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Started by upstream project "BIOFORMATS-test-repo" build number 102 originally caused by: Started by upstream project "Trigger" build number 113 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/jenkins11176676418244353963.sh + '[' samples = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_15747_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 -Duser.language=fr -Duser.country=FR 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 test-automated: [testng] File leak detector installed [testng] 01:24:36,098 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:24:36,100 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:24:36,100 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:36,101 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:36,101 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:24:36,101 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:24:36,102 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:24:36,102 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:36,102 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:36,103 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:24:36,103 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:24:36,103 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:24:36,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:24:36,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:24:36,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:24:36,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:24:36,385 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:24:36,386 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:24:36,386 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:24:36,387 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:24:36,387 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:24:36,388 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:24:36,388 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 286 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-24 01:24:36,402] [main] java.version = 1.8.0_342 [testng] 01:24:36,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:24:36,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:36,470 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-24_01-24-36.log] [testng] 01:24:36,472 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-06-24 01:24:36,474] [main] testng.directory = /data [testng] [2024-06-24 01:24:36,475] [main] testng.configDirectory = /config [testng] [2024-06-24 01:24:36,492] [main] testng.multiplier = 1.0 [testng] [2024-06-24 01:24:36,492] [main] testng.in-memory = false [testng] [2024-06-24 01:24:36,492] [main] testng.allow-missing = false [testng] [2024-06-24 01:24:36,493] [main] user.language = fr [testng] [2024-06-24 01:24:36,493] [main] user.country = FR [testng] [2024-06-24 01:24:36,493] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-06-24 01:25:03,282] [main] ---------------------------------------- [testng] [2024-06-24 01:25:03,283] [main] Total files: 164 [testng] [2024-06-24 01:25:03,283] [main] Scan time: 26.789 s (163 ms/file) [testng] [2024-06-24 01:25:03,283] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-24 01:25:15,602] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:25:15,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:25:15,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:15,604 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-24_01-25-15.log] [testng] 01:25:15,605 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14c9a2b7 - End of configuration. [testng] [2024-06-24 01:25:15,648] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 01:25:15,649 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:25:15,649 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:15,650 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-24_01-25-15.log] [testng] 01:25:15,651 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4269d9ea - End of configuration. [testng] [2024-06-24 01:25:15,669] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 01:25:15,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:25:15,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:15,671 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-24_01-25-15.log] [testng] 01:25:15,671 |-INFO in ch.qos.logback.core.sift.SiftProcessor@781ec6e9 - End of configuration. [testng] [2024-06-24 01:25:15,737] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:25:15,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:25:15,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:15,738 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-24_01-25-15.log] [testng] 01:25:15,739 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4149496e - End of configuration. [testng] [2024-06-24 01:25:15,791] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk: [testng] 01:25:15,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:25:15,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:15,792 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-24_01-25-15.log] [testng] 01:25:15,793 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f65c2e0 - End of configuration. [testng] [2024-06-24 01:25:15,916] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 01:25:15,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:25:15,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:15,917 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-24_01-25-15.log] [testng] 01:25:15,918 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79e800fb - End of configuration. [testng] [2024-06-24 01:25:15,927] [pool-1-thread-7] Initializing /data/ome/embryo.lsm: [testng] 01:25:15,928 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:25:15,928 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:15,929 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-24_01-25-15.log] [testng] 01:25:15,929 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d0e942 - End of configuration. [testng] [2024-06-24 01:25:15,967] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 01:25:15,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:25:15,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:15,968 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-24_01-25-15.log] [testng] 01:25:15,969 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ddce935 - End of configuration. [testng] [2024-06-24 01:25:15,982] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 01:25:15,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:25:15,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:15,984 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-24_01-25-15.log] [testng] 01:25:15,984 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64603732 - End of configuration. [testng] [2024-06-24 01:25:16,008] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 01:25:16,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:25:16,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:16,009 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-24_01-25-16.log] [testng] 01:25:16,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16c96318 - End of configuration. [testng] [2024-06-24 01:25:16,020] [pool-1-thread-3] Initializing /data/ome/worm.tiff: [testng] 01:25:16,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:25:16,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:16,022 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-24_01-25-16.log] [testng] 01:25:16,023 |-INFO in ch.qos.logback.core.sift.SiftProcessor@87b22e4 - End of configuration. [testng] [2024-06-24 01:25:16,094] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:25:16,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:25:16,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:16,095 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-24_01-25-16.log] [testng] 01:25:16,096 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d294c6 - End of configuration. [testng] [2024-06-24 01:25:19,010] [pool-1-thread-6] Initializing /data/ome/C1.lsm: [testng] [2024-06-24 01:25:19,029] [pool-1-thread-1] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-06-24 01:25:19,053] [pool-1-thread-5] Initializing /data/sdub/sdub.pattern: [testng] [2024-06-24 01:25:19,192] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-06-24 01:25:19,201] [pool-1-thread-10] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-06-24 01:25:19,227] [pool-1-thread-2] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-06-24 01:25:19,233] [pool-1-thread-9] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-06-24 01:25:19,319] [pool-1-thread-11] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-06-24 01:25:19,484] [pool-1-thread-4] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-06-24 01:25:19,621] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-06-24 01:25:19,686] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-06-24 01:25:19,877] [pool-1-thread-6] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-06-24 01:25:19,911] [pool-1-thread-11] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-06-24 01:25:20,000] [pool-1-thread-3] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-06-24 01:25:20,093] [pool-1-thread-1] Initializing /data/ome/cb_1.r3d: [testng] [2024-06-24 01:25:20,271] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-06-24 01:25:20,284] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-06-24 01:25:20,532] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-06-24 01:25:20,658] [pool-1-thread-8] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-06-24 01:25:20,912] [pool-1-thread-5] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-06-24 01:25:20,978] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-06-24 01:25:21,015] [pool-1-thread-3] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-06-24 01:25:21,257] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-06-24 01:25:21,266] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-06-24 01:25:21,435] [pool-1-thread-3] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-06-24 01:25:21,561] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-06-24 01:25:21,598] [pool-1-thread-10] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-06-24 01:25:22,346] [pool-1-thread-4] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-06-24 01:25:22,481] [pool-1-thread-2] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-06-24 01:25:22,565] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-06-24 01:25:22,692] [pool-1-thread-3] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-06-24 01:25:22,717] [pool-1-thread-9] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-06-24 01:25:22,793] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-06-24 01:25:22,940] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-06-24 01:25:22,949] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-06-24 01:25:23,029] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-06-24 01:25:23,088] [pool-1-thread-6] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-06-24 01:25:23,356] [pool-1-thread-7] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-06-24 01:25:24,234] [pool-1-thread-3] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-06-24 01:25:24,294] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-06-24 01:25:24,332] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-06-24 01:25:24,465] [pool-1-thread-4] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-06-24 01:25:24,487] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-06-24 01:25:24,556] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-06-24 01:25:24,616] [pool-1-thread-8] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-06-24 01:25:24,914] [pool-1-thread-6] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-06-24 01:25:25,113] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Speedway.jpg: [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 31 seconds Finished: SUCCESS