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Started by upstream project "BIOFORMATS-test-repo" build number 39 originally caused by: Started by upstream project "Trigger" build number 45 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins17063240731420158590.sh + '[' samples = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_5414_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 01:23:48,002 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:23:48,005 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:23:48,005 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:23:48,007 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:23:48,008 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:23:48,009 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:23:48,009 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:23:48,009 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:23:48,010 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:23:48,011 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:23:48,012 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:23:48,012 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:23:48,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:23:48,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:23:48,334 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:23:48,334 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:23:48,342 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:23:48,342 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:23:48,342 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:23:48,343 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:23:48,343 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:23:48,344 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:23:48,344 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 334 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-20 01:23:48,356] [main] java.version = 11.0.16 [testng] 01:23:48,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:23:48,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:48,437 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-20_01-23-48.log] [testng] 01:23:48,440 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-04-20 01:23:48,445] [main] testng.directory = /data [testng] [2024-04-20 01:23:48,445] [main] testng.configDirectory = /config [testng] [2024-04-20 01:23:48,463] [main] testng.multiplier = 1.0 [testng] [2024-04-20 01:23:48,466] [main] testng.in-memory = false [testng] [2024-04-20 01:23:48,466] [main] testng.allow-missing = false [testng] [2024-04-20 01:23:48,466] [main] user.language = en [testng] [2024-04-20 01:23:48,466] [main] user.country = ${user.country} [testng] [2024-04-20 01:23:48,466] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-20 01:24:09,562] [main] ---------------------------------------- [testng] [2024-04-20 01:24:09,562] [main] Total files: 164 [testng] [2024-04-20 01:24:09,562] [main] Scan time: 21.095 s (128 ms/file) [testng] [2024-04-20 01:24:09,562] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-20 01:24:19,868] [pool-1-thread-1] Initializing /data/ome/C1.lsm: [testng] 01:24:19,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:24:19,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:19,874 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-20_01-24-19.log] [testng] 01:24:19,874 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e0e00ca - End of configuration. [testng] [2024-04-20 01:24:19,912] [pool-1-thread-12] Initializing /data/openjpeg/Facade.bmp: [testng] 01:24:19,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:24:19,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:19,912 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-20_01-24-19.log] [testng] 01:24:19,913 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cfc6f9b - End of configuration. [testng] [2024-04-20 01:24:19,930] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:24:19,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:24:19,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:19,931 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-20_01-24-19.log] [testng] 01:24:19,931 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ac839d - End of configuration. [testng] [2024-04-20 01:24:19,949] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] 01:24:19,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:24:19,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:19,951 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-20_01-24-19.log] [testng] 01:24:19,951 |-INFO in ch.qos.logback.core.sift.SiftProcessor@727340a3 - End of configuration. [testng] [2024-04-20 01:24:19,978] [pool-1-thread-9] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] 01:24:19,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:24:19,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:19,979 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-20_01-24-19.log] [testng] 01:24:19,979 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12572679 - End of configuration. [testng] [2024-04-20 01:24:20,041] [pool-1-thread-8] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:24:20,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:24:20,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:20,042 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-20_01-24-20.log] [testng] 01:24:20,042 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10f4e939 - End of configuration. [testng] [2024-04-20 01:24:20,082] [pool-1-thread-7] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 01:24:20,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:24:20,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:20,083 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-20_01-24-20.log] [testng] 01:24:20,084 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a517560 - End of configuration. [testng] [2024-04-20 01:24:20,330] [pool-1-thread-6] Initializing /data/openjpeg/Rome.ppm: [testng] 01:24:20,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:24:20,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:20,331 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-20_01-24-20.log] [testng] 01:24:20,331 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c40f4be - End of configuration. [testng] [2024-04-20 01:24:20,341] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:24:20,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:24:20,342 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:20,342 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-20_01-24-20.log] [testng] 01:24:20,343 |-INFO in ch.qos.logback.core.sift.SiftProcessor@707b02f0 - End of configuration. [testng] [2024-04-20 01:24:20,379] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 01:24:20,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:24:20,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:20,380 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-20_01-24-20.log] [testng] 01:24:20,381 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59edaedc - End of configuration. [testng] [2024-04-20 01:24:20,394] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 01:24:20,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:24:20,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:20,396 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-20_01-24-20.log] [testng] 01:24:20,396 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2545e30a - End of configuration. [testng] [2024-04-20 01:24:20,479] [pool-1-thread-2] Initializing /data/sdub/sdub.pattern: [testng] 01:24:20,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:24:20,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:20,481 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-20_01-24-20.log] [testng] 01:24:20,481 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2644be84 - End of configuration. [testng] [2024-04-20 01:24:22,653] [pool-1-thread-6] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-04-20 01:24:22,676] [pool-1-thread-10] Initializing /data/ome/654Atemp.stk: [testng] [2024-04-20 01:24:22,788] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-04-20 01:24:22,794] [pool-1-thread-5] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-04-20 01:24:22,833] [pool-1-thread-1] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-04-20 01:24:22,841] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-04-20 01:24:23,282] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-04-20 01:24:23,298] [pool-1-thread-8] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-04-20 01:24:23,317] [pool-1-thread-9] Initializing /data/ome/worm.tiff: [testng] [2024-04-20 01:24:23,358] [pool-1-thread-1] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-04-20 01:24:23,455] [pool-1-thread-2] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-04-20 01:24:23,517] [pool-1-thread-4] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-04-20 01:24:23,832] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-04-20 01:24:23,838] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-04-20 01:24:24,067] [pool-1-thread-8] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-04-20 01:24:24,079] [pool-1-thread-1] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-04-20 01:24:24,989] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-04-20 01:24:25,014] [pool-1-thread-5] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-04-20 01:24:25,118] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-04-20 01:24:25,167] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-04-20 01:24:25,231] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-04-20 01:24:25,605] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-04-20 01:24:25,724] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-04-20 01:24:25,746] [pool-1-thread-10] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-04-20 01:24:25,763] [pool-1-thread-5] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-04-20 01:24:25,840] [pool-1-thread-8] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-04-20 01:24:26,220] [pool-1-thread-4] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-04-20 01:24:26,477] [pool-1-thread-8] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-04-20 01:24:26,530] [pool-1-thread-10] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-04-20 01:24:26,716] [pool-1-thread-5] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-04-20 01:24:26,776] [pool-1-thread-3] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-04-20 01:24:26,931] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-04-20 01:24:26,976] [pool-1-thread-9] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-04-20 01:24:27,788] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-04-20 01:24:27,919] [pool-1-thread-3] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-04-20 01:24:28,045] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-04-20 01:24:28,085] [pool-1-thread-10] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-04-20 01:24:28,211] [pool-1-thread-4] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-04-20 01:24:28,294] [pool-1-thread-6] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-04-20 01:24:28,502] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] [2024-04-20 01:24:28,816] [pool-1-thread-6] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-04-20 01:24:28,960] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-04-20 01:24:29,085] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-04-20 01:24:29,160] [pool-1-thread-8] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-04-20 01:24:29,487] [pool-1-thread-4] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-04-20 01:24:29,792] [pool-1-thread-8] Initializing /data/ome/embryo.lsm: [testng] [2024-04-20 01:24:29,885] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.ppm: [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 15 seconds Finished: SUCCESS