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Started by upstream project "BIOFORMATS-test-repo" build number 208 originally caused by: Started by upstream project "Trigger" build number 234 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/jenkins9041641312967333951.sh + '[' samples = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_32974_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 01:33:33,013 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:33:33,015 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 01:33:33,015 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:33:33,016 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:33:33,016 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:33:33,016 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:33:33,017 |-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] 01:33:33,017 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:33:33,017 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:33:33,018 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:33:33,018 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:33:33,019 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:33:33,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:33:33,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:33:33,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:33:33,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:33:33,241 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:33:33,242 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:33:33,242 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:33:33,243 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:33:33,243 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 01:33:33,244 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 01:33:33,244 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 227 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-03 01:33:33,258] [main] java.version = 21 [testng] 01:33:33,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:33:33,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:33,312 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-03_01-33-33.log] [testng] 01:33:33,313 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-10-03 01:33:33,315] [main] testng.directory = /data [testng] [2024-10-03 01:33:33,315] [main] testng.configDirectory = /config [testng] [2024-10-03 01:33:33,323] [main] testng.multiplier = 1.0 [testng] [2024-10-03 01:33:33,324] [main] testng.in-memory = false [testng] [2024-10-03 01:33:33,324] [main] testng.allow-missing = false [testng] [2024-10-03 01:33:33,324] [main] user.language = en [testng] [2024-10-03 01:33:33,324] [main] user.country = ${user.country} [testng] [2024-10-03 01:33:33,324] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-03 01:34:08,803] [main] ---------------------------------------- [testng] [2024-10-03 01:34:08,803] [main] Total files: 164 [testng] [2024-10-03 01:34:08,803] [main] Scan time: 35.479 s (216 ms/file) [testng] [2024-10-03 01:34:08,804] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-03 01:34:37,741] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 01:34:37,741 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:34:37,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:37,743 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-03_01-34-37.log] [testng] 01:34:37,743 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22b4ff3e - End of configuration. [testng] [2024-10-03 01:34:37,814] [pool-1-thread-12] Initializing /data/ome/tiffany.color.tiff: [testng] 01:34:37,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:34:37,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:37,815 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-03_01-34-37.log] [testng] 01:34:37,816 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5885929d - End of configuration. [testng] [2024-10-03 01:34:39,048] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 01:34:39,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:34:39,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:39,049 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-03_01-34-39.log] [testng] 01:34:39,050 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e02ceca - End of configuration. [testng] [2024-10-03 01:34:39,141] [pool-1-thread-10] Initializing /data/openjpeg/Facade.bmp: [testng] 01:34:39,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:34:39,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:39,142 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-03_01-34-39.log] [testng] 01:34:39,143 |-INFO in ch.qos.logback.core.sift.SiftProcessor@377bbd54 - End of configuration. [testng] [2024-10-03 01:34:39,202] [pool-1-thread-9] Initializing /data/sdub/sdub.pattern: [testng] 01:34:39,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:34:39,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:39,203 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-03_01-34-39.log] [testng] 01:34:39,203 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f0650b8 - End of configuration. [testng] [2024-10-03 01:34:43,147] [pool-1-thread-8] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] 01:34:43,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:34:43,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:43,149 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-03_01-34-43.log] [testng] 01:34:43,149 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65350b87 - End of configuration. [testng] [2024-10-03 01:34:43,367] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] 01:34:43,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:34:43,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:43,368 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-03_01-34-43.log] [testng] 01:34:43,368 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71301bfb - End of configuration. [testng] [2024-10-03 01:34:43,623] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] 01:34:43,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:34:43,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:43,624 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-03_01-34-43.log] [testng] 01:34:43,624 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31b78629 - End of configuration. [testng] [2024-10-03 01:34:43,656] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:34:43,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:34:43,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:43,657 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-03_01-34-43.log] [testng] 01:34:43,657 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a9894c1 - End of configuration. [testng] [2024-10-03 01:34:43,683] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:34:43,683 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:34:43,683 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:43,684 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-03_01-34-43.log] [testng] 01:34:43,685 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c7a5853 - End of configuration. [testng] [2024-10-03 01:34:43,854] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 01:34:43,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:34:43,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:43,855 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-03_01-34-43.log] [testng] 01:34:43,856 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7926de0f - End of configuration. [testng] [2024-10-03 01:34:44,202] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:34:44,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:34:44,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:44,203 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-03_01-34-44.log] [testng] 01:34:44,204 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46204784 - End of configuration. [testng] [2024-10-03 01:34:46,457] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-10-03 01:34:46,490] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-10-03 01:34:46,995] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-10-03 01:34:47,276] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-10-03 01:34:47,428] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-10-03 01:34:47,482] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-10-03 01:34:47,557] [pool-1-thread-1] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-10-03 01:34:48,107] [pool-1-thread-4] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-10-03 01:34:49,024] [pool-1-thread-7] Initializing /data/ome/worm.tiff: [testng] [2024-10-03 01:34:50,307] [pool-1-thread-2] Initializing /data/ome/embryo.lsm: [testng] [2024-10-03 01:34:50,576] [pool-1-thread-12] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-10-03 01:34:51,470] [pool-1-thread-11] Initializing /data/ome/654Atemp.stk: [testng] [2024-10-03 01:34:53,124] [pool-1-thread-5] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-10-03 01:34:53,231] [pool-1-thread-8] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-10-03 01:34:54,222] [pool-1-thread-6] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-10-03 01:34:55,017] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-10-03 01:34:55,323] [pool-1-thread-5] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-10-03 01:34:55,955] [pool-1-thread-10] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-10-03 01:34:56,469] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-10-03 01:34:56,698] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-10-03 01:34:57,154] [pool-1-thread-12] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-10-03 01:34:57,888] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-10-03 01:34:58,149] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-10-03 01:34:58,593] [pool-1-thread-7] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-10-03 01:34:58,922] [pool-1-thread-3] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-10-03 01:34:59,148] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-10-03 01:34:59,778] [pool-1-thread-12] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-10-03 01:35:15,439] [pool-1-thread-5] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-10-03 01:35:16,746] [pool-1-thread-7] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-10-03 01:35:16,913] [pool-1-thread-10] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-10-03 01:35:17,299] [pool-1-thread-8] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-10-03 01:35:17,753] [pool-1-thread-6] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-10-03 01:35:18,179] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-10-03 01:35:18,300] [pool-1-thread-1] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-10-03 01:35:18,668] [pool-1-thread-11] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-10-03 01:35:20,046] [pool-1-thread-7] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-10-03 01:35:21,691] [pool-1-thread-8] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-10-03 01:35:21,946] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-10-03 01:35:22,723] [pool-1-thread-10] Initializing /data/ome/cb_1.r3d: [testng] [2024-10-03 01:35:23,591] [pool-1-thread-1] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-10-03 01:35:24,454] [pool-1-thread-7] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-10-03 01:35:24,986] [pool-1-thread-6] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-10-03 01:35:25,148] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-10-03 01:35:26,210] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-10-03 01:35:27,255] [pool-1-thread-9] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-10-03 01:35:28,826] [pool-1-thread-10] Initializing /data/ome/C1.lsm: [testng] [2024-10-03 01:35:29,508] [pool-1-thread-3] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 3 minutes 49 seconds Finished: SUCCESS