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Started by upstream project "BIOFORMATS-test-repo" build number 227 originally caused by: Started by upstream project "Trigger" build number 252 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins13847972277789145892.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35573_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] 08:25:57,781 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 08:25:57,783 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 08:25:57,783 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:25:57,784 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:25:57,784 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 08:25:57,784 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 08:25:57,785 |-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] 08:25:57,785 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:25:57,785 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:25:57,785 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 08:25:57,786 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 08:25:57,786 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 08:25:58,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 08:25:58,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 08:25:58,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 08:25:58,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 08:25:58,041 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 08:25:58,041 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 08:25:58,041 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 08:25:58,041 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 08:25:58,042 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 08:25:58,042 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 08:25:58,042 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 257 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-18 08:25:58,052] [main] java.version = 1.8.0_342 [testng] 08:25:58,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:25:58,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:25:58,098 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-18_08-25-58.log] [testng] 08:25:58,100 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-18 08:25:58,101] [main] testng.directory = /data [testng] [2024-10-18 08:25:58,102] [main] testng.configDirectory = /config [testng] [2024-10-18 08:25:58,113] [main] testng.multiplier = 1.0 [testng] [2024-10-18 08:25:58,114] [main] testng.in-memory = false [testng] [2024-10-18 08:25:58,114] [main] testng.allow-missing = false [testng] [2024-10-18 08:25:58,114] [main] user.language = en [testng] [2024-10-18 08:25:58,114] [main] user.country = ${user.country} [testng] [2024-10-18 08:25:58,114] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-18 08:30:58,522] [main] ---------------------------------------- [testng] [2024-10-18 08:30:58,523] [main] Total files: 164 [testng] [2024-10-18 08:30:58,523] [main] Scan time: 300.408 s (1831 ms/file) [testng] [2024-10-18 08:30:58,523] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-18 08:41:45,638] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 08:41:45,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 08:41:45,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:41:45,640 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-18_08-41-45.log] [testng] 08:41:45,640 |-INFO in ch.qos.logback.core.sift.SiftProcessor@500dffe1 - End of configuration. [testng] [2024-10-18 08:41:52,831] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 08:41:52,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 08:41:52,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:41:52,832 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-18_08-41-52.log] [testng] 08:41:52,832 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34e21dd - End of configuration. [testng] [2024-10-18 08:41:53,617] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 08:41:53,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 08:41:53,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:41:53,618 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-18_08-41-53.log] [testng] 08:41:53,618 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61bef709 - End of configuration. [testng] [2024-10-18 08:41:58,632] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm: [testng] 08:41:58,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 08:41:58,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:41:58,632 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-18_08-41-58.log] [testng] 08:41:58,633 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b3cca71 - End of configuration. [testng] [2024-10-18 08:42:03,547] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk: [testng] 08:42:03,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 08:42:03,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:03,547 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-18_08-42-03.log] [testng] 08:42:03,548 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48fcb28e - End of configuration. [testng] [2024-10-18 08:42:15,731] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 08:42:15,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 08:42:15,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:15,732 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-18_08-42-15.log] [testng] 08:42:15,733 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75186d06 - End of configuration. [testng] [2024-10-18 08:42:16,698] [pool-1-thread-7] Initializing /data/ome/embryo.lsm: [testng] 08:42:16,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 08:42:16,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:16,699 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-18_08-42-16.log] [testng] 08:42:16,699 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e22c87a - End of configuration. [testng] [2024-10-18 08:42:22,195] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 08:42:22,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 08:42:22,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:22,196 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-18_08-42-22.log] [testng] 08:42:22,196 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66a1d392 - End of configuration. [testng] [2024-10-18 08:42:23,253] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 08:42:23,253 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 08:42:23,253 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:23,253 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-18_08-42-23.log] [testng] 08:42:23,254 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c46f658 - End of configuration. [testng] [2024-10-18 08:42:28,495] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 08:42:28,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 08:42:28,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:28,496 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-18_08-42-28.log] [testng] 08:42:28,496 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e10d0e6 - End of configuration. [testng] [2024-10-18 08:42:29,278] [pool-1-thread-3] Initializing /data/ome/worm.tiff: [testng] 08:42:29,279 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 08:42:29,279 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:29,279 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-18_08-42-29.log] [testng] 08:42:29,280 |-INFO in ch.qos.logback.core.sift.SiftProcessor@97dae36 - End of configuration. [testng] [2024-10-18 08:42:40,626] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 08:42:40,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 08:42:40,627 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:40,627 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-18_08-42-40.log] [testng] 08:42:40,628 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a148311 - End of configuration. [testng] [2024-10-18 08:43:03,547] [pool-1-thread-4] Initializing /data/ome/C1.lsm: [testng] [2024-10-18 08:43:12,351] [pool-1-thread-12] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-10-18 08:43:13,878] [pool-1-thread-8] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-10-18 08:43:24,228] [pool-1-thread-6] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-10-18 08:43:35,619] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-10-18 08:43:39,267] [pool-1-thread-12] Initializing /data/sdub/sdub.pattern: [testng] [2024-10-18 08:45:11,823] [pool-1-thread-10] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-10-18 08:45:19,691] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-10-18 08:45:21,141] [pool-1-thread-7] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-10-18 08:45:32,519] [pool-1-thread-11] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-10-18 08:45:39,693] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-10-18 08:45:47,018] [pool-1-thread-1] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-10-18 08:45:52,346] [pool-1-thread-4] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-10-18 08:45:57,766] [pool-1-thread-5] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-10-18 08:46:14,832] [pool-1-thread-8] Initializing /data/ome/cb_1.r3d: [testng] [2024-10-18 08:46:17,459] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-10-18 08:46:29,411] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-10-18 08:46:31,689] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-10-18 08:46:43,058] [pool-1-thread-4] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-10-18 08:46:56,156] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-10-18 08:46:58,690] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-10-18 08:46:59,861] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-10-18 08:47:01,284] [pool-1-thread-9] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-10-18 08:47:04,625] [pool-1-thread-8] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-10-18 08:47:08,493] [pool-1-thread-2] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-10-18 08:47:17,803] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-10-18 08:47:24,059] [pool-1-thread-3] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-10-18 08:47:34,597] [pool-1-thread-7] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-10-18 08:47:37,127] [pool-1-thread-6] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-10-18 08:47:43,579] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-10-18 08:47:48,024] [pool-1-thread-2] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-10-18 08:47:56,231] [pool-1-thread-4] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-10-18 08:48:13,341] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-10-18 08:48:14,848] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-10-18 08:48:16,209] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-10-18 08:48:26,038] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-10-18 08:48:32,912] [pool-1-thread-10] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-10-18 08:48:49,752] [pool-1-thread-7] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-10-18 08:53:04,814] [pool-1-thread-8] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-10-18 08:53:15,713] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-10-18 08:53:21,839] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-10-18 08:53:23,092] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-10-18 08:53:24,246] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-10-18 08:53:25,290] [pool-1-thread-11] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-10-18 08:53:43,121] [pool-1-thread-6] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-10-18 08:53:52,589] [pool-1-thread-9] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-10-18 08:54:04,481] [pool-1-thread-8] 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: 51 minutes 6 seconds Finished: SUCCESS