Started by upstream project "BIOFORMATS-test-repo" build number 184 originally caused by: Started by upstream project "Trigger" build number 206 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins11893353453973878032.sh + '[' samples = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_29038_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] 10:45:47,209 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 10:45:47,211 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 10:45:47,211 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:45:47,212 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:45:47,213 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 10:45:47,213 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 10:45:47,213 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 10:45:47,213 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:45:47,214 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:45:47,214 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 10:45:47,215 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 10:45:47,215 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 10:45:47,429 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 10:45:47,429 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 10:45:47,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 10:45:47,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 10:45:47,462 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 10:45:47,463 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 10:45:47,463 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 10:45:47,463 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 10:45:47,463 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 10:45:47,464 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 10:45:47,464 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 250 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-11 10:45:47,474] [main] java.version = 17.0.2 [testng] 10:45:47,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 10:45:47,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:45:47,522 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-11_10-45-47.log] [testng] 10:45:47,524 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-09-11 10:45:47,526] [main] testng.directory = /data [testng] [2024-09-11 10:45:47,527] [main] testng.configDirectory = /config [testng] [2024-09-11 10:45:47,537] [main] testng.multiplier = 1.0 [testng] [2024-09-11 10:45:47,538] [main] testng.in-memory = false [testng] [2024-09-11 10:45:47,538] [main] testng.allow-missing = false [testng] [2024-09-11 10:45:47,538] [main] user.language = en [testng] [2024-09-11 10:45:47,539] [main] user.country = ${user.country} [testng] [2024-09-11 10:45:47,539] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-11 10:46:07,105] [main] ---------------------------------------- [testng] [2024-09-11 10:46:07,106] [main] Total files: 164 [testng] [2024-09-11 10:46:07,106] [main] Scan time: 19.566 s (119 ms/file) [testng] [2024-09-11 10:46:07,106] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-11 10:46:16,339] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] 10:46:16,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:46:16,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:46:16,341 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-11_10-46-16.log] [testng] 10:46:16,342 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4587c321 - End of configuration. [testng] [2024-09-11 10:46:16,422] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 10:46:16,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:46:16,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:46:16,423 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-11_10-46-16.log] [testng] 10:46:16,424 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6543fac1 - End of configuration. [testng] [2024-09-11 10:46:16,445] [pool-1-thread-11] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 10:46:16,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:46:16,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:46:16,446 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-11_10-46-16.log] [testng] 10:46:16,447 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74c8b280 - End of configuration. [testng] [2024-09-11 10:46:16,512] [pool-1-thread-10] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] 10:46:16,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:46:16,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:46:16,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-11_10-46-16.log] [testng] 10:46:16,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a5e5610 - End of configuration. [testng] [2024-09-11 10:46:16,620] [pool-1-thread-9] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 10:46:16,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:46:16,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:46:16,621 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-11_10-46-16.log] [testng] 10:46:16,622 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66dd7483 - End of configuration. [testng] [2024-09-11 10:46:16,651] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 10:46:16,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:46:16,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:46:16,654 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-11_10-46-16.log] [testng] 10:46:16,654 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57423d07 - End of configuration. [testng] [2024-09-11 10:46:16,673] [pool-1-thread-7] Initializing /data/openjpeg/Facade.bmp: [testng] 10:46:16,674 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:46:16,674 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:46:16,675 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-11_10-46-16.log] [testng] 10:46:16,675 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e2e225b - End of configuration. [testng] [2024-09-11 10:46:16,696] [pool-1-thread-6] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 10:46:16,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:46:16,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:46:16,698 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-11_10-46-16.log] [testng] 10:46:16,698 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75cc45e7 - End of configuration. [testng] [2024-09-11 10:46:16,787] [pool-1-thread-5] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 10:46:16,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:46:16,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:46:16,788 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-11_10-46-16.log] [testng] 10:46:16,788 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b83f79 - End of configuration. [testng] [2024-09-11 10:46:16,903] [pool-1-thread-4] Initializing /data/ome/Adultmidsection.lsm: [testng] 10:46:16,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:46:16,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:46:16,907 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-11_10-46-16.log] [testng] 10:46:16,908 |-INFO in ch.qos.logback.core.sift.SiftProcessor@518f9006 - End of configuration. [testng] [2024-09-11 10:46:16,953] [pool-1-thread-3] Initializing /data/ome/worm.tiff: [testng] 10:46:16,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:46:16,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:46:16,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-11_10-46-16.log] [testng] 10:46:16,955 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34dd50fa - End of configuration. [testng] [2024-09-11 10:46:17,167] [pool-1-thread-2] Initializing /data/ome/cb_1.r3d: [testng] 10:46:17,167 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:46:17,167 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:46:17,168 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-11_10-46-17.log] [testng] 10:46:17,168 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7747cd08 - End of configuration. [testng] [2024-09-11 10:46:19,086] [pool-1-thread-8] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-09-11 10:46:19,547] [pool-1-thread-11] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-09-11 10:46:19,613] [pool-1-thread-2] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-09-11 10:46:20,033] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-09-11 10:46:20,132] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-09-11 10:46:20,189] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-09-11 10:46:20,426] [pool-1-thread-6] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-09-11 10:46:20,513] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-09-11 10:46:20,524] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-09-11 10:46:20,603] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-09-11 10:46:20,750] [pool-1-thread-7] Initializing /data/ome/embryo.lsm: [testng] [2024-09-11 10:46:20,883] [pool-1-thread-11] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-09-11 10:46:21,018] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-09-11 10:46:21,024] [pool-1-thread-3] Initializing /data/ome/654Atemp.stk: [testng] [2024-09-11 10:46:21,231] [pool-1-thread-12] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-09-11 10:46:21,252] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-09-11 10:46:21,589] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-09-11 10:46:21,884] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-09-11 10:46:21,919] [pool-1-thread-6] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-09-11 10:46:21,959] [pool-1-thread-7] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-09-11 10:46:23,639] [pool-1-thread-4] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-09-11 10:46:23,675] [pool-1-thread-12] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-09-11 10:46:23,705] [pool-1-thread-10] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-09-11 10:46:23,721] [pool-1-thread-11] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-09-11 10:46:23,775] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-09-11 10:46:24,036] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-09-11 10:46:24,215] [pool-1-thread-11] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-09-11 10:46:24,265] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-09-11 10:46:24,305] [pool-1-thread-5] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-09-11 10:46:24,962] [pool-1-thread-1] Initializing /data/ome/C1.lsm: [testng] [2024-09-11 10:46:25,010] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-09-11 10:46:25,138] [pool-1-thread-8] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-09-11 10:46:25,343] [pool-1-thread-10] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-09-11 10:46:25,470] [pool-1-thread-6] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-09-11 10:46:25,831] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-09-11 10:46:25,931] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-09-11 10:46:25,993] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-09-11 10:46:26,149] [pool-1-thread-2] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-09-11 10:46:26,317] [pool-1-thread-9] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-09-11 10:46:26,332] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-09-11 10:46:26,441] [pool-1-thread-3] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-09-11 10:46:26,751] [pool-1-thread-11] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-09-11 10:46:26,867] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-09-11 10:46:27,002] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-09-11 10:46:27,102] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-09-11 10:46:27,189] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-09-11 10:46:27,616] [pool-1-thread-11] Initializing /data/sdub/sdub.pattern: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 2 minutes 13 seconds Finished: SUCCESS