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Started by upstream project "BIOFORMATS-test-repo" build number 301 originally caused by: Started by upstream project "Trigger" build number 323 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins13073254738147680920.sh + '[' samples = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_47593_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 00:58:42,450 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:58:42,452 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 00:58:42,452 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:58:42,453 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:58:42,453 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:58:42,454 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:58:42,454 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:58:42,454 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:58:42,455 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:58:42,455 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:58:42,455 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:58:42,456 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:58:42,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:58:42,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:58:42,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:58:42,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:58:42,645 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:58:42,645 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:58:42,645 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:58:42,645 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:58:42,645 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 00:58:42,646 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 00:58:42,646 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 191 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-28 00:58:42,655] [main] java.version = 11.0.16 [testng] 00:58:42,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:58:42,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:58:42,699 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-28_00-58-42.log] [testng] 00:58:42,701 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-12-28 00:58:42,703] [main] testng.directory = /data [testng] [2024-12-28 00:58:42,703] [main] testng.configDirectory = /config [testng] [2024-12-28 00:58:42,712] [main] testng.multiplier = 1.0 [testng] [2024-12-28 00:58:42,714] [main] testng.in-memory = false [testng] [2024-12-28 00:58:42,714] [main] testng.allow-missing = false [testng] [2024-12-28 00:58:42,714] [main] user.language = en [testng] [2024-12-28 00:58:42,714] [main] user.country = ${user.country} [testng] [2024-12-28 00:58:42,714] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-28 00:59:55,846] [main] ---------------------------------------- [testng] [2024-12-28 00:59:55,846] [main] Total files: 164 [testng] [2024-12-28 00:59:55,847] [main] Scan time: 73.132 s (445 ms/file) [testng] [2024-12-28 00:59:55,847] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-28 01:02:24,040] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.ppm: [testng] 01:02:24,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:02:24,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:24,043 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-28_01-02-24.log] [testng] 01:02:24,044 |-INFO in ch.qos.logback.core.sift.SiftProcessor@279e4a92 - End of configuration. [testng] [2024-12-28 01:02:24,224] [pool-1-thread-12] Initializing /data/ome/anusgfpzs.lsm: [testng] 01:02:24,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:02:24,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:24,224 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-28_01-02-24.log] [testng] 01:02:24,225 |-INFO in ch.qos.logback.core.sift.SiftProcessor@309d08b5 - End of configuration. [testng] [2024-12-28 01:02:24,958] [pool-1-thread-11] Initializing /data/ome/C1lowmusgfp.lsm: [testng] 01:02:24,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:02:24,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:24,959 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-28_01-02-24.log] [testng] 01:02:24,959 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75fbc125 - End of configuration. [testng] [2024-12-28 01:02:25,816] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 01:02:25,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:02:25,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:25,817 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-28_01-02-25.log] [testng] 01:02:25,817 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a13d5c0 - End of configuration. [testng] [2024-12-28 01:02:26,500] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 01:02:26,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:02:26,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:26,500 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-28_01-02-26.log] [testng] 01:02:26,501 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d04fbc5 - End of configuration. [testng] [2024-12-28 01:02:26,645] [pool-1-thread-8] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] 01:02:26,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:02:26,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:26,646 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-28_01-02-26.log] [testng] 01:02:26,647 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32db520c - End of configuration. [testng] [2024-12-28 01:02:28,141] [pool-1-thread-7] Initializing /data/ome/compressed2ChZ.lsm: [testng] 01:02:28,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:02:28,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:28,142 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-28_01-02-28.log] [testng] 01:02:28,142 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a5074e4 - End of configuration. [testng] [2024-12-28 01:02:29,363] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 01:02:29,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:02:29,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:29,364 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-28_01-02-29.log] [testng] 01:02:29,364 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5367d4f2 - End of configuration. [testng] [2024-12-28 01:02:30,734] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv: [testng] 01:02:30,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:02:30,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:30,735 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-28_01-02-30.log] [testng] 01:02:30,735 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ef00d08 - End of configuration. [testng] [2024-12-28 01:02:30,931] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 01:02:30,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:02:30,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:30,932 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-28_01-02-30.log] [testng] 01:02:30,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a7ac56a - End of configuration. [testng] [2024-12-28 01:02:31,091] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:02:31,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:02:31,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:31,092 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-28_01-02-31.log] [testng] 01:02:31,092 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b975c30 - End of configuration. [testng] [2024-12-28 01:02:31,219] [pool-1-thread-2] Initializing /data/openjpeg/thumb_facade.jpg: [testng] 01:02:31,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:02:31,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:31,220 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-28_01-02-31.log] [testng] 01:02:31,220 |-INFO in ch.qos.logback.core.sift.SiftProcessor@377701a7 - End of configuration. [testng] [2024-12-28 01:02:36,288] [pool-1-thread-4] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-12-28 01:02:38,207] [pool-1-thread-1] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-12-28 01:02:38,418] [pool-1-thread-9] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-12-28 01:02:41,018] [pool-1-thread-3] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-12-28 01:02:41,711] [pool-1-thread-5] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-12-28 01:02:45,647] [pool-1-thread-2] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-12-28 01:02:47,446] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-12-28 01:02:48,311] [pool-1-thread-10] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-12-28 01:02:49,880] [pool-1-thread-1] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-12-28 01:02:51,047] [pool-1-thread-11] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-12-28 01:02:51,249] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-12-28 01:02:51,392] [pool-1-thread-7] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-12-28 01:02:51,708] [pool-1-thread-8] Initializing /data/ome/C1.lsm: [testng] [2024-12-28 01:02:55,090] [pool-1-thread-3] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-12-28 01:02:58,340] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-12-28 01:03:00,332] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-12-28 01:03:01,354] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-12-28 01:03:03,052] [pool-1-thread-10] Initializing /data/ome/worm.tiff: [testng] [2024-12-28 01:03:05,638] [pool-1-thread-2] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-12-28 01:03:09,440] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-12-28 01:03:10,276] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-12-28 01:03:11,911] [pool-1-thread-9] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-12-28 01:03:54,253] [pool-1-thread-12] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-12-28 01:03:55,395] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-12-28 01:03:56,531] [pool-1-thread-8] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-12-28 01:03:57,573] [pool-1-thread-7] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-12-28 01:03:58,880] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-12-28 01:04:02,270] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-12-28 01:04:03,661] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-12-28 01:04:03,857] [pool-1-thread-3] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-12-28 01:04:05,742] [pool-1-thread-7] Initializing /data/ome/embryo.lsm: [testng] [2024-12-28 01:04:07,258] [pool-1-thread-11] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-12-28 01:04:10,040] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern: [testng] [2024-12-28 01:04:20,934] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-12-28 01:04:22,952] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-12-28 01:04:24,426] [pool-1-thread-2] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-12-28 01:04:25,532] [pool-1-thread-7] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-12-28 01:04:27,453] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-12-28 01:04:27,597] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-12-28 01:04:27,815] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-12-28 01:04:29,656] [pool-1-thread-3] Initializing /data/ome/cb_1.r3d: [testng] [2024-12-28 01:04:30,849] [pool-1-thread-2] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-12-28 01:04:34,317] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-12-28 01:04:34,807] [pool-1-thread-12] Initializing /data/ome/654Atemp.stk: [testng] [2024-12-28 01:04:36,546] [pool-1-thread-4] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-12-28 01:04:37,329] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-12-28 01:04:37,612] [pool-1-thread-1] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 8 minutes 35 seconds Finished: SUCCESS