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Started by upstream project "BIOFORMATS-test-repo" build number 123 originally caused by: Started by upstream project "Trigger" build number 140 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/jenkins8799692907606519682.sh + '[' samples = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_19191_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] 01:24:17,433 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:24:17,434 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:24:17,434 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:17,435 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:17,435 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:24:17,436 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:24:17,436 |-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] 01:24:17,436 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:17,436 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:17,437 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:24:17,437 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:24:17,438 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:24:17,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:24:17,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:24:17,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:24:17,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:24:17,638 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:24:17,638 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:24:17,638 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:24:17,639 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:24:17,639 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:24:17,640 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:24:17,640 |-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] [2024-07-17 01:24:17,650] [main] java.version = 17.0.2 [testng] 01:24:17,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:24:17,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:17,698 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-17_01-24-17.log] [testng] 01:24:17,699 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-07-17 01:24:17,702] [main] testng.directory = /data [testng] [2024-07-17 01:24:17,702] [main] testng.configDirectory = /config [testng] [2024-07-17 01:24:17,711] [main] testng.multiplier = 1.0 [testng] [2024-07-17 01:24:17,712] [main] testng.in-memory = false [testng] [2024-07-17 01:24:17,712] [main] testng.allow-missing = false [testng] [2024-07-17 01:24:17,712] [main] user.language = en [testng] [2024-07-17 01:24:17,713] [main] user.country = ${user.country} [testng] [2024-07-17 01:24:17,713] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-17 01:24:37,373] [main] ---------------------------------------- [testng] [2024-07-17 01:24:37,373] [main] Total files: 164 [testng] [2024-07-17 01:24:37,373] [main] Scan time: 19.66 s (119 ms/file) [testng] [2024-07-17 01:24:37,373] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-17 01:24:45,608] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:24:45,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:24:45,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:45,610 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-17_01-24-45.log] [testng] 01:24:45,610 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41179e5a - End of configuration. [testng] [2024-07-17 01:24:45,653] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 01:24:45,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:24:45,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:45,654 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-17_01-24-45.log] [testng] 01:24:45,655 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d1bfe7f - End of configuration. [testng] [2024-07-17 01:24:45,688] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:24:45,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:24:45,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:45,689 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-17_01-24-45.log] [testng] 01:24:45,690 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72538368 - End of configuration. [testng] [2024-07-17 01:24:45,697] [pool-1-thread-10] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:24:45,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:24:45,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:45,701 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-17_01-24-45.log] [testng] 01:24:45,702 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75fc4baf - End of configuration. [testng] [2024-07-17 01:24:45,742] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 01:24:45,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:24:45,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:45,743 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-17_01-24-45.log] [testng] 01:24:45,743 |-INFO in ch.qos.logback.core.sift.SiftProcessor@166a90ed - End of configuration. [testng] [2024-07-17 01:24:45,754] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:24:45,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:24:45,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:45,755 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-17_01-24-45.log] [testng] 01:24:45,756 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f3a00cc - End of configuration. [testng] [2024-07-17 01:24:45,777] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:24:45,778 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:24:45,778 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:45,779 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-17_01-24-45.log] [testng] 01:24:45,780 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b889c5d - End of configuration. [testng] [2024-07-17 01:24:45,824] [pool-1-thread-6] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 01:24:45,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:24:45,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:45,826 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-17_01-24-45.log] [testng] 01:24:45,827 |-INFO in ch.qos.logback.core.sift.SiftProcessor@152740d3 - End of configuration. [testng] [2024-07-17 01:24:45,945] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 01:24:45,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:24:45,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:45,947 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-17_01-24-45.log] [testng] 01:24:45,947 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1996fa6a - End of configuration. [testng] [2024-07-17 01:24:45,956] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] 01:24:45,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:24:45,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:45,957 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-17_01-24-45.log] [testng] 01:24:45,958 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2457b2d4 - End of configuration. [testng] [2024-07-17 01:24:46,008] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 01:24:46,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:24:46,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:46,009 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-17_01-24-46.log] [testng] 01:24:46,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29b9d632 - End of configuration. [testng] [2024-07-17 01:24:46,023] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 01:24:46,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:24:46,024 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:46,024 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-17_01-24-46.log] [testng] 01:24:46,025 |-INFO in ch.qos.logback.core.sift.SiftProcessor@116d3f53 - End of configuration. [testng] [2024-07-17 01:24:47,826] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-07-17 01:24:47,834] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-07-17 01:24:47,841] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-07-17 01:24:47,851] [pool-1-thread-1] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-07-17 01:24:47,858] [pool-1-thread-4] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-07-17 01:24:47,999] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-07-17 01:24:48,009] [pool-1-thread-7] Initializing /data/sdub/sdub.pattern: [testng] [2024-07-17 01:24:48,412] [pool-1-thread-3] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-07-17 01:24:48,432] [pool-1-thread-2] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-07-17 01:24:48,514] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-07-17 01:24:48,560] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-07-17 01:24:48,759] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-07-17 01:24:48,767] [pool-1-thread-8] Initializing /data/ome/worm.tiff: [testng] [2024-07-17 01:24:48,940] [pool-1-thread-5] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-07-17 01:24:48,990] [pool-1-thread-12] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-07-17 01:24:49,148] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-07-17 01:24:49,375] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-07-17 01:24:49,389] [pool-1-thread-12] Initializing /data/ome/654Atemp.stk: [testng] [2024-07-17 01:24:49,789] [pool-1-thread-2] Initializing /data/ome/embryo.lsm: [testng] [2024-07-17 01:24:49,819] [pool-1-thread-6] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-07-17 01:24:50,231] [pool-1-thread-7] Initializing /data/ome/C1.lsm: [testng] [2024-07-17 01:24:50,350] [pool-1-thread-11] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-07-17 01:24:51,333] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] [2024-07-17 01:24:51,427] [pool-1-thread-2] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-07-17 01:24:51,646] [pool-1-thread-3] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-07-17 01:24:52,498] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-07-17 01:24:52,520] [pool-1-thread-5] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-07-17 01:24:52,587] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-07-17 01:24:52,869] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-07-17 01:24:52,925] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-07-17 01:24:53,080] [pool-1-thread-1] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-07-17 01:24:53,187] [pool-1-thread-7] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-07-17 01:24:53,243] [pool-1-thread-10] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-07-17 01:24:53,273] [pool-1-thread-5] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-07-17 01:24:53,567] [pool-1-thread-4] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-07-17 01:24:53,591] [pool-1-thread-6] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-07-17 01:24:53,605] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-07-17 01:24:53,727] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-07-17 01:24:53,805] [pool-1-thread-2] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-07-17 01:24:53,824] [pool-1-thread-6] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-07-17 01:24:54,072] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-07-17 01:24:54,140] [pool-1-thread-5] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-07-17 01:24:54,195] [pool-1-thread-4] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-07-17 01:24:54,216] [pool-1-thread-10] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-07-17 01:24:54,420] [pool-1-thread-1] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-07-17 01:24:54,467] [pool-1-thread-7] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-07-17 01:24:54,539] [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 12 seconds Finished: SUCCESS