![[Jenkins]](/jenkins/static/eed02e22/images/svgs/logo.svg){kind=logo}
Started by upstream project "BIOFORMATS-test-repo" build number 279 originally caused by: Started by upstream project "Trigger" build number 299 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins15712020797659282797.sh + '[' samples = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43973_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] 00:32:10,681 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:32:10,682 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:32:10,682 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:32:10,683 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:32:10,684 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:32:10,684 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:32:10,684 |-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] 00:32:10,684 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:32:10,685 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:32:10,685 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:32:10,686 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:32:10,686 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:32:10,869 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:32:10,869 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:32:10,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:32:10,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:32:10,912 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:32:10,913 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:32:10,913 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:32:10,914 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:32:10,914 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:32:10,915 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:32:10,915 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 230 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-04 00:32:10,925] [main] java.version = 17.0.2 [testng] 00:32:10,928 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:32:10,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:10,970 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-04_00-32-10.log] [testng] 00:32:10,972 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-04 00:32:10,974] [main] testng.directory = /data [testng] [2024-12-04 00:32:10,974] [main] testng.configDirectory = /config [testng] [2024-12-04 00:32:10,983] [main] testng.multiplier = 1.0 [testng] [2024-12-04 00:32:10,984] [main] testng.in-memory = false [testng] [2024-12-04 00:32:10,984] [main] testng.allow-missing = false [testng] [2024-12-04 00:32:10,984] [main] user.language = en [testng] [2024-12-04 00:32:10,984] [main] user.country = ${user.country} [testng] [2024-12-04 00:32:10,984] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-04 00:32:45,937] [main] ---------------------------------------- [testng] [2024-12-04 00:32:45,937] [main] Total files: 164 [testng] [2024-12-04 00:32:45,937] [main] Scan time: 34.953 s (213 ms/file) [testng] [2024-12-04 00:32:45,937] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-04 00:33:34,075] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] 00:33:34,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:33:34,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:34,076 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-04_00-33-34.log] [testng] 00:33:34,076 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10623b2f - End of configuration. [testng] [2024-12-04 00:33:35,361] [pool-1-thread-12] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 00:33:35,362 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:33:35,362 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:35,362 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-04_00-33-35.log] [testng] 00:33:35,363 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f4cc7aa - End of configuration. [testng] [2024-12-04 00:33:35,855] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:33:35,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:33:35,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:35,856 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-04_00-33-35.log] [testng] 00:33:35,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5952fd83 - End of configuration. [testng] [2024-12-04 00:33:36,736] [pool-1-thread-10] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 00:33:36,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:33:36,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:36,737 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-04_00-33-36.log] [testng] 00:33:36,738 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c88ec - End of configuration. [testng] [2024-12-04 00:33:37,030] [pool-1-thread-9] Initializing /data/openjpeg/thumb_facade.jpg: [testng] 00:33:37,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:33:37,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:37,031 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-04_00-33-37.log] [testng] 00:33:37,032 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f33c897 - End of configuration. [testng] [2024-12-04 00:33:37,134] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 00:33:37,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:33:37,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:37,135 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-04_00-33-37.log] [testng] 00:33:37,136 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32a428f3 - End of configuration. [testng] [2024-12-04 00:33:37,232] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:33:37,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:33:37,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:37,233 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-04_00-33-37.log] [testng] 00:33:37,233 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18eff806 - End of configuration. [testng] [2024-12-04 00:33:37,639] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] 00:33:37,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:33:37,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:37,639 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-04_00-33-37.log] [testng] 00:33:37,640 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a49a255 - End of configuration. [testng] [2024-12-04 00:33:38,190] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:33:38,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:33:38,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:38,192 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-04_00-33-38.log] [testng] 00:33:38,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e1a1e58 - End of configuration. [testng] [2024-12-04 00:33:38,723] [pool-1-thread-4] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 00:33:38,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:33:38,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:38,724 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-04_00-33-38.log] [testng] 00:33:38,724 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d5e1c72 - End of configuration. [testng] [2024-12-04 00:33:38,854] [pool-1-thread-3] Initializing /data/ome/tiffany.color.tiff: [testng] 00:33:38,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:33:38,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:38,855 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-04_00-33-38.log] [testng] 00:33:38,855 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8a5b823 - End of configuration. [testng] [2024-12-04 00:33:39,994] [pool-1-thread-2] Initializing /data/ome/anusgfpzs.lsm: [testng] 00:33:39,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:33:39,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:39,995 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-04_00-33-39.log] [testng] 00:33:39,995 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25904576 - End of configuration. [testng] [2024-12-04 00:33:43,351] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-12-04 00:33:43,389] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-12-04 00:33:43,463] [pool-1-thread-10] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-12-04 00:33:43,802] [pool-1-thread-9] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-12-04 00:33:44,366] [pool-1-thread-6] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-12-04 00:33:45,096] [pool-1-thread-12] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-12-04 00:33:45,224] [pool-1-thread-2] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-12-04 00:33:45,845] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-12-04 00:33:47,476] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-12-04 00:33:47,611] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-12-04 00:33:47,738] [pool-1-thread-9] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-12-04 00:33:48,556] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] [2024-12-04 00:33:48,794] [pool-1-thread-12] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-12-04 00:33:49,765] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-12-04 00:33:50,509] [pool-1-thread-3] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-12-04 00:33:51,848] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-12-04 00:33:52,031] [pool-1-thread-8] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-12-04 00:33:52,819] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-12-04 00:33:53,560] [pool-1-thread-4] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-12-04 00:33:54,368] [pool-1-thread-2] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-12-04 00:33:55,318] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-12-04 00:33:56,024] [pool-1-thread-5] Initializing /data/ome/C1.lsm: [testng] [2024-12-04 00:33:56,836] [pool-1-thread-7] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-12-04 00:33:58,978] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-12-04 00:33:59,981] [pool-1-thread-8] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-12-04 00:34:00,199] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-12-04 00:34:00,305] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-12-04 00:34:00,757] [pool-1-thread-10] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-12-04 00:34:00,912] [pool-1-thread-6] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-12-04 00:34:02,256] [pool-1-thread-4] Initializing /data/ome/654Atemp.stk: [testng] [2024-12-04 00:34:04,195] [pool-1-thread-9] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-12-04 00:34:26,934] [pool-1-thread-2] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-12-04 00:34:27,655] [pool-1-thread-12] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-12-04 00:34:28,339] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-12-04 00:34:28,483] [pool-1-thread-8] Initializing /data/ome/worm.tiff: [testng] [2024-12-04 00:34:31,720] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-12-04 00:34:32,634] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-12-04 00:34:33,990] [pool-1-thread-5] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-12-04 00:34:34,985] [pool-1-thread-2] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-12-04 00:34:35,654] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-12-04 00:34:36,347] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern: [testng] [2024-12-04 00:34:42,714] [pool-1-thread-1] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-12-04 00:34:43,317] [pool-1-thread-4] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-12-04 00:34:43,559] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-12-04 00:34:44,362] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-12-04 00:34:44,698] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-12-04 00:34:45,199] [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: 4 minutes 13 seconds Finished: SUCCESS