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Started by upstream project "BIOFORMATS-test-repo" build number 272 originally caused by: Started by upstream project "Trigger" build number 294 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins5053259298922021203.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42825_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] 00:34:21,155 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:34:21,157 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:34:21,157 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:34:21,158 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:34:21,158 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:34:21,158 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:34:21,158 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:34:21,158 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:34:21,159 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:34:21,159 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:34:21,159 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:34:21,159 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:34:21,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:34:21,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:34:21,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:34:21,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:34:21,443 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:34:21,443 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:34:21,444 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:34:21,444 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:34:21,444 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:34:21,445 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:34:21,445 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 286 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-29 00:34:21,457] [main] java.version = 1.8.0_342 [testng] 00:34:21,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:34:21,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:21,511 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-29_00-34-21.log] [testng] 00:34:21,513 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-29 00:34:21,515] [main] testng.directory = /data [testng] [2024-11-29 00:34:21,515] [main] testng.configDirectory = /config [testng] [2024-11-29 00:34:21,529] [main] testng.multiplier = 1.0 [testng] [2024-11-29 00:34:21,530] [main] testng.in-memory = false [testng] [2024-11-29 00:34:21,530] [main] testng.allow-missing = false [testng] [2024-11-29 00:34:21,530] [main] user.language = en [testng] [2024-11-29 00:34:21,530] [main] user.country = ${user.country} [testng] [2024-11-29 00:34:21,530] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-29 00:35:09,227] [main] ---------------------------------------- [testng] [2024-11-29 00:35:09,227] [main] Total files: 164 [testng] [2024-11-29 00:35:09,228] [main] Scan time: 47.697 s (290 ms/file) [testng] [2024-11-29 00:35:09,228] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-29 00:36:19,430] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:36:19,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:36:19,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:19,432 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-29_00-36-19.log] [testng] 00:36:19,432 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d251121 - End of configuration. [testng] [2024-11-29 00:36:20,473] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 00:36:20,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:36:20,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:20,474 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-29_00-36-20.log] [testng] 00:36:20,474 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34b8064a - End of configuration. [testng] [2024-11-29 00:36:20,611] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 00:36:20,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:36:20,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:20,612 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-29_00-36-20.log] [testng] 00:36:20,612 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a3c1a53 - End of configuration. [testng] [2024-11-29 00:36:21,383] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm: [testng] 00:36:21,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:36:21,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:21,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-29_00-36-21.log] [testng] 00:36:21,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20096708 - End of configuration. [testng] [2024-11-29 00:36:21,837] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk: [testng] 00:36:21,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:36:21,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:21,838 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-29_00-36-21.log] [testng] 00:36:21,838 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dc0c17c - End of configuration. [testng] [2024-11-29 00:36:22,925] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 00:36:22,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:36:22,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:22,926 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-29_00-36-22.log] [testng] 00:36:22,926 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5827d8bd - End of configuration. [testng] [2024-11-29 00:36:23,019] [pool-1-thread-7] Initializing /data/ome/embryo.lsm: [testng] 00:36:23,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:36:23,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:23,020 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-29_00-36-23.log] [testng] 00:36:23,020 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ce261a1 - End of configuration. [testng] [2024-11-29 00:36:23,569] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 00:36:23,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:36:23,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:23,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-29_00-36-23.log] [testng] 00:36:23,570 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d7c78b0 - End of configuration. [testng] [2024-11-29 00:36:23,691] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 00:36:23,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:36:23,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:23,692 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-29_00-36-23.log] [testng] 00:36:23,692 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29c08edb - End of configuration. [testng] [2024-11-29 00:36:24,050] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 00:36:24,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:36:24,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:24,051 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-29_00-36-24.log] [testng] 00:36:24,051 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61bef709 - End of configuration. [testng] [2024-11-29 00:36:24,107] [pool-1-thread-3] Initializing /data/ome/worm.tiff: [testng] 00:36:24,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:36:24,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:24,108 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-29_00-36-24.log] [testng] 00:36:24,108 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75186d06 - End of configuration. [testng] [2024-11-29 00:36:25,182] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:36:25,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:36:25,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:25,183 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-29_00-36-25.log] [testng] 00:36:25,183 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66a1d392 - End of configuration. [testng] [2024-11-29 00:36:28,717] [pool-1-thread-6] Initializing /data/ome/C1.lsm: [testng] [2024-11-29 00:36:29,077] [pool-1-thread-4] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-11-29 00:36:29,377] [pool-1-thread-12] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-11-29 00:36:29,700] [pool-1-thread-8] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-11-29 00:36:30,179] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-11-29 00:36:30,273] [pool-1-thread-7] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-11-29 00:36:30,604] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern: [testng] [2024-11-29 00:36:33,982] [pool-1-thread-1] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-11-29 00:36:34,416] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-11-29 00:36:35,180] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-11-29 00:36:35,664] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-11-29 00:36:36,925] [pool-1-thread-5] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-11-29 00:36:37,046] [pool-1-thread-2] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-11-29 00:36:37,543] [pool-1-thread-9] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-11-29 00:36:38,739] [pool-1-thread-6] Initializing /data/ome/cb_1.r3d: [testng] [2024-11-29 00:36:39,001] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-11-29 00:36:39,483] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-11-29 00:36:39,871] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-11-29 00:36:40,771] [pool-1-thread-2] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-11-29 00:36:41,548] [pool-1-thread-5] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-11-29 00:36:41,722] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-11-29 00:36:42,281] [pool-1-thread-6] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-11-29 00:36:42,398] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-11-29 00:36:42,588] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-11-29 00:36:42,876] [pool-1-thread-12] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-11-29 00:36:43,270] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-11-29 00:36:43,835] [pool-1-thread-5] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-11-29 00:36:45,428] [pool-1-thread-4] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-11-29 00:36:45,577] [pool-1-thread-6] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-11-29 00:36:45,908] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-11-29 00:36:45,977] [pool-1-thread-3] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-11-29 00:36:46,759] [pool-1-thread-9] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-11-29 00:36:47,104] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-11-29 00:36:47,189] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-11-29 00:36:47,627] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-11-29 00:36:49,511] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-11-29 00:36:49,801] [pool-1-thread-4] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-11-29 00:36:51,039] [pool-1-thread-7] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-11-29 00:37:09,427] [pool-1-thread-2] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-11-29 00:37:09,751] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-11-29 00:37:10,714] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-11-29 00:37:12,047] [pool-1-thread-9] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-11-29 00:37:13,068] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-11-29 00:37:13,794] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-11-29 00:37:14,391] [pool-1-thread-11] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-11-29 00:37:15,890] [pool-1-thread-2] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-11-29 00:37:16,776] [pool-1-thread-4] 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: 4 minutes 13 seconds Finished: SUCCESS