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Started by upstream project "BIOFORMATS-test-repo" build number 362 originally caused by: Started by upstream project "Trigger" build number 388 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/jenkins10900775771864618291.sh + '[' samples = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_57663_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] 00:33:55,011 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:33:55,012 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 00:33:55,012 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:33:55,013 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:33:55,013 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:33:55,014 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:33:55,014 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:33:55,014 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:33:55,015 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:33:55,015 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:33:55,016 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:33:55,016 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:33:55,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:33:55,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:33:55,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:33:55,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:33:55,230 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:33:55,230 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:33:55,230 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:33:55,231 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:33:55,231 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 00:33:55,232 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 00:33:55,232 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 217 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-02 00:33:55,246] [main] java.version = 17.0.2 [testng] 00:33:55,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:33:55,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:55,305 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-02_00-33-55.log] [testng] 00:33:55,307 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-02 00:33:55,309] [main] testng.directory = /data [testng] [2025-03-02 00:33:55,309] [main] testng.configDirectory = /config [testng] [2025-03-02 00:33:55,318] [main] testng.multiplier = 1.0 [testng] [2025-03-02 00:33:55,319] [main] testng.in-memory = false [testng] [2025-03-02 00:33:55,319] [main] testng.allow-missing = false [testng] [2025-03-02 00:33:55,319] [main] user.language = en [testng] [2025-03-02 00:33:55,319] [main] user.country = ${user.country} [testng] [2025-03-02 00:33:55,319] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-02 00:34:35,419] [main] ---------------------------------------- [testng] [2025-03-02 00:34:35,419] [main] Total files: 164 [testng] [2025-03-02 00:34:35,419] [main] Scan time: 40.1 s (244 ms/file) [testng] [2025-03-02 00:34:35,419] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-02 00:35:49,693] [pool-1-thread-1] Initializing /data/ome/011B1_Morph.HTD: [testng] 00:35:49,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:35:49,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:49,695 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-02_00-35-49.log] [testng] 00:35:49,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@264a6f5b - End of configuration. [testng] [2025-03-02 00:35:50,782] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 00:35:50,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:35:50,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:50,783 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-02_00-35-50.log] [testng] 00:35:50,783 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6900ff27 - End of configuration. [testng] [2025-03-02 00:35:50,853] [pool-1-thread-11] Initializing /data/ome/CHOBI_d3d.dv: [testng] 00:35:50,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:35:50,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:50,859 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-02_00-35-50.log] [testng] 00:35:50,864 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d2f5ab7 - End of configuration. [testng] [2025-03-02 00:35:51,032] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern: [testng] 00:35:51,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:35:51,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:51,033 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-02_00-35-51.log] [testng] 00:35:51,033 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dccad9b - End of configuration. [testng] [2025-03-02 00:35:57,155] [pool-1-thread-9] Initializing /data/openjpeg/Rome.ppm: [testng] 00:35:57,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:35:57,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:57,156 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-02_00-35-57.log] [testng] 00:35:57,157 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1876d509 - End of configuration. [testng] [2025-03-02 00:35:57,257] [pool-1-thread-8] Initializing /data/ome/tinyTest.d3d.dv: [testng] 00:35:57,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:35:57,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:57,258 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-02_00-35-57.log] [testng] 00:35:57,259 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c43c096 - End of configuration. [testng] [2025-03-02 00:35:57,457] [pool-1-thread-7] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] 00:35:57,458 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:35:57,458 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:57,458 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-02_00-35-57.log] [testng] 00:35:57,459 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13ea67fe - End of configuration. [testng] [2025-03-02 00:35:59,153] [pool-1-thread-6] Initializing /data/ome/Cpharynxzs1.lsm: [testng] 00:35:59,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:35:59,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:59,155 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-02_00-35-59.log] [testng] 00:35:59,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@119c4253 - End of configuration. [testng] [2025-03-02 00:35:59,931] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 00:35:59,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:35:59,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:59,932 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-02_00-35-59.log] [testng] 00:35:59,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ebc1589 - End of configuration. [testng] [2025-03-02 00:36:00,026] [pool-1-thread-4] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:36:00,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:36:00,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:00,029 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-02_00-36-00.log] [testng] 00:36:00,029 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72538368 - End of configuration. [testng] [2025-03-02 00:36:01,135] [pool-1-thread-3] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] 00:36:01,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:36:01,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:01,136 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-02_00-36-01.log] [testng] 00:36:01,136 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75fc4baf - End of configuration. [testng] [2025-03-02 00:36:02,546] [pool-1-thread-2] Initializing /data/ome/worm.tiff: [testng] 00:36:02,546 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:36:02,546 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:02,547 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-02_00-36-02.log] [testng] 00:36:02,547 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1365dc19 - End of configuration. [testng] [2025-03-02 00:36:06,859] [pool-1-thread-12] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2025-03-02 00:36:07,439] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2025-03-02 00:36:07,547] [pool-1-thread-8] Initializing /data/openjpeg/Rome.bmp: [testng] [2025-03-02 00:36:07,882] [pool-1-thread-11] Initializing /data/ome/tiffany.color.tiff: [testng] [2025-03-02 00:36:09,423] [pool-1-thread-5] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2025-03-02 00:36:10,137] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2025-03-02 00:36:10,500] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2025-03-02 00:36:10,653] [pool-1-thread-9] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2025-03-02 00:36:12,123] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2025-03-02 00:36:12,865] [pool-1-thread-5] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2025-03-02 00:36:14,140] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2025-03-02 00:36:14,615] [pool-1-thread-6] Initializing /data/openjpeg/Rome.jp2: [testng] [2025-03-02 00:36:15,861] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2025-03-02 00:36:16,050] [pool-1-thread-4] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2025-03-02 00:36:17,361] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2025-03-02 00:36:18,657] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2025-03-02 00:36:18,934] [pool-1-thread-8] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2025-03-02 00:36:20,433] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2025-03-02 00:36:20,594] [pool-1-thread-7] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2025-03-02 00:36:20,942] [pool-1-thread-11] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2025-03-02 00:36:21,493] [pool-1-thread-9] Initializing /data/ome/anusgfpzs.lsm: [testng] [2025-03-02 00:36:22,924] [pool-1-thread-5] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2025-03-02 00:36:23,436] [pool-1-thread-3] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2025-03-02 00:36:25,316] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2025-03-02 00:36:26,138] [pool-1-thread-4] Initializing /data/TAABA/TAABA.pattern: [testng] [2025-03-02 00:36:51,271] [pool-1-thread-6] Initializing /data/ome/Adultmidsection.lsm: [testng] [2025-03-02 00:36:52,526] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2025-03-02 00:36:52,667] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2025-03-02 00:36:53,215] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2025-03-02 00:36:53,982] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2025-03-02 00:36:55,721] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2025-03-02 00:36:56,304] [pool-1-thread-2] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2025-03-02 00:36:57,524] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2025-03-02 00:36:58,337] [pool-1-thread-8] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2025-03-02 00:36:59,040] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2025-03-02 00:36:59,827] [pool-1-thread-7] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2025-03-02 00:37:00,462] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2025-03-02 00:37:01,424] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2025-03-02 00:37:02,507] [pool-1-thread-11] Initializing /data/ome/C1.lsm: [testng] [2025-03-02 00:37:03,522] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2025-03-02 00:37:04,277] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2025-03-02 00:37:05,065] [pool-1-thread-8] Initializing /data/ome/654Atemp.stk: [testng] [2025-03-02 00:37:06,888] [pool-1-thread-6] Initializing /data/ome/cb_1.r3d: [testng] [2025-03-02 00:37:07,198] [pool-1-thread-5] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2025-03-02 00:37:07,623] [pool-1-thread-10] Initializing /data/openjpeg/Facade.pnm: [testng] [2025-03-02 00:37:08,709] [pool-1-thread-7] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2025-03-02 00:37:09,393] [pool-1-thread-11] Initializing /data/openjpeg/Facade.bmp: [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 36 seconds Finished: SUCCESS