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Started by upstream project "BIOFORMATS-test-repo" build number 300 originally caused by: Started by upstream project "Trigger" build number 322 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/jenkins15895886576433415960.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_47428_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] 00:38:40,381 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:38:40,383 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:38:40,383 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:38:40,384 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:38:40,384 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:38:40,385 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:38:40,385 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:38:40,385 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:38:40,385 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:38:40,386 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:38:40,386 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:38:40,386 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:38:40,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:38:40,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:38:40,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:38:40,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:38:40,650 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:38:40,650 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:38:40,650 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:38:40,651 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:38:40,651 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:38:40,652 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:38:40,652 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 267 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-27 00:38:40,662] [main] java.version = 1.8.0_342 [testng] 00:38:40,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:38:40,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:40,709 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-27_00-38-40.log] [testng] 00:38:40,711 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-27 00:38:40,713] [main] testng.directory = /data [testng] [2024-12-27 00:38:40,713] [main] testng.configDirectory = /config [testng] [2024-12-27 00:38:40,727] [main] testng.multiplier = 1.0 [testng] [2024-12-27 00:38:40,727] [main] testng.in-memory = false [testng] [2024-12-27 00:38:40,728] [main] testng.allow-missing = false [testng] [2024-12-27 00:38:40,728] [main] user.language = en [testng] [2024-12-27 00:38:40,728] [main] user.country = ${user.country} [testng] [2024-12-27 00:38:40,728] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-27 00:39:12,980] [main] ---------------------------------------- [testng] [2024-12-27 00:39:12,980] [main] Total files: 164 [testng] [2024-12-27 00:39:12,980] [main] Scan time: 32.252 s (196 ms/file) [testng] [2024-12-27 00:39:12,980] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-27 00:39:53,502] [pool-1-thread-1] Initializing /data/TAABA/TAABA.pattern: [testng] 00:39:53,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:39:53,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:53,504 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-27_00-39-53.log] [testng] 00:39:53,504 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74dd7227 - End of configuration. [testng] [2024-12-27 00:40:21,119] [pool-1-thread-12] Initializing /data/ome/worm.tiff: [testng] 00:40:21,119 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:40:21,119 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:21,120 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-27_00-40-21.log] [testng] 00:40:21,121 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10a2f26d - End of configuration. [testng] [2024-12-27 00:40:22,881] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 00:40:22,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:40:22,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:22,882 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-27_00-40-22.log] [testng] 00:40:22,883 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a283af5 - End of configuration. [testng] [2024-12-27 00:40:22,976] [pool-1-thread-10] Initializing /data/ome/Cpharynxzs1.lsm: [testng] 00:40:22,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:40:22,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:22,977 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-27_00-40-22.log] [testng] 00:40:22,977 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f5a9d43 - End of configuration. [testng] [2024-12-27 00:40:23,563] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] 00:40:23,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:40:23,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:23,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-27_00-40-23.log] [testng] 00:40:23,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b9d1e51 - End of configuration. [testng] [2024-12-27 00:40:24,480] [pool-1-thread-8] Initializing /data/ome/C1.lsm: [testng] 00:40:24,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:40:24,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:24,481 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-27_00-40-24.log] [testng] 00:40:24,481 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bfd24b5 - End of configuration. [testng] [2024-12-27 00:40:25,046] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:40:25,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:40:25,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:25,047 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-27_00-40-25.log] [testng] 00:40:25,047 |-INFO in ch.qos.logback.core.sift.SiftProcessor@799b275d - End of configuration. [testng] [2024-12-27 00:40:25,580] [pool-1-thread-6] Initializing /data/openjpeg/thumb_facade.jpg: [testng] 00:40:25,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:40:25,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:25,581 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-27_00-40-25.log] [testng] 00:40:25,582 |-INFO in ch.qos.logback.core.sift.SiftProcessor@200b9f16 - End of configuration. [testng] [2024-12-27 00:40:25,741] [pool-1-thread-5] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 00:40:25,741 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:40:25,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:25,742 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-27_00-40-25.log] [testng] 00:40:25,743 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f444476 - End of configuration. [testng] [2024-12-27 00:40:26,481] [pool-1-thread-4] Initializing /data/ome/anusgfpzs.lsm: [testng] 00:40:26,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:40:26,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:26,482 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-27_00-40-26.log] [testng] 00:40:26,482 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66f7efe5 - End of configuration. [testng] [2024-12-27 00:40:27,106] [pool-1-thread-3] Initializing /data/openjpeg/Rome.jp2: [testng] 00:40:27,106 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:40:27,106 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:27,107 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-27_00-40-27.log] [testng] 00:40:27,107 |-INFO in ch.qos.logback.core.sift.SiftProcessor@484fa178 - End of configuration. [testng] [2024-12-27 00:40:27,632] [pool-1-thread-2] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 00:40:27,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:40:27,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:27,633 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-27_00-40-27.log] [testng] 00:40:27,634 |-INFO in ch.qos.logback.core.sift.SiftProcessor@249fd3ac - End of configuration. [testng] [2024-12-27 00:40:31,261] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-12-27 00:40:33,416] [pool-1-thread-6] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-12-27 00:40:35,473] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-12-27 00:40:36,696] [pool-1-thread-7] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-12-27 00:40:36,890] [pool-1-thread-2] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-12-27 00:40:37,080] [pool-1-thread-4] Initializing /data/sdub/sdub.pattern: [testng] [2024-12-27 00:40:45,869] [pool-1-thread-8] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-12-27 00:40:47,144] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-12-27 00:40:47,369] [pool-1-thread-3] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-12-27 00:40:48,871] [pool-1-thread-5] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-12-27 00:40:49,480] [pool-1-thread-9] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-12-27 00:40:51,306] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-12-27 00:40:52,034] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-12-27 00:40:52,181] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-12-27 00:40:53,939] [pool-1-thread-7] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-12-27 00:40:55,515] [pool-1-thread-12] Initializing /data/ome/654Atemp.stk: [testng] [2024-12-27 00:40:57,627] [pool-1-thread-6] Initializing /data/ome/cb_1.r3d: [testng] [2024-12-27 00:40:59,139] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-12-27 00:41:01,962] [pool-1-thread-10] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-12-27 00:41:03,940] [pool-1-thread-6] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-12-27 00:41:04,624] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-12-27 00:41:06,981] [pool-1-thread-7] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-12-27 00:41:09,759] [pool-1-thread-3] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-12-27 00:41:09,917] [pool-1-thread-9] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-12-27 00:41:10,309] [pool-1-thread-10] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-12-27 00:41:10,814] [pool-1-thread-2] Initializing /data/ome/embryo.lsm: [testng] [2024-12-27 00:41:11,909] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-12-27 00:41:13,039] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-12-27 00:41:13,302] [pool-1-thread-12] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-12-27 00:41:14,191] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-12-27 00:41:15,149] [pool-1-thread-3] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-12-27 00:41:16,120] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-12-27 00:41:16,774] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-12-27 00:41:17,119] [pool-1-thread-6] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-12-27 00:41:17,699] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-12-27 00:41:17,859] [pool-1-thread-2] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-12-27 00:41:18,832] [pool-1-thread-10] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-12-27 00:41:20,879] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-12-27 00:41:21,094] [pool-1-thread-12] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-12-27 00:41:22,102] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-12-27 00:41:22,439] [pool-1-thread-5] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-12-27 00:41:24,715] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-12-27 00:41:25,535] [pool-1-thread-6] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-12-27 00:41:26,859] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-12-27 00:41:27,667] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-12-27 00:41:28,392] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-12-27 00:41:28,745] [pool-1-thread-10] Initializing /data/openjpeg/Facade.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 4 minutes 16 seconds Finished: SUCCESS