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Started by upstream project "BIOFORMATS-test-repo" build number 285 originally caused by: Started by upstream project "Trigger" build number 304 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins11187518436859012208.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_44959_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] 00:37:03,099 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:37:03,101 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:37:03,101 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:03,102 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:03,103 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:37:03,103 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:37:03,103 |-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] 00:37:03,103 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:03,104 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:03,104 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:37:03,104 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:37:03,104 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:37:03,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:37:03,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:37:03,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:37:03,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:37:03,389 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:37:03,389 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:37:03,389 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:37:03,389 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:37:03,390 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:37:03,391 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:37:03,391 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 287 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-09 00:37:03,403] [main] java.version = 1.8.0_342 [testng] 00:37:03,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:37:03,407 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:03,453 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-09_00-37-03.log] [testng] 00:37:03,455 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-09 00:37:03,457] [main] testng.directory = /data [testng] [2024-12-09 00:37:03,457] [main] testng.configDirectory = /config [testng] [2024-12-09 00:37:03,470] [main] testng.multiplier = 1.0 [testng] [2024-12-09 00:37:03,470] [main] testng.in-memory = false [testng] [2024-12-09 00:37:03,471] [main] testng.allow-missing = false [testng] [2024-12-09 00:37:03,471] [main] user.language = fr [testng] [2024-12-09 00:37:03,471] [main] user.country = FR [testng] [2024-12-09 00:37:03,471] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-09 00:37:33,533] [main] ---------------------------------------- [testng] [2024-12-09 00:37:33,533] [main] Total files: 164 [testng] [2024-12-09 00:37:33,534] [main] Scan time: 30.062 s (183 ms/file) [testng] [2024-12-09 00:37:33,534] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-09 00:38:29,301] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 00:38:29,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:38:29,302 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:29,302 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-09_00-38-29.log] [testng] 00:38:29,303 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1069d977 - End of configuration. [testng] [2024-12-09 00:38:29,593] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 00:38:29,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:38:29,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:29,594 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-09_00-38-29.log] [testng] 00:38:29,594 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75b1a85e - End of configuration. [testng] [2024-12-09 00:38:29,955] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 00:38:29,955 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:38:29,955 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:29,955 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-09_00-38-29.log] [testng] 00:38:29,956 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6aeb1a10 - End of configuration. [testng] [2024-12-09 00:38:30,357] [pool-1-thread-10] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] 00:38:30,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:38:30,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:30,358 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-09_00-38-30.log] [testng] 00:38:30,359 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d81323e - End of configuration. [testng] [2024-12-09 00:38:31,018] [pool-1-thread-9] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 00:38:31,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:38:31,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:31,019 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-09_00-38-31.log] [testng] 00:38:31,019 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2501a9fb - End of configuration. [testng] [2024-12-09 00:38:31,866] [pool-1-thread-8] Initializing /data/ome/C1midmusnorm.lsm: [testng] 00:38:31,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:38:31,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:31,867 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-09_00-38-31.log] [testng] 00:38:31,867 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fac0149 - End of configuration. [testng] [2024-12-09 00:38:32,425] [pool-1-thread-7] Initializing /data/openjpeg/Facade.bmp: [testng] 00:38:32,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:38:32,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:32,426 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-09_00-38-32.log] [testng] 00:38:32,427 |-INFO in ch.qos.logback.core.sift.SiftProcessor@699ed949 - End of configuration. [testng] [2024-12-09 00:38:32,513] [pool-1-thread-6] Initializing /data/TAABA/TAABA.pattern: [testng] 00:38:32,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:38:32,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:32,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-09_00-38-32.log] [testng] 00:38:32,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@284792a4 - End of configuration. [testng] [2024-12-09 00:38:58,420] [pool-1-thread-5] Initializing /data/ome/tiffany.color.tiff: [testng] 00:38:58,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:38:58,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:58,421 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-09_00-38-58.log] [testng] 00:38:58,421 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5757863 - End of configuration. [testng] [2024-12-09 00:39:00,601] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] 00:39:00,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:39:00,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:00,602 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-09_00-39-00.log] [testng] 00:39:00,603 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30a6141c - End of configuration. [testng] [2024-12-09 00:39:00,906] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 00:39:00,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:39:00,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:00,907 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-09_00-39-00.log] [testng] 00:39:00,908 |-INFO in ch.qos.logback.core.sift.SiftProcessor@673aa7f2 - End of configuration. [testng] [2024-12-09 00:39:01,022] [pool-1-thread-2] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:39:01,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:39:01,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:01,023 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-09_00-39-01.log] [testng] 00:39:01,023 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c892d31 - End of configuration. [testng] [2024-12-09 00:39:06,152] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-12-09 00:39:07,102] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-12-09 00:39:08,723] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-12-09 00:39:08,866] [pool-1-thread-3] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-12-09 00:39:10,046] [pool-1-thread-12] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-12-09 00:39:10,309] [pool-1-thread-8] Initializing /data/ome/654Atemp.stk: [testng] [2024-12-09 00:39:13,980] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-12-09 00:39:14,108] [pool-1-thread-3] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-12-09 00:39:14,738] [pool-1-thread-7] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-12-09 00:39:16,439] [pool-1-thread-2] Initializing /data/ome/worm.tiff: [testng] [2024-12-09 00:39:17,774] [pool-1-thread-12] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-12-09 00:39:18,232] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-12-09 00:39:18,298] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-12-09 00:39:19,470] [pool-1-thread-9] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-12-09 00:39:20,579] [pool-1-thread-10] Initializing /data/ome/C1.lsm: [testng] [2024-12-09 00:39:21,033] [pool-1-thread-1] Initializing /data/ome/embryo.lsm: [testng] [2024-12-09 00:39:23,158] [pool-1-thread-5] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-12-09 00:39:25,017] [pool-1-thread-3] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-12-09 00:39:28,086] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-12-09 00:39:29,073] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-12-09 00:39:29,243] [pool-1-thread-8] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-12-09 00:39:30,145] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-12-09 00:39:31,271] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-12-09 00:39:31,501] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-12-09 00:39:33,372] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-12-09 00:39:34,286] [pool-1-thread-5] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-12-09 00:39:35,463] [pool-1-thread-3] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-12-09 00:39:35,993] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-12-09 00:39:36,112] [pool-1-thread-12] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-12-09 00:39:36,185] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-12-09 00:39:36,403] [pool-1-thread-4] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-12-09 00:39:37,766] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-12-09 00:39:38,019] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-12-09 00:39:39,439] [pool-1-thread-4] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-12-09 00:39:40,052] [pool-1-thread-2] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-12-09 00:39:40,748] [pool-1-thread-9] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-12-09 00:39:42,044] [pool-1-thread-1] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-12-09 00:39:42,427] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-12-09 00:39:43,655] [pool-1-thread-3] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-12-09 00:39:44,503] [pool-1-thread-2] Initializing /data/sdub/sdub.pattern: [testng] [2024-12-09 00:39:52,802] [pool-1-thread-5] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-12-09 00:39:53,780] [pool-1-thread-12] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-12-09 00:39:53,939] [pool-1-thread-1] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-12-09 00:39:56,474] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-12-09 00:39:57,468] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-12-09 00:39:59,466] [pool-1-thread-12] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-12-09 00:40:00,490] [pool-1-thread-4] Initializing /data/openjpeg/FacadeERROPJ.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 32 seconds Finished: SUCCESS