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Started by upstream project "BIOFORMATS-test-repo" build number 209 originally caused by: Started by upstream project "Trigger" build number 235 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins1780067951009507801.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_33138_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 test-automated: [testng] File leak detector installed [testng] 01:32:24,764 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:32:24,765 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:32:24,765 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:32:24,766 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:32:24,766 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:32:24,766 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:32:24,767 |-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] 01:32:24,767 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:32:24,767 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:32:24,768 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:32:24,768 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:32:24,768 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:32:25,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:32:25,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:32:25,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:32:25,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:32:25,068 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:32:25,069 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:32:25,069 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:32:25,069 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:32:25,069 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:32:25,070 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:32:25,070 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 303 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-04 01:32:25,081] [main] java.version = 1.8.0_342 [testng] 01:32:25,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:32:25,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:25,134 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-04_01-32-25.log] [testng] 01:32:25,135 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-10-04 01:32:25,138] [main] testng.directory = /data [testng] [2024-10-04 01:32:25,138] [main] testng.configDirectory = /config [testng] [2024-10-04 01:32:25,151] [main] testng.multiplier = 1.0 [testng] [2024-10-04 01:32:25,151] [main] testng.in-memory = false [testng] [2024-10-04 01:32:25,151] [main] testng.allow-missing = false [testng] [2024-10-04 01:32:25,151] [main] user.language = en [testng] [2024-10-04 01:32:25,151] [main] user.country = ${user.country} [testng] [2024-10-04 01:32:25,151] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-04 01:33:05,071] [main] ---------------------------------------- [testng] [2024-10-04 01:33:05,072] [main] Total files: 164 [testng] [2024-10-04 01:33:05,072] [main] Scan time: 39.919 s (243 ms/file) [testng] [2024-10-04 01:33:05,072] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-04 01:33:43,434] [pool-1-thread-1] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 01:33:43,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:33:43,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:43,435 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-04_01-33-43.log] [testng] 01:33:43,436 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b79098f - End of configuration. [testng] [2024-10-04 01:33:43,847] [pool-1-thread-12] Initializing /data/ome/tiffany.color.tiff: [testng] 01:33:43,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:33:43,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:43,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-04_01-33-43.log] [testng] 01:33:43,848 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20862982 - End of configuration. [testng] [2024-10-04 01:33:44,324] [pool-1-thread-11] Initializing /data/ome/C1lowmusgfp.lsm: [testng] 01:33:44,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:33:44,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:44,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-04_01-33-44.log] [testng] 01:33:44,326 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dc0c17c - End of configuration. [testng] [2024-10-04 01:33:44,598] [pool-1-thread-10] Initializing /data/ome/C1.lsm: [testng] 01:33:44,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:33:44,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:44,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-04_01-33-44.log] [testng] 01:33:44,599 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2331ee1 - End of configuration. [testng] [2024-10-04 01:33:44,738] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 01:33:44,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:33:44,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:44,739 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-04_01-33-44.log] [testng] 01:33:44,739 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a148311 - End of configuration. [testng] [2024-10-04 01:33:44,770] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 01:33:44,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:33:44,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:44,771 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-04_01-33-44.log] [testng] 01:33:44,771 |-INFO in ch.qos.logback.core.sift.SiftProcessor@716ea815 - End of configuration. [testng] [2024-10-04 01:33:45,059] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] 01:33:45,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:33:45,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:45,060 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-04_01-33-45.log] [testng] 01:33:45,061 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22c10d98 - End of configuration. [testng] [2024-10-04 01:33:45,092] [pool-1-thread-6] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:33:45,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:33:45,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:45,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-04_01-33-45.log] [testng] 01:33:45,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@588cc7d2 - End of configuration. [testng] [2024-10-04 01:33:45,296] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 01:33:45,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:33:45,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:45,297 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-04_01-33-45.log] [testng] 01:33:45,298 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44deeb35 - End of configuration. [testng] [2024-10-04 01:33:45,405] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:33:45,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:33:45,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:45,406 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-04_01-33-45.log] [testng] 01:33:45,406 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51b5eb98 - End of configuration. [testng] [2024-10-04 01:33:45,573] [pool-1-thread-3] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 01:33:45,573 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:33:45,573 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:45,574 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-04_01-33-45.log] [testng] 01:33:45,574 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6db7869e - End of configuration. [testng] [2024-10-04 01:33:45,924] [pool-1-thread-2] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] 01:33:45,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:33:45,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:45,925 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-04_01-33-45.log] [testng] 01:33:45,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63d5a684 - End of configuration. [testng] [2024-10-04 01:33:48,162] [pool-1-thread-7] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-10-04 01:33:48,965] [pool-1-thread-9] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-10-04 01:33:49,271] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-10-04 01:33:49,358] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-10-04 01:33:49,668] [pool-1-thread-5] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-10-04 01:33:50,090] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-10-04 01:33:50,132] [pool-1-thread-6] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-10-04 01:33:50,286] [pool-1-thread-2] Initializing /data/ome/cb_1.r3d: [testng] [2024-10-04 01:33:50,424] [pool-1-thread-8] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-10-04 01:33:50,564] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-10-04 01:33:50,811] [pool-1-thread-3] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-10-04 01:33:51,120] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-10-04 01:33:51,470] [pool-1-thread-12] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-10-04 01:33:51,620] [pool-1-thread-4] Initializing /data/ome/worm.tiff: [testng] [2024-10-04 01:33:52,119] [pool-1-thread-9] Initializing /data/ome/embryo.lsm: [testng] [2024-10-04 01:33:52,334] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-10-04 01:33:52,387] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-10-04 01:33:52,551] [pool-1-thread-6] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-10-04 01:33:52,755] [pool-1-thread-8] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-10-04 01:33:53,122] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-10-04 01:33:53,446] [pool-1-thread-7] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-10-04 01:33:53,549] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-10-04 01:33:53,628] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-10-04 01:33:54,230] [pool-1-thread-5] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-10-04 01:33:54,510] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-10-04 01:33:54,631] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk: [testng] [2024-10-04 01:33:55,861] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-10-04 01:33:56,155] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-10-04 01:33:56,291] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-10-04 01:33:56,349] [pool-1-thread-6] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-10-04 01:33:56,534] [pool-1-thread-2] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-10-04 01:33:57,373] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-10-04 01:33:57,498] [pool-1-thread-5] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-10-04 01:33:57,627] [pool-1-thread-8] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-10-04 01:33:57,867] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-10-04 01:33:58,138] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-10-04 01:33:58,539] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-10-04 01:33:58,690] [pool-1-thread-6] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-10-04 01:33:58,942] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-10-04 01:33:59,016] [pool-1-thread-10] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-10-04 01:33:59,096] [pool-1-thread-5] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-10-04 01:34:00,035] [pool-1-thread-6] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-10-04 01:34:00,631] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-10-04 01:34:00,853] [pool-1-thread-9] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-10-04 01:34:08,746] [pool-1-thread-8] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-10-04 01:34:09,098] [pool-1-thread-10] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-10-04 01:34:09,314] [pool-1-thread-7] Initializing /data/sdub/sdub.pattern: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 3 minutes 12 seconds Finished: SUCCESS