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Started by upstream project "BIOFORMATS-test-repo" build number 71 originally caused by: Started by upstream project "Trigger" build number 79 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/jenkins8379855304290700217.sh + '[' samples = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_10663_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] 03:54:46,845 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:54:46,847 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 03:54:46,847 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:54:46,848 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:54:46,849 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:54:46,849 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:54:46,849 |-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] 03:54:46,849 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:54:46,850 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:54:46,851 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:54:46,851 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:54:46,852 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:54:47,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:54:47,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:54:47,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:54:47,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:54:47,159 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:54:47,159 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:54:47,159 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:54:47,159 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:54:47,160 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 03:54:47,160 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 03:54:47,160 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 310 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-22 03:54:47,171] [main] java.version = 17.0.2 [testng] 03:54:47,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:54:47,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:47,226 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-22_03-54-47.log] [testng] 03:54:47,228 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-05-22 03:54:47,232] [main] testng.directory = /data [testng] [2024-05-22 03:54:47,232] [main] testng.configDirectory = /config [testng] [2024-05-22 03:54:47,246] [main] testng.multiplier = 1.0 [testng] [2024-05-22 03:54:47,248] [main] testng.in-memory = false [testng] [2024-05-22 03:54:47,248] [main] testng.allow-missing = false [testng] [2024-05-22 03:54:47,248] [main] user.language = en [testng] [2024-05-22 03:54:47,248] [main] user.country = ${user.country} [testng] [2024-05-22 03:54:47,249] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-22 03:55:06,470] [main] ---------------------------------------- [testng] [2024-05-22 03:55:06,470] [main] Total files: 164 [testng] [2024-05-22 03:55:06,470] [main] Scan time: 19.221 s (117 ms/file) [testng] [2024-05-22 03:55:06,471] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-22 03:55:15,170] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] 03:55:15,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:55:15,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:55:15,173 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-22_03-55-15.log] [testng] 03:55:15,173 |-INFO in ch.qos.logback.core.sift.SiftProcessor@349a8c26 - End of configuration. [testng] [2024-05-22 03:55:15,221] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 03:55:15,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:55:15,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:55:15,223 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-22_03-55-15.log] [testng] 03:55:15,223 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38b75c39 - End of configuration. [testng] [2024-05-22 03:55:15,272] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 03:55:15,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:55:15,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:55:15,273 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-22_03-55-15.log] [testng] 03:55:15,273 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2179e7cf - End of configuration. [testng] [2024-05-22 03:55:15,281] [pool-1-thread-10] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 03:55:15,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:55:15,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:55:15,283 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-22_03-55-15.log] [testng] 03:55:15,283 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20634cc8 - End of configuration. [testng] [2024-05-22 03:55:15,330] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 03:55:15,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:55:15,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:55:15,331 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-22_03-55-15.log] [testng] 03:55:15,332 |-INFO in ch.qos.logback.core.sift.SiftProcessor@160567df - End of configuration. [testng] [2024-05-22 03:55:15,344] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 03:55:15,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:55:15,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:55:15,345 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-22_03-55-15.log] [testng] 03:55:15,346 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dc22be - End of configuration. [testng] [2024-05-22 03:55:15,361] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 03:55:15,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:55:15,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:55:15,362 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-22_03-55-15.log] [testng] 03:55:15,363 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15832c43 - End of configuration. [testng] [2024-05-22 03:55:15,403] [pool-1-thread-6] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 03:55:15,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:55:15,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:55:15,404 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-22_03-55-15.log] [testng] 03:55:15,405 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10a9e7c4 - End of configuration. [testng] [2024-05-22 03:55:15,489] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 03:55:15,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:55:15,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:55:15,490 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-22_03-55-15.log] [testng] 03:55:15,490 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12dbf165 - End of configuration. [testng] [2024-05-22 03:55:15,501] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] 03:55:15,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:55:15,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:55:15,503 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-22_03-55-15.log] [testng] 03:55:15,504 |-INFO in ch.qos.logback.core.sift.SiftProcessor@408cc8ce - End of configuration. [testng] [2024-05-22 03:55:15,567] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 03:55:15,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:55:15,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:55:15,568 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-22_03-55-15.log] [testng] 03:55:15,568 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6016ef06 - End of configuration. [testng] [2024-05-22 03:55:15,590] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 03:55:15,590 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:55:15,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:55:15,592 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-22_03-55-15.log] [testng] 03:55:15,592 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36762f40 - End of configuration. [testng] [2024-05-22 03:55:17,627] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-05-22 03:55:17,635] [pool-1-thread-2] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-05-22 03:55:17,669] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-05-22 03:55:17,681] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-05-22 03:55:17,693] [pool-1-thread-7] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-05-22 03:55:17,707] [pool-1-thread-12] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-05-22 03:55:17,922] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-05-22 03:55:17,930] [pool-1-thread-3] Initializing /data/sdub/sdub.pattern: [testng] [2024-05-22 03:55:18,386] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-05-22 03:55:18,393] [pool-1-thread-11] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-05-22 03:55:18,487] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-05-22 03:55:18,493] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-05-22 03:55:18,564] [pool-1-thread-7] Initializing /data/ome/worm.tiff: [testng] [2024-05-22 03:55:18,616] [pool-1-thread-8] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-05-22 03:55:18,859] [pool-1-thread-4] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-05-22 03:55:18,867] [pool-1-thread-10] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-05-22 03:55:19,272] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-05-22 03:55:19,280] [pool-1-thread-4] Initializing /data/ome/654Atemp.stk: [testng] [2024-05-22 03:55:19,528] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2024-05-22 03:55:19,683] [pool-1-thread-11] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-05-22 03:55:19,719] [pool-1-thread-3] Initializing /data/ome/C1.lsm: [testng] [2024-05-22 03:55:19,759] [pool-1-thread-2] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-05-22 03:55:20,691] [pool-1-thread-10] Initializing /data/ome/cb_1.r3d: [testng] [2024-05-22 03:55:20,797] [pool-1-thread-8] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-05-22 03:55:20,876] [pool-1-thread-12] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-05-22 03:55:21,544] [pool-1-thread-6] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-05-22 03:55:21,577] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-05-22 03:55:21,653] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-05-22 03:55:21,860] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-05-22 03:55:21,994] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-05-22 03:55:22,000] [pool-1-thread-1] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-05-22 03:55:22,048] [pool-1-thread-4] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-05-22 03:55:22,273] [pool-1-thread-10] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-05-22 03:55:22,294] [pool-1-thread-6] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-05-22 03:55:22,328] [pool-1-thread-11] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-05-22 03:55:22,348] [pool-1-thread-7] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-05-22 03:55:22,370] [pool-1-thread-8] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-05-22 03:55:22,445] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-05-22 03:55:22,458] [pool-1-thread-1] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-05-22 03:55:22,502] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-05-22 03:55:22,551] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-05-22 03:55:22,739] [pool-1-thread-11] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-05-22 03:55:22,780] [pool-1-thread-10] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-05-22 03:55:22,821] [pool-1-thread-7] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-05-22 03:55:22,919] [pool-1-thread-4] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-05-22 03:55:22,924] [pool-1-thread-5] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-05-22 03:55:22,938] [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 4 seconds Finished: SUCCESS