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Started by upstream project "BIOFORMATS-test-repo" build number 7 originally caused by: Started by upstream project "Trigger" build number 10 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/jenkins11063871368522387843.sh + '[' samples = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_984_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 00:25:43,979 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:25:43,980 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 00:25:43,980 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:25:43,981 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:25:43,981 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:25:43,982 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:25:43,982 |-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] 00:25:43,982 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:25:43,983 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:25:43,983 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:25:43,984 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:25:43,984 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:25:44,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:25:44,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:25:44,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:25:44,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:25:44,185 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:25:44,185 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:25:44,185 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:25:44,185 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:25:44,185 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 00:25:44,186 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 00:25:44,186 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 203 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-21 00:25:44,195] [main] java.version = 21 [testng] 00:25:44,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:25:44,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:25:44,240 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-21_00-25-44.log] [testng] 00:25:44,241 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-03-21 00:25:44,243] [main] testng.directory = /data [testng] [2024-03-21 00:25:44,243] [main] testng.configDirectory = /config [testng] [2024-03-21 00:25:44,252] [main] testng.multiplier = 1.0 [testng] [2024-03-21 00:25:44,253] [main] testng.in-memory = false [testng] [2024-03-21 00:25:44,253] [main] testng.allow-missing = false [testng] [2024-03-21 00:25:44,253] [main] user.language = en [testng] [2024-03-21 00:25:44,253] [main] user.country = ${user.country} [testng] [2024-03-21 00:25:44,253] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-21 00:26:06,590] [main] ---------------------------------------- [testng] [2024-03-21 00:26:06,590] [main] Total files: 164 [testng] [2024-03-21 00:26:06,590] [main] Scan time: 22.337 s (136 ms/file) [testng] [2024-03-21 00:26:06,591] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-21 00:26:23,804] [pool-1-thread-1] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 00:26:23,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:26:23,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:23,806 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-21_00-26-23.log] [testng] 00:26:23,807 |-INFO in ch.qos.logback.core.sift.SiftProcessor@559d43cd - End of configuration. [testng] [2024-03-21 00:26:24,021] [pool-1-thread-12] Initializing /data/sdub/sdub.pattern: [testng] 00:26:24,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:26:24,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:24,023 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-21_00-26-24.log] [testng] 00:26:24,023 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31264c57 - End of configuration. [testng] [2024-03-21 00:26:24,545] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] 00:26:24,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:26:24,546 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:24,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-21_00-26-24.log] [testng] 00:26:24,547 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7880b379 - End of configuration. [testng] [2024-03-21 00:26:24,559] [pool-1-thread-10] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 00:26:24,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:26:24,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:24,560 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-21_00-26-24.log] [testng] 00:26:24,561 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71ee1e1a - End of configuration. [testng] [2024-03-21 00:26:24,787] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 00:26:24,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:26:24,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:24,789 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-21_00-26-24.log] [testng] 00:26:24,789 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56a8e1ff - End of configuration. [testng] [2024-03-21 00:26:24,831] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 00:26:24,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:26:24,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:24,832 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-21_00-26-24.log] [testng] 00:26:24,833 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79529903 - End of configuration. [testng] [2024-03-21 00:26:24,862] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] 00:26:24,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:26:24,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:24,863 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-21_00-26-24.log] [testng] 00:26:24,864 |-INFO in ch.qos.logback.core.sift.SiftProcessor@aa39c8a - End of configuration. [testng] [2024-03-21 00:26:24,877] [pool-1-thread-6] Initializing /data/openjpeg/Facade.pnm: [testng] 00:26:24,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:26:24,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:24,879 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-21_00-26-24.log] [testng] 00:26:24,879 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73008fda - End of configuration. [testng] [2024-03-21 00:26:24,892] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 00:26:24,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:26:24,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:24,893 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-21_00-26-24.log] [testng] 00:26:24,894 |-INFO in ch.qos.logback.core.sift.SiftProcessor@528ff37b - End of configuration. [testng] [2024-03-21 00:26:24,906] [pool-1-thread-4] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 00:26:24,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:26:24,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:24,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-21_00-26-24.log] [testng] 00:26:24,908 |-INFO in ch.qos.logback.core.sift.SiftProcessor@398f196b - End of configuration. [testng] [2024-03-21 00:26:25,036] [pool-1-thread-3] Initializing /data/openjpeg/Rome.jp2: [testng] 00:26:25,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:26:25,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:25,037 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-21_00-26-25.log] [testng] 00:26:25,037 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b64d1d1 - End of configuration. [testng] [2024-03-21 00:26:25,106] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 00:26:25,106 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:26:25,106 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:25,107 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-21_00-26-25.log] [testng] 00:26:25,107 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4112e0ce - End of configuration. [testng] [2024-03-21 00:26:26,977] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-03-21 00:26:26,997] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-03-21 00:26:27,017] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-03-21 00:26:27,033] [pool-1-thread-2] Initializing /data/ome/654Atemp.stk: [testng] [2024-03-21 00:26:27,215] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-03-21 00:26:27,753] [pool-1-thread-4] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-03-21 00:26:27,781] [pool-1-thread-6] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-03-21 00:26:28,725] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-03-21 00:26:28,905] [pool-1-thread-8] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-03-21 00:26:29,257] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-03-21 00:26:29,437] [pool-1-thread-4] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-03-21 00:26:29,523] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-03-21 00:26:29,623] [pool-1-thread-5] Initializing /data/ome/C1.lsm: [testng] [2024-03-21 00:26:29,757] [pool-1-thread-11] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-03-21 00:26:29,984] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-03-21 00:26:30,016] [pool-1-thread-4] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-03-21 00:26:30,173] [pool-1-thread-1] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-03-21 00:26:30,559] [pool-1-thread-2] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-03-21 00:26:30,673] [pool-1-thread-10] Initializing /data/ome/worm.tiff: [testng] [2024-03-21 00:26:30,772] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-03-21 00:26:30,795] [pool-1-thread-7] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-03-21 00:26:30,809] [pool-1-thread-8] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-03-21 00:26:31,103] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-03-21 00:26:31,379] [pool-1-thread-2] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-03-21 00:26:31,421] [pool-1-thread-4] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-03-21 00:26:31,973] [pool-1-thread-11] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-03-21 00:26:32,052] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-03-21 00:26:32,097] [pool-1-thread-1] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-03-21 00:26:34,978] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-03-21 00:26:35,348] [pool-1-thread-8] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-03-21 00:26:35,397] [pool-1-thread-5] Initializing /data/ome/cb_1.r3d: [testng] [2024-03-21 00:26:35,635] [pool-1-thread-11] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-03-21 00:26:35,850] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-03-21 00:26:36,020] [pool-1-thread-7] Initializing /data/ome/embryo.lsm: [testng] [2024-03-21 00:26:36,110] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-03-21 00:26:36,282] [pool-1-thread-8] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-03-21 00:26:36,521] [pool-1-thread-5] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-03-21 00:26:36,651] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-03-21 00:26:36,843] [pool-1-thread-10] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-03-21 00:26:37,004] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-03-21 00:26:37,586] [pool-1-thread-7] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-03-21 00:26:37,814] [pool-1-thread-10] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-03-21 00:26:37,922] [pool-1-thread-8] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-03-21 00:26:38,539] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-03-21 00:26:38,557] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-03-21 00:26:38,675] [pool-1-thread-5] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-03-21 00:26:38,936] [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 14 seconds Finished: SUCCESS