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Started by upstream project "BIOFORMATS-test-repo" build number 248 originally caused by: Started by upstream project "Trigger" build number 272 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins14105483689807647070.sh + '[' samples = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_39018_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 00:37:42,953 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:37:42,954 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 00:37:42,954 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:42,955 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:42,956 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:37:42,956 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:37:42,956 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:37:42,956 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:42,957 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:42,957 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:37:42,958 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:37:42,958 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:37:43,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:37:43,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:37:43,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:37:43,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:37:43,143 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:37:43,143 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:37:43,143 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:37:43,143 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:37:43,143 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 00:37:43,144 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 00:37:43,144 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 187 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-07 00:37:43,153] [main] java.version = 21 [testng] 00:37:43,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:37:43,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:43,196 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-07_00-37-43.log] [testng] 00:37:43,197 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-11-07 00:37:43,199] [main] testng.directory = /data [testng] [2024-11-07 00:37:43,199] [main] testng.configDirectory = /config [testng] [2024-11-07 00:37:43,207] [main] testng.multiplier = 1.0 [testng] [2024-11-07 00:37:43,208] [main] testng.in-memory = false [testng] [2024-11-07 00:37:43,208] [main] testng.allow-missing = false [testng] [2024-11-07 00:37:43,208] [main] user.language = en [testng] [2024-11-07 00:37:43,208] [main] user.country = ${user.country} [testng] [2024-11-07 00:37:43,208] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-07 00:38:22,433] [main] ---------------------------------------- [testng] [2024-11-07 00:38:22,433] [main] Total files: 164 [testng] [2024-11-07 00:38:22,433] [main] Scan time: 39.225 s (239 ms/file) [testng] [2024-11-07 00:38:22,434] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-07 00:39:23,517] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:39:23,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:39:23,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:23,518 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-07_00-39-23.log] [testng] 00:39:23,519 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5cedc35b - End of configuration. [testng] [2024-11-07 00:39:23,835] [pool-1-thread-12] Initializing /data/openjpeg/Facade.pnm: [testng] 00:39:23,835 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:39:23,835 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:23,836 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-07_00-39-23.log] [testng] 00:39:23,837 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6492bb3f - End of configuration. [testng] [2024-11-07 00:39:24,061] [pool-1-thread-11] Initializing /data/ome/C1.lsm: [testng] 00:39:24,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:39:24,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:24,062 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-07_00-39-24.log] [testng] 00:39:24,062 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bba0814 - End of configuration. [testng] [2024-11-07 00:39:24,490] [pool-1-thread-10] Initializing /data/openjpeg/Facade.bmp: [testng] 00:39:24,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:39:24,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:24,491 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-07_00-39-24.log] [testng] 00:39:24,491 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d23af89 - End of configuration. [testng] [2024-11-07 00:39:24,549] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 00:39:24,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:39:24,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:24,550 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-07_00-39-24.log] [testng] 00:39:24,551 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d911d22 - End of configuration. [testng] [2024-11-07 00:39:24,613] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 00:39:24,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:39:24,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:24,614 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-07_00-39-24.log] [testng] 00:39:24,615 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29a81142 - End of configuration. [testng] [2024-11-07 00:39:24,709] [pool-1-thread-7] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] 00:39:24,710 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:39:24,710 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:24,711 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-07_00-39-24.log] [testng] 00:39:24,711 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e72f393 - End of configuration. [testng] [2024-11-07 00:39:25,831] [pool-1-thread-6] Initializing /data/openjpeg/Rome.jp2: [testng] 00:39:25,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:39:25,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:25,832 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-07_00-39-25.log] [testng] 00:39:25,832 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3499b443 - End of configuration. [testng] [2024-11-07 00:39:26,234] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv: [testng] 00:39:26,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:39:26,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:26,235 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-07_00-39-26.log] [testng] 00:39:26,235 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c40c7b0 - End of configuration. [testng] [2024-11-07 00:39:26,354] [pool-1-thread-4] Initializing /data/ome/011B1_Morph.HTD: [testng] 00:39:26,354 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:39:26,354 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:26,355 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-07_00-39-26.log] [testng] 00:39:26,355 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57ca05f - End of configuration. [testng] [2024-11-07 00:39:27,236] [pool-1-thread-3] Initializing /data/ome/654Atemp.stk: [testng] 00:39:27,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:39:27,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:27,237 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-07_00-39-27.log] [testng] 00:39:27,237 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8ec34be - End of configuration. [testng] [2024-11-07 00:39:28,003] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] 00:39:28,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:39:28,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:28,004 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-07_00-39-28.log] [testng] 00:39:28,004 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57a411f5 - End of configuration. [testng] [2024-11-07 00:39:30,670] [pool-1-thread-9] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-11-07 00:39:30,802] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-11-07 00:39:31,745] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-11-07 00:39:31,889] [pool-1-thread-10] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-11-07 00:39:32,772] [pool-1-thread-2] Initializing /data/sdub/sdub.pattern: [testng] [2024-11-07 00:39:37,669] [pool-1-thread-8] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-11-07 00:39:38,861] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-11-07 00:39:39,063] [pool-1-thread-1] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-11-07 00:39:39,689] [pool-1-thread-11] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-11-07 00:39:40,501] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-11-07 00:39:40,954] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-11-07 00:39:41,388] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-11-07 00:39:42,016] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-11-07 00:39:42,524] [pool-1-thread-5] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-11-07 00:39:43,551] [pool-1-thread-8] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-11-07 00:40:01,914] [pool-1-thread-3] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-11-07 00:40:03,252] [pool-1-thread-12] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-11-07 00:40:03,873] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-11-07 00:40:04,695] [pool-1-thread-10] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-11-07 00:40:05,381] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-11-07 00:40:05,935] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-11-07 00:40:06,566] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-11-07 00:40:07,482] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-11-07 00:40:08,417] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-11-07 00:40:09,023] [pool-1-thread-6] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-11-07 00:40:10,863] [pool-1-thread-11] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-11-07 00:40:11,415] [pool-1-thread-1] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-11-07 00:40:12,173] [pool-1-thread-3] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-11-07 00:40:13,004] [pool-1-thread-10] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-11-07 00:40:14,338] [pool-1-thread-9] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-11-07 00:40:15,899] [pool-1-thread-6] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-11-07 00:40:17,532] [pool-1-thread-1] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-11-07 00:40:18,295] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-11-07 00:40:18,700] [pool-1-thread-3] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-11-07 00:40:19,084] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-11-07 00:40:19,711] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2024-11-07 00:40:20,275] [pool-1-thread-11] Initializing /data/ome/worm.tiff: [testng] [2024-11-07 00:40:21,887] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-11-07 00:40:22,261] [pool-1-thread-3] Initializing /data/ome/cb_1.r3d: [testng] [2024-11-07 00:40:22,825] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-11-07 00:40:23,440] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-11-07 00:40:24,836] [pool-1-thread-6] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-11-07 00:40:25,396] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-11-07 00:40:25,491] [pool-1-thread-12] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-11-07 00:40:25,965] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-11-07 00:40:26,527] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-11-07 00:40:28,508] [pool-1-thread-1] Initializing /data/ome/tiffany.color.tiff: [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 59 seconds Finished: SUCCESS