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Started by upstream project "BIOFORMATS-test-repo" build number 18 originally caused by: Started by upstream project "Trigger" build number 21 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/jenkins2758263086269729101.sh + '[' samples = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_2134_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] 00:23:40,999 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:23:41,001 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 00:23:41,001 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:23:41,002 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:23:41,003 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:23:41,003 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:23:41,004 |-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] 00:23:41,004 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:23:41,004 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:23:41,005 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:23:41,006 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:23:41,006 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:23:41,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:23:41,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:23:41,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:23:41,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:23:41,300 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:23:41,301 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:23:41,301 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:23:41,302 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:23:41,302 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 00:23:41,303 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 00:23:41,303 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 299 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-31 00:23:41,316] [main] java.version = 17.0.2 [testng] 00:23:41,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:23:41,322 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:41,387 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-31_00-23-41.log] [testng] 00:23:41,390 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-03-31 00:23:41,394] [main] testng.directory = /data [testng] [2024-03-31 00:23:41,395] [main] testng.configDirectory = /config [testng] [2024-03-31 00:23:41,406] [main] testng.multiplier = 1.0 [testng] [2024-03-31 00:23:41,407] [main] testng.in-memory = false [testng] [2024-03-31 00:23:41,408] [main] testng.allow-missing = false [testng] [2024-03-31 00:23:41,408] [main] user.language = en [testng] [2024-03-31 00:23:41,408] [main] user.country = ${user.country} [testng] [2024-03-31 00:23:41,408] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-31 00:24:03,819] [main] ---------------------------------------- [testng] [2024-03-31 00:24:03,819] [main] Total files: 164 [testng] [2024-03-31 00:24:03,819] [main] Scan time: 22.411 s (136 ms/file) [testng] [2024-03-31 00:24:03,819] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-31 00:24:13,897] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] 00:24:13,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:24:13,898 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:13,899 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-31_00-24-13.log] [testng] 00:24:13,900 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e917786 - End of configuration. [testng] [2024-03-31 00:24:13,947] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 00:24:13,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:24:13,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:13,948 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-31_00-24-13.log] [testng] 00:24:13,948 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dc8fb78 - End of configuration. [testng] [2024-03-31 00:24:13,999] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 00:24:13,999 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:24:13,999 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:14,000 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-31_00-24-14.log] [testng] 00:24:14,001 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43e3e7f5 - End of configuration. [testng] [2024-03-31 00:24:14,011] [pool-1-thread-10] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:24:14,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:24:14,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:14,015 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-31_00-24-14.log] [testng] 00:24:14,015 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c912598 - End of configuration. [testng] [2024-03-31 00:24:14,070] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 00:24:14,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:24:14,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:14,071 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-31_00-24-14.log] [testng] 00:24:14,071 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cfa7f6d - End of configuration. [testng] [2024-03-31 00:24:14,081] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 00:24:14,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:24:14,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:14,083 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-31_00-24-14.log] [testng] 00:24:14,083 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c174121 - End of configuration. [testng] [2024-03-31 00:24:14,100] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:24:14,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:24:14,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:14,102 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-31_00-24-14.log] [testng] 00:24:14,103 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3332d204 - End of configuration. [testng] [2024-03-31 00:24:14,178] [pool-1-thread-6] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 00:24:14,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:24:14,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:14,180 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-31_00-24-14.log] [testng] 00:24:14,181 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f8d7cc2 - End of configuration. [testng] [2024-03-31 00:24:14,313] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 00:24:14,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:24:14,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:14,314 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-31_00-24-14.log] [testng] 00:24:14,315 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fd87ef7 - End of configuration. [testng] [2024-03-31 00:24:14,323] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] 00:24:14,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:24:14,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:14,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-31_00-24-14.log] [testng] 00:24:14,326 |-INFO in ch.qos.logback.core.sift.SiftProcessor@282a07d2 - End of configuration. [testng] [2024-03-31 00:24:14,383] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 00:24:14,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:24:14,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:14,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-31_00-24-14.log] [testng] 00:24:14,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fbae551 - End of configuration. [testng] [2024-03-31 00:24:14,403] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 00:24:14,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:24:14,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:14,405 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-31_00-24-14.log] [testng] 00:24:14,406 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67f430e3 - End of configuration. [testng] [2024-03-31 00:24:15,948] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-03-31 00:24:16,190] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern: [testng] [2024-03-31 00:24:16,600] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-03-31 00:24:17,007] [pool-1-thread-9] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-03-31 00:24:17,876] [pool-1-thread-1] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-03-31 00:24:17,889] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-03-31 00:24:18,152] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-03-31 00:24:18,165] [pool-1-thread-7] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-03-31 00:24:18,252] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-03-31 00:24:18,376] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-03-31 00:24:18,457] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-03-31 00:24:18,574] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-03-31 00:24:18,585] [pool-1-thread-2] Initializing /data/ome/worm.tiff: [testng] [2024-03-31 00:24:18,871] [pool-1-thread-12] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-03-31 00:24:19,605] [pool-1-thread-10] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-03-31 00:24:20,155] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-03-31 00:24:20,355] [pool-1-thread-5] Initializing /data/ome/654Atemp.stk: [testng] [2024-03-31 00:24:20,682] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-03-31 00:24:20,916] [pool-1-thread-3] Initializing /data/ome/embryo.lsm: [testng] [2024-03-31 00:24:21,041] [pool-1-thread-9] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-03-31 00:24:21,187] [pool-1-thread-10] Initializing /data/ome/C1.lsm: [testng] [2024-03-31 00:24:21,255] [pool-1-thread-6] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-03-31 00:24:23,547] [pool-1-thread-7] Initializing /data/ome/cb_1.r3d: [testng] [2024-03-31 00:24:23,825] [pool-1-thread-10] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-03-31 00:24:23,998] [pool-1-thread-12] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-03-31 00:24:24,829] [pool-1-thread-3] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-03-31 00:24:24,899] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-03-31 00:24:24,991] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-03-31 00:24:25,195] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-03-31 00:24:25,261] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-03-31 00:24:25,491] [pool-1-thread-7] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-03-31 00:24:25,505] [pool-1-thread-4] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-03-31 00:24:25,526] [pool-1-thread-8] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-03-31 00:24:25,554] [pool-1-thread-2] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-03-31 00:24:25,583] [pool-1-thread-3] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-03-31 00:24:25,757] [pool-1-thread-5] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-03-31 00:24:25,814] [pool-1-thread-1] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-03-31 00:24:26,008] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-03-31 00:24:26,050] [pool-1-thread-1] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-03-31 00:24:26,112] [pool-1-thread-7] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-03-31 00:24:26,336] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-03-31 00:24:26,386] [pool-1-thread-2] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-03-31 00:24:26,413] [pool-1-thread-8] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-03-31 00:24:26,577] [pool-1-thread-5] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-03-31 00:24:26,832] [pool-1-thread-10] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-03-31 00:24:26,860] [pool-1-thread-3] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-03-31 00:24:27,046] [pool-1-thread-7] 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 46 seconds Finished: SUCCESS