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Started by upstream project "BIOFORMATS-test-repo" build number 291 originally caused by: Started by upstream project "Trigger" build number 310 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/jenkins12224780768711082425.sh + '[' samples = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_45943_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 [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 00:43:11,304 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:43:11,305 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:43:11,305 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:43:11,306 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:43:11,306 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:43:11,307 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:43:11,307 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:43:11,307 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:43:11,307 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:43:11,308 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:43:11,308 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:43:11,308 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:43:11,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:43:11,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:43:11,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:43:11,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:43:11,495 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:43:11,495 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:43:11,495 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:43:11,495 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:43:11,495 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:43:11,496 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:43:11,496 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 189 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-15 00:43:11,505] [main] java.version = 17.0.2 [testng] 00:43:11,508 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:43:11,508 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:11,548 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-15_00-43-11.log] [testng] 00:43:11,549 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-15 00:43:11,551] [main] testng.directory = /data [testng] [2024-12-15 00:43:11,551] [main] testng.configDirectory = /config [testng] [2024-12-15 00:43:11,560] [main] testng.multiplier = 1.0 [testng] [2024-12-15 00:43:11,560] [main] testng.in-memory = false [testng] [2024-12-15 00:43:11,560] [main] testng.allow-missing = false [testng] [2024-12-15 00:43:11,560] [main] user.language = en [testng] [2024-12-15 00:43:11,560] [main] user.country = ${user.country} [testng] [2024-12-15 00:43:11,561] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-15 00:44:22,154] [main] ---------------------------------------- [testng] [2024-12-15 00:44:22,154] [main] Total files: 164 [testng] [2024-12-15 00:44:22,154] [main] Scan time: 70.593 s (430 ms/file) [testng] [2024-12-15 00:44:22,154] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-15 00:46:48,883] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] 00:46:48,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:46:48,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:48,884 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-15_00-46-48.log] [testng] 00:46:48,884 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a678a8b - End of configuration. [testng] [2024-12-15 00:46:50,880] [pool-1-thread-12] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 00:46:50,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:46:50,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:50,881 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-15_00-46-50.log] [testng] 00:46:50,881 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1334f822 - End of configuration. [testng] [2024-12-15 00:46:51,967] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:46:51,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:46:51,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:51,968 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-15_00-46-51.log] [testng] 00:46:51,968 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37dcbf02 - End of configuration. [testng] [2024-12-15 00:46:53,419] [pool-1-thread-10] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 00:46:53,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:46:53,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:53,420 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-15_00-46-53.log] [testng] 00:46:53,420 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12c4c5e2 - End of configuration. [testng] [2024-12-15 00:46:53,846] [pool-1-thread-9] Initializing /data/openjpeg/thumb_facade.jpg: [testng] 00:46:53,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:46:53,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:53,847 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-15_00-46-53.log] [testng] 00:46:53,847 |-INFO in ch.qos.logback.core.sift.SiftProcessor@379064b1 - End of configuration. [testng] [2024-12-15 00:46:54,021] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 00:46:54,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:46:54,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:54,022 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-15_00-46-54.log] [testng] 00:46:54,023 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f6a1903 - End of configuration. [testng] [2024-12-15 00:46:54,213] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:46:54,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:46:54,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:54,214 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-15_00-46-54.log] [testng] 00:46:54,214 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67811bc7 - End of configuration. [testng] [2024-12-15 00:46:54,997] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] 00:46:54,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:46:54,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:54,998 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-15_00-46-54.log] [testng] 00:46:54,999 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48868ad6 - End of configuration. [testng] [2024-12-15 00:46:56,329] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:46:56,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:46:56,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:56,330 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-15_00-46-56.log] [testng] 00:46:56,331 |-INFO in ch.qos.logback.core.sift.SiftProcessor@442f9fdc - End of configuration. [testng] [2024-12-15 00:46:58,091] [pool-1-thread-4] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 00:46:58,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:46:58,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:58,092 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-15_00-46-58.log] [testng] 00:46:58,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29664303 - End of configuration. [testng] [2024-12-15 00:46:58,477] [pool-1-thread-3] Initializing /data/ome/tiffany.color.tiff: [testng] 00:46:58,477 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:46:58,477 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:58,478 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-15_00-46-58.log] [testng] 00:46:58,479 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20d5bfaa - End of configuration. [testng] [2024-12-15 00:47:00,760] [pool-1-thread-2] Initializing /data/ome/anusgfpzs.lsm: [testng] 00:47:00,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:47:00,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:00,761 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-15_00-47-00.log] [testng] 00:47:00,761 |-INFO in ch.qos.logback.core.sift.SiftProcessor@495fbf76 - End of configuration. [testng] [2024-12-15 00:47:07,305] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-12-15 00:47:07,536] [pool-1-thread-10] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-12-15 00:47:09,470] [pool-1-thread-8] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-12-15 00:47:10,318] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-12-15 00:47:11,897] [pool-1-thread-7] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-12-15 00:47:12,922] [pool-1-thread-10] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-12-15 00:47:13,191] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-12-15 00:47:13,365] [pool-1-thread-6] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-12-15 00:47:15,305] [pool-1-thread-2] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-12-15 00:47:16,489] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-12-15 00:47:17,540] [pool-1-thread-5] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-12-15 00:47:18,482] [pool-1-thread-11] Initializing /data/ome/cb_1.r3d: [testng] [2024-12-15 00:47:20,790] [pool-1-thread-9] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-12-15 00:47:22,906] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-12-15 00:47:24,307] [pool-1-thread-10] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-12-15 00:47:26,317] [pool-1-thread-3] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-12-15 00:47:26,582] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-12-15 00:47:26,919] [pool-1-thread-1] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-12-15 00:47:27,461] [pool-1-thread-8] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-12-15 00:47:29,891] [pool-1-thread-11] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-12-15 00:47:31,122] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-12-15 00:47:31,843] [pool-1-thread-7] Initializing /data/ome/C1.lsm: [testng] [2024-12-15 00:47:34,127] [pool-1-thread-6] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-12-15 00:47:36,360] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-12-15 00:47:38,141] [pool-1-thread-1] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-12-15 00:47:38,522] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-12-15 00:47:38,787] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-12-15 00:47:40,313] [pool-1-thread-9] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-12-15 00:47:40,574] [pool-1-thread-2] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-12-15 00:47:43,110] [pool-1-thread-8] Initializing /data/ome/654Atemp.stk: [testng] [2024-12-15 00:47:46,871] [pool-1-thread-11] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-12-15 00:48:34,696] [pool-1-thread-3] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-12-15 00:48:36,013] [pool-1-thread-5] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-12-15 00:48:37,613] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-12-15 00:48:38,242] [pool-1-thread-7] Initializing /data/ome/worm.tiff: [testng] [2024-12-15 00:48:43,070] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-12-15 00:48:44,378] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-12-15 00:48:45,684] [pool-1-thread-12] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-12-15 00:48:48,026] [pool-1-thread-4] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-12-15 00:48:53,036] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-12-15 00:48:54,215] [pool-1-thread-3] Initializing /data/sdub/sdub.pattern: [testng] [2024-12-15 00:49:11,790] [pool-1-thread-9] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-12-15 00:49:14,330] [pool-1-thread-2] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-12-15 00:49:15,828] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-12-15 00:49:17,040] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-12-15 00:49:17,493] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-12-15 00:49:18,486] [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: 9 minutes 43 seconds Finished: SUCCESS