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Started by upstream project "BIOFORMATS-test-repo" build number 78 originally caused by: Started by upstream project "Trigger" build number 86 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/jenkins5828270492158993169.sh + '[' samples = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_11811_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] 01:24:54,728 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:24:54,730 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:24:54,730 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:54,732 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:54,733 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:24:54,733 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:24:54,734 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:24:54,734 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:54,735 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:54,736 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:24:54,736 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:24:54,736 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:24:54,980 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:24:54,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:24:55,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:24:55,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:24:55,024 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:24:55,024 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:24:55,024 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:24:55,025 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:24:55,025 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:24:55,026 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:24:55,026 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 291 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-29 01:24:55,036] [main] java.version = 17.0.2 [testng] 01:24:55,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:24:55,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:55,095 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-29_01-24-55.log] [testng] 01:24:55,096 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-05-29 01:24:55,101] [main] testng.directory = /data [testng] [2024-05-29 01:24:55,102] [main] testng.configDirectory = /config [testng] [2024-05-29 01:24:55,116] [main] testng.multiplier = 1.0 [testng] [2024-05-29 01:24:55,118] [main] testng.in-memory = false [testng] [2024-05-29 01:24:55,118] [main] testng.allow-missing = false [testng] [2024-05-29 01:24:55,118] [main] user.language = en [testng] [2024-05-29 01:24:55,118] [main] user.country = ${user.country} [testng] [2024-05-29 01:24:55,118] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-29 01:25:14,783] [main] ---------------------------------------- [testng] [2024-05-29 01:25:14,783] [main] Total files: 164 [testng] [2024-05-29 01:25:14,783] [main] Scan time: 19.665 s (119 ms/file) [testng] [2024-05-29 01:25:14,783] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-29 01:25:22,911] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:25:22,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:25:22,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:22,912 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-29_01-25-22.log] [testng] 01:25:22,913 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b225ce3 - End of configuration. [testng] [2024-05-29 01:25:22,949] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 01:25:22,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:25:22,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:22,950 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-29_01-25-22.log] [testng] 01:25:22,950 |-INFO in ch.qos.logback.core.sift.SiftProcessor@160567df - End of configuration. [testng] [2024-05-29 01:25:22,987] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:25:22,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:25:22,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:22,989 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-29_01-25-22.log] [testng] 01:25:22,989 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dc22be - End of configuration. [testng] [2024-05-29 01:25:22,997] [pool-1-thread-10] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:25:22,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:25:22,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:22,998 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-29_01-25-22.log] [testng] 01:25:22,999 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15832c43 - End of configuration. [testng] [2024-05-29 01:25:23,049] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 01:25:23,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:25:23,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:23,051 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-29_01-25-23.log] [testng] 01:25:23,051 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c912598 - End of configuration. [testng] [2024-05-29 01:25:23,063] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:25:23,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:25:23,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:23,064 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-29_01-25-23.log] [testng] 01:25:23,065 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70b58ee2 - End of configuration. [testng] [2024-05-29 01:25:23,093] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:25:23,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:25:23,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:23,094 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-29_01-25-23.log] [testng] 01:25:23,095 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5006bddf - End of configuration. [testng] [2024-05-29 01:25:23,134] [pool-1-thread-6] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 01:25:23,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:25:23,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:23,136 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-29_01-25-23.log] [testng] 01:25:23,136 |-INFO in ch.qos.logback.core.sift.SiftProcessor@580346cc - End of configuration. [testng] [2024-05-29 01:25:23,240] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 01:25:23,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:25:23,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:23,241 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-29_01-25-23.log] [testng] 01:25:23,242 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38a4f0ac - End of configuration. [testng] [2024-05-29 01:25:23,250] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] 01:25:23,250 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:25:23,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:23,251 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-29_01-25-23.log] [testng] 01:25:23,252 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ad31aab - End of configuration. [testng] [2024-05-29 01:25:23,290] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 01:25:23,290 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:25:23,290 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:23,291 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-29_01-25-23.log] [testng] 01:25:23,291 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17493967 - End of configuration. [testng] [2024-05-29 01:25:23,304] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 01:25:23,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:25:23,305 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:23,305 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-29_01-25-23.log] [testng] 01:25:23,306 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fd87ef7 - End of configuration. [testng] [2024-05-29 01:25:25,093] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-05-29 01:25:25,099] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-05-29 01:25:25,105] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-05-29 01:25:25,112] [pool-1-thread-4] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-05-29 01:25:25,122] [pool-1-thread-1] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-05-29 01:25:25,304] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-05-29 01:25:25,310] [pool-1-thread-7] Initializing /data/sdub/sdub.pattern: [testng] [2024-05-29 01:25:25,696] [pool-1-thread-3] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-05-29 01:25:25,813] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-05-29 01:25:25,864] [pool-1-thread-9] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-05-29 01:25:25,957] [pool-1-thread-4] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-05-29 01:25:26,048] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-05-29 01:25:26,308] [pool-1-thread-5] Initializing /data/ome/worm.tiff: [testng] [2024-05-29 01:25:26,359] [pool-1-thread-11] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-05-29 01:25:26,366] [pool-1-thread-12] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-05-29 01:25:26,691] [pool-1-thread-8] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-05-29 01:25:26,756] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-05-29 01:25:26,889] [pool-1-thread-11] Initializing /data/ome/654Atemp.stk: [testng] [2024-05-29 01:25:27,140] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2024-05-29 01:25:27,571] [pool-1-thread-9] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-05-29 01:25:27,628] [pool-1-thread-7] Initializing /data/ome/C1.lsm: [testng] [2024-05-29 01:25:27,951] [pool-1-thread-1] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-05-29 01:25:28,773] [pool-1-thread-8] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-05-29 01:25:28,815] [pool-1-thread-6] Initializing /data/ome/cb_1.r3d: [testng] [2024-05-29 01:25:28,967] [pool-1-thread-12] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-05-29 01:25:29,611] [pool-1-thread-7] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-05-29 01:25:29,703] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-05-29 01:25:29,721] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-05-29 01:25:29,942] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-05-29 01:25:30,007] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-05-29 01:25:30,046] [pool-1-thread-10] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-05-29 01:25:30,077] [pool-1-thread-9] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-05-29 01:25:30,119] [pool-1-thread-2] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-05-29 01:25:30,157] [pool-1-thread-11] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-05-29 01:25:30,379] [pool-1-thread-6] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-05-29 01:25:30,397] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-05-29 01:25:30,408] [pool-1-thread-7] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-05-29 01:25:30,416] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-05-29 01:25:30,492] [pool-1-thread-8] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-05-29 01:25:30,622] [pool-1-thread-7] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-05-29 01:25:30,689] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-05-29 01:25:30,773] [pool-1-thread-2] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-05-29 01:25:30,778] [pool-1-thread-11] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-05-29 01:25:30,859] [pool-1-thread-6] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-05-29 01:25:31,032] [pool-1-thread-7] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-05-29 01:25:31,038] [pool-1-thread-10] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-05-29 01:25:31,102] [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 5 seconds Finished: SUCCESS