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Started by upstream project "BIOFORMATS-test-repo" build number 194 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins12836718584689839672.sh + '[' samples = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_30678_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 11:10:18,883 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:10:18,884 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 11:10:18,884 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:10:18,885 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:10:18,885 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:10:18,886 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:10:18,886 |-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] 11:10:18,886 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:10:18,887 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:10:18,887 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:10:18,887 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:10:18,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:10:19,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:10:19,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:10:19,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:10:19,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:10:19,088 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:10:19,088 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:10:19,088 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:10:19,088 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:10:19,088 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 11:10:19,089 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 11:10:19,089 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 202 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-19 11:10:19,098] [main] java.version = 21 [testng] 11:10:19,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:10:19,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:10:19,144 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-19_11-10-19.log] [testng] 11:10:19,146 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-09-19 11:10:19,147] [main] testng.directory = /data [testng] [2024-09-19 11:10:19,148] [main] testng.configDirectory = /config [testng] [2024-09-19 11:10:19,156] [main] testng.multiplier = 1.0 [testng] [2024-09-19 11:10:19,157] [main] testng.in-memory = false [testng] [2024-09-19 11:10:19,157] [main] testng.allow-missing = false [testng] [2024-09-19 11:10:19,157] [main] user.language = en [testng] [2024-09-19 11:10:19,157] [main] user.country = ${user.country} [testng] [2024-09-19 11:10:19,157] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-19 11:11:20,442] [main] ---------------------------------------- [testng] [2024-09-19 11:11:20,442] [main] Total files: 164 [testng] [2024-09-19 11:11:20,442] [main] Scan time: 61.284 s (373 ms/file) [testng] [2024-09-19 11:11:20,443] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-19 11:12:48,606] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 11:12:48,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:12:48,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:48,608 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-19_11-12-48.log] [testng] 11:12:48,608 |-INFO in ch.qos.logback.core.sift.SiftProcessor@101ba4e6 - End of configuration. [testng] [2024-09-19 11:12:48,720] [pool-1-thread-12] Initializing /data/ome/tiffany.color.tiff: [testng] 11:12:48,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:12:48,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:48,721 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-19_11-12-48.log] [testng] 11:12:48,721 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1da968b6 - End of configuration. [testng] [2024-09-19 11:12:50,077] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 11:12:50,077 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:12:50,077 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:50,078 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-19_11-12-50.log] [testng] 11:12:50,078 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3658a15b - End of configuration. [testng] [2024-09-19 11:12:50,197] [pool-1-thread-10] Initializing /data/openjpeg/Facade.bmp: [testng] 11:12:50,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:12:50,198 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:50,198 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-19_11-12-50.log] [testng] 11:12:50,199 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e284641 - End of configuration. [testng] [2024-09-19 11:12:50,340] [pool-1-thread-9] Initializing /data/sdub/sdub.pattern: [testng] 11:12:50,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:12:50,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:50,341 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-19_11-12-50.log] [testng] 11:12:50,341 |-INFO in ch.qos.logback.core.sift.SiftProcessor@626856d3 - End of configuration. [testng] [2024-09-19 11:12:57,976] [pool-1-thread-8] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] 11:12:57,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:12:57,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:57,977 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-19_11-12-57.log] [testng] 11:12:57,978 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8ec34be - End of configuration. [testng] [2024-09-19 11:12:58,679] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] 11:12:58,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:12:58,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:58,680 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-19_11-12-58.log] [testng] 11:12:58,680 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57a411f5 - End of configuration. [testng] [2024-09-19 11:12:59,656] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] 11:12:59,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:12:59,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:59,657 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-19_11-12-59.log] [testng] 11:12:59,658 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e878776 - End of configuration. [testng] [2024-09-19 11:12:59,772] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 11:12:59,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:12:59,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:59,773 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-19_11-12-59.log] [testng] 11:12:59,774 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42fa3168 - End of configuration. [testng] [2024-09-19 11:12:59,892] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 11:12:59,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:12:59,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:12:59,893 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-19_11-12-59.log] [testng] 11:12:59,894 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3579ff3e - End of configuration. [testng] [2024-09-19 11:13:00,463] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 11:13:00,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:13:00,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:13:00,464 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-19_11-13-00.log] [testng] 11:13:00,464 |-INFO in ch.qos.logback.core.sift.SiftProcessor@270e021d - End of configuration. [testng] [2024-09-19 11:13:00,576] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 11:13:00,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:13:00,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:13:00,576 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-19_11-13-00.log] [testng] 11:13:00,577 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a90c1a3 - End of configuration. [testng] [2024-09-19 11:13:03,985] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-09-19 11:13:04,453] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-09-19 11:13:04,960] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-09-19 11:13:05,086] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-09-19 11:13:05,222] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-09-19 11:13:05,338] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-09-19 11:13:06,410] [pool-1-thread-3] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-09-19 11:13:07,196] [pool-1-thread-4] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-09-19 11:13:08,541] [pool-1-thread-2] Initializing /data/ome/embryo.lsm: [testng] [2024-09-19 11:13:09,283] [pool-1-thread-7] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-09-19 11:13:10,416] [pool-1-thread-8] Initializing /data/ome/worm.tiff: [testng] [2024-09-19 11:13:11,825] [pool-1-thread-12] Initializing /data/ome/654Atemp.stk: [testng] [2024-09-19 11:13:13,837] [pool-1-thread-10] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-09-19 11:13:14,023] [pool-1-thread-6] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-09-19 11:13:16,133] [pool-1-thread-11] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-09-19 11:13:16,964] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-09-19 11:13:18,410] [pool-1-thread-5] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-09-19 11:13:20,272] [pool-1-thread-10] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-09-19 11:13:21,660] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-09-19 11:13:23,289] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-09-19 11:13:23,561] [pool-1-thread-7] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-09-19 11:13:25,535] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-09-19 11:13:25,907] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-09-19 11:13:27,247] [pool-1-thread-8] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-09-19 11:13:28,261] [pool-1-thread-4] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-09-19 11:13:29,557] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-09-19 11:13:30,284] [pool-1-thread-8] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-09-19 11:13:51,556] [pool-1-thread-5] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-09-19 11:13:52,642] [pool-1-thread-7] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-09-19 11:13:53,125] [pool-1-thread-12] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-09-19 11:13:53,454] [pool-1-thread-11] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-09-19 11:13:54,057] [pool-1-thread-6] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-09-19 11:13:55,302] [pool-1-thread-10] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-09-19 11:13:55,510] [pool-1-thread-4] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-09-19 11:13:56,337] [pool-1-thread-3] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-09-19 11:13:56,969] [pool-1-thread-12] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-09-19 11:13:59,121] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-09-19 11:13:59,352] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-09-19 11:13:59,525] [pool-1-thread-7] Initializing /data/ome/cb_1.r3d: [testng] [2024-09-19 11:13:59,852] [pool-1-thread-6] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-09-19 11:14:00,889] [pool-1-thread-12] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-09-19 11:14:01,940] [pool-1-thread-10] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-09-19 11:14:02,148] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-09-19 11:14:02,509] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-09-19 11:14:03,527] [pool-1-thread-9] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-09-19 11:14:04,596] [pool-1-thread-4] Initializing /data/ome/C1.lsm: [testng] [2024-09-19 11:14:05,146] [pool-1-thread-11] 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: 5 minutes 42 seconds Finished: SUCCESS