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Started by upstream project "BIOFORMATS-test-repo" build number 282 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/jenkins17028836051558611145.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_44467_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] 10:20:22,165 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 10:20:22,167 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 10:20:22,167 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:20:22,168 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:20:22,169 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 10:20:22,169 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 10:20:22,169 |-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] 10:20:22,169 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:20:22,170 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:20:22,170 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 10:20:22,170 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 10:20:22,170 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 10:20:22,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 10:20:22,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 10:20:22,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 10:20:22,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 10:20:22,437 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 10:20:22,437 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 10:20:22,437 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 10:20:22,437 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 10:20:22,437 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 10:20:22,438 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 10:20:22,438 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 268 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-06 10:20:22,448] [main] java.version = 1.8.0_342 [testng] 10:20:22,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 10:20:22,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:20:22,499 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-06_10-20-22.log] [testng] 10:20:22,501 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-06 10:20:22,503] [main] testng.directory = /data [testng] [2024-12-06 10:20:22,503] [main] testng.configDirectory = /config [testng] [2024-12-06 10:20:22,515] [main] testng.multiplier = 1.0 [testng] [2024-12-06 10:20:22,516] [main] testng.in-memory = false [testng] [2024-12-06 10:20:22,516] [main] testng.allow-missing = false [testng] [2024-12-06 10:20:22,516] [main] user.language = en [testng] [2024-12-06 10:20:22,516] [main] user.country = ${user.country} [testng] [2024-12-06 10:20:22,516] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-06 10:21:11,931] [main] ---------------------------------------- [testng] [2024-12-06 10:21:11,931] [main] Total files: 164 [testng] [2024-12-06 10:21:11,931] [main] Scan time: 49.415 s (301 ms/file) [testng] [2024-12-06 10:21:11,931] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-06 10:22:17,795] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 10:22:17,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:22:17,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:22:17,796 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-06_10-22-17.log] [testng] 10:22:17,797 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5eb8fc3 - End of configuration. [testng] [2024-12-06 10:22:18,465] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 10:22:18,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:22:18,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:22:18,465 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-06_10-22-18.log] [testng] 10:22:18,466 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b693221 - End of configuration. [testng] [2024-12-06 10:22:18,541] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 10:22:18,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:22:18,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:22:18,543 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-06_10-22-18.log] [testng] 10:22:18,543 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17d95eff - End of configuration. [testng] [2024-12-06 10:22:18,987] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm: [testng] 10:22:18,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:22:18,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:22:18,988 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-06_10-22-18.log] [testng] 10:22:18,989 |-INFO in ch.qos.logback.core.sift.SiftProcessor@598037ed - End of configuration. [testng] [2024-12-06 10:22:19,442] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk: [testng] 10:22:19,442 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:22:19,442 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:22:19,443 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-06_10-22-19.log] [testng] 10:22:19,443 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6665b28 - End of configuration. [testng] [2024-12-06 10:22:20,587] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 10:22:20,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:22:20,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:22:20,588 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-06_10-22-20.log] [testng] 10:22:20,588 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bea91b6 - End of configuration. [testng] [2024-12-06 10:22:20,670] [pool-1-thread-7] Initializing /data/ome/embryo.lsm: [testng] 10:22:20,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:22:20,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:22:20,670 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-06_10-22-20.log] [testng] 10:22:20,671 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5cdfe440 - End of configuration. [testng] [2024-12-06 10:22:21,165] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 10:22:21,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:22:21,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:22:21,166 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-06_10-22-21.log] [testng] 10:22:21,166 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6346da7c - End of configuration. [testng] [2024-12-06 10:22:21,261] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 10:22:21,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:22:21,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:22:21,262 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-06_10-22-21.log] [testng] 10:22:21,262 |-INFO in ch.qos.logback.core.sift.SiftProcessor@305884b1 - End of configuration. [testng] [2024-12-06 10:22:21,704] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 10:22:21,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:22:21,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:22:21,705 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-06_10-22-21.log] [testng] 10:22:21,706 |-INFO in ch.qos.logback.core.sift.SiftProcessor@567dc1f8 - End of configuration. [testng] [2024-12-06 10:22:21,771] [pool-1-thread-3] Initializing /data/ome/worm.tiff: [testng] 10:22:21,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:22:21,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:22:21,772 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-06_10-22-21.log] [testng] 10:22:21,772 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a3c1a53 - End of configuration. [testng] [2024-12-06 10:22:22,715] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 10:22:22,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:22:22,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:22:22,715 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-06_10-22-22.log] [testng] 10:22:22,716 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22490d60 - End of configuration. [testng] [2024-12-06 10:22:26,317] [pool-1-thread-4] Initializing /data/ome/C1.lsm: [testng] [2024-12-06 10:22:27,279] [pool-1-thread-6] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-12-06 10:22:27,582] [pool-1-thread-12] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-12-06 10:22:27,683] [pool-1-thread-8] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-12-06 10:22:28,798] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-12-06 10:22:28,924] [pool-1-thread-10] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-12-06 10:22:29,525] [pool-1-thread-7] Initializing /data/sdub/sdub.pattern: [testng] [2024-12-06 10:22:36,264] [pool-1-thread-11] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-12-06 10:22:37,357] [pool-1-thread-2] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-12-06 10:22:38,136] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-12-06 10:22:38,255] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-12-06 10:22:39,427] [pool-1-thread-6] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-12-06 10:22:39,932] [pool-1-thread-5] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-12-06 10:22:40,102] [pool-1-thread-3] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-12-06 10:22:41,723] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] [2024-12-06 10:22:42,097] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-12-06 10:22:42,671] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-12-06 10:22:42,764] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-12-06 10:22:43,691] [pool-1-thread-6] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-12-06 10:22:44,291] [pool-1-thread-11] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-12-06 10:22:44,979] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-12-06 10:22:45,643] [pool-1-thread-4] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-12-06 10:22:45,919] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-12-06 10:22:46,043] [pool-1-thread-2] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-12-06 10:22:46,399] [pool-1-thread-12] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-12-06 10:22:46,689] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-12-06 10:22:47,516] [pool-1-thread-5] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-12-06 10:22:48,601] [pool-1-thread-8] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-12-06 10:22:49,397] [pool-1-thread-1] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-12-06 10:22:49,918] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-12-06 10:22:50,039] [pool-1-thread-4] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-12-06 10:22:50,526] [pool-1-thread-3] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-12-06 10:22:51,472] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-12-06 10:22:51,576] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-12-06 10:22:51,760] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-12-06 10:22:53,189] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-12-06 10:22:53,429] [pool-1-thread-9] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-12-06 10:22:54,589] [pool-1-thread-8] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-12-06 10:23:14,593] [pool-1-thread-10] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-12-06 10:23:15,252] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-12-06 10:23:15,784] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-12-06 10:23:16,483] [pool-1-thread-4] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-12-06 10:23:18,443] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-12-06 10:23:18,560] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-12-06 10:23:18,708] [pool-1-thread-2] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-12-06 10:23:20,296] [pool-1-thread-10] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-12-06 10:23:21,044] [pool-1-thread-9] 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 18 seconds Finished: SUCCESS