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Started by upstream project "BIOFORMATS-test-repo" build number 117 originally caused by: Started by upstream project "Trigger" build number 134 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins12182534842628155733.sh + '[' samples = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_18207_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 01:27:09,632 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:27:09,633 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 01:27:09,633 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:27:09,634 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:27:09,635 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:27:09,635 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:27:09,635 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:27:09,635 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:27:09,636 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:27:09,636 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:27:09,637 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:27:09,637 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:27:09,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:27:09,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:27:09,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:27:09,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:27:09,831 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:27:09,831 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:27:09,831 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:27:09,832 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:27:09,832 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 01:27:09,833 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 01:27:09,833 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 197 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-11 01:27:09,841] [main] java.version = 21 [testng] 01:27:09,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:27:09,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:09,904 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-11_01-27-09.log] [testng] 01:27:09,907 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-07-11 01:27:09,909] [main] testng.directory = /data [testng] [2024-07-11 01:27:09,909] [main] testng.configDirectory = /config [testng] [2024-07-11 01:27:09,924] [main] testng.multiplier = 1.0 [testng] [2024-07-11 01:27:09,925] [main] testng.in-memory = false [testng] [2024-07-11 01:27:09,926] [main] testng.allow-missing = false [testng] [2024-07-11 01:27:09,926] [main] user.language = en [testng] [2024-07-11 01:27:09,926] [main] user.country = ${user.country} [testng] [2024-07-11 01:27:09,926] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-11 01:27:31,084] [main] ---------------------------------------- [testng] [2024-07-11 01:27:31,084] [main] Total files: 164 [testng] [2024-07-11 01:27:31,085] [main] Scan time: 21.158 s (129 ms/file) [testng] [2024-07-11 01:27:31,085] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-11 01:27:40,430] [pool-1-thread-1] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 01:27:40,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:27:40,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:40,432 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-11_01-27-40.log] [testng] 01:27:40,433 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6963d493 - End of configuration. [testng] [2024-07-11 01:27:40,448] [pool-1-thread-12] Initializing /data/sdub/sdub.pattern: [testng] 01:27:40,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:27:40,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:40,449 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-11_01-27-40.log] [testng] 01:27:40,449 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cd8e08b - End of configuration. [testng] [2024-07-11 01:27:40,709] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] 01:27:40,710 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:27:40,710 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:40,711 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-11_01-27-40.log] [testng] 01:27:40,711 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bd16688 - End of configuration. [testng] [2024-07-11 01:27:40,723] [pool-1-thread-10] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 01:27:40,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:27:40,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:40,725 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-11_01-27-40.log] [testng] 01:27:40,725 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15f51157 - End of configuration. [testng] [2024-07-11 01:27:41,013] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 01:27:41,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:27:41,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:41,014 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-11_01-27-41.log] [testng] 01:27:41,014 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d034c8e - End of configuration. [testng] [2024-07-11 01:27:41,038] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:27:41,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:27:41,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:41,040 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-11_01-27-41.log] [testng] 01:27:41,040 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b41f3a1 - End of configuration. [testng] [2024-07-11 01:27:41,054] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] 01:27:41,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:27:41,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:41,055 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-11_01-27-41.log] [testng] 01:27:41,056 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5095471d - End of configuration. [testng] [2024-07-11 01:27:41,091] [pool-1-thread-6] Initializing /data/openjpeg/Facade.pnm: [testng] 01:27:41,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:27:41,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:41,092 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-11_01-27-41.log] [testng] 01:27:41,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c48d0d1 - End of configuration. [testng] [2024-07-11 01:27:41,101] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 01:27:41,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:27:41,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:41,103 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-11_01-27-41.log] [testng] 01:27:41,103 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31264c57 - End of configuration. [testng] [2024-07-11 01:27:41,112] [pool-1-thread-4] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 01:27:41,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:27:41,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:41,113 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-11_01-27-41.log] [testng] 01:27:41,114 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7880b379 - End of configuration. [testng] [2024-07-11 01:27:41,204] [pool-1-thread-3] Initializing /data/openjpeg/Rome.jp2: [testng] 01:27:41,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:27:41,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:41,205 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-11_01-27-41.log] [testng] 01:27:41,205 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9ea9de2 - End of configuration. [testng] [2024-07-11 01:27:41,220] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 01:27:41,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:27:41,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:41,222 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-11_01-27-41.log] [testng] 01:27:41,222 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c148d0d - End of configuration. [testng] [2024-07-11 01:27:43,701] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-07-11 01:27:43,707] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-07-11 01:27:43,716] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-07-11 01:27:43,727] [pool-1-thread-2] Initializing /data/ome/654Atemp.stk: [testng] [2024-07-11 01:27:43,834] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-07-11 01:27:44,155] [pool-1-thread-6] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-07-11 01:27:44,162] [pool-1-thread-12] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-07-11 01:27:45,038] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-07-11 01:27:45,161] [pool-1-thread-4] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-07-11 01:27:45,230] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-07-11 01:27:45,301] [pool-1-thread-3] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-07-11 01:27:45,356] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-07-11 01:27:45,434] [pool-1-thread-10] Initializing /data/ome/C1.lsm: [testng] [2024-07-11 01:27:45,453] [pool-1-thread-3] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-07-11 01:27:45,627] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-07-11 01:27:45,792] [pool-1-thread-2] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-07-11 01:27:45,847] [pool-1-thread-10] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-07-11 01:27:45,890] [pool-1-thread-8] Initializing /data/ome/worm.tiff: [testng] [2024-07-11 01:27:45,929] [pool-1-thread-3] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-07-11 01:27:46,119] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-07-11 01:27:46,182] [pool-1-thread-7] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-07-11 01:27:46,237] [pool-1-thread-2] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-07-11 01:27:46,393] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-07-11 01:27:46,401] [pool-1-thread-1] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-07-11 01:27:46,436] [pool-1-thread-3] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-07-11 01:27:46,517] [pool-1-thread-10] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-07-11 01:27:46,549] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-07-11 01:27:46,698] [pool-1-thread-4] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-07-11 01:27:47,689] [pool-1-thread-5] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-07-11 01:27:47,999] [pool-1-thread-11] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-07-11 01:27:48,088] [pool-1-thread-5] Initializing /data/ome/cb_1.r3d: [testng] [2024-07-11 01:27:48,268] [pool-1-thread-3] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-07-11 01:27:48,307] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-07-11 01:27:48,319] [pool-1-thread-2] Initializing /data/ome/embryo.lsm: [testng] [2024-07-11 01:27:48,457] [pool-1-thread-11] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-07-11 01:27:48,787] [pool-1-thread-2] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-07-11 01:27:48,857] [pool-1-thread-3] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-07-11 01:27:49,346] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-07-11 01:27:49,396] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-07-11 01:27:49,490] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-07-11 01:27:49,502] [pool-1-thread-3] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-07-11 01:27:49,757] [pool-1-thread-7] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-07-11 01:27:49,884] [pool-1-thread-5] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-07-11 01:27:49,993] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-07-11 01:27:50,006] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-07-11 01:27:50,141] [pool-1-thread-5] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-07-11 01:27:50,248] [pool-1-thread-8] Initializing /data/ome/compressed2ChZ.lsm: [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 11 seconds Finished: SUCCESS