.pattern: [testng] [2024-06-05 01:25:32,243] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-06-05 01:25:32,250] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-06-05 01:25:32,257] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-06-05 01:25:32,265] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-06-05 01:25:32,564] [pool-1-thread-9] Initializing /data/ome/worm.tiff: [testng] [2024-06-05 01:25:32,626] [pool-1-thread-12] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-06-05 01:25:32,977] [pool-1-thread-5] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-06-05 01:25:32,983] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-06-05 01:25:33,198] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-06-05 01:25:33,346] [pool-1-thread-5] Initializing /data/ome/654Atemp.stk: [testng] [2024-06-05 01:25:33,530] [pool-1-thread-1] Initializing /data/ome/embryo.lsm: [testng] [2024-06-05 01:25:33,567] [pool-1-thread-6] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-06-05 01:25:33,693] [pool-1-thread-7] Initializing /data/ome/C1.lsm: [testng] [2024-06-05 01:25:33,929] [pool-1-thread-3] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-06-05 01:25:34,786] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] [2024-06-05 01:25:34,877] [pool-1-thread-11] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-06-05 01:25:34,963] [pool-1-thread-1] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-06-05 01:25:35,481] [pool-1-thread-7] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-06-05 01:25:35,515] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-06-05 01:25:35,598] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-06-05 01:25:35,789] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-06-05 01:25:35,810] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-06-05 01:25:35,892] [pool-1-thread-2] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-06-05 01:25:35,957] [pool-1-thread-7] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-06-05 01:25:36,111] [pool-1-thread-4] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-06-05 01:25:36,150] [pool-1-thread-6] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-06-05 01:25:36,172] [pool-1-thread-5] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-06-05 01:25:36,216] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-06-05 01:25:36,273] [pool-1-thread-2] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-06-05 01:25:36,467] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-06-05 01:25:36,544] [pool-1-thread-11] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-06-05 01:25:36,660] [pool-1-thread-6] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-06-05 01:25:36,761] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-06-05 01:25:36,824] [pool-1-thread-9] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-06-05 01:25:36,836] [pool-1-thread-4] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-06-05 01:25:36,950] [pool-1-thread-10] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-06-05 01:25:37,046] [pool-1-thread-7] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-06-05 01:25:37,081] [pool-1-thread-8] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-06-05 01:25:37,127] [pool-1-thread-6] 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 34 seconds Finished: SUCCESS