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Started by upstream project "BIOFORMATS-test-repo" build number 238 originally caused by: Started by upstream project "Trigger" build number 263 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/jenkins17149360728576820083.sh + '[' samples = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37378_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] 00:32:01,076 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:32:01,078 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 00:32:01,078 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:32:01,079 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:32:01,080 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:32:01,080 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:32:01,081 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:32:01,081 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:32:01,081 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:32:01,082 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:32:01,082 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:32:01,082 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:32:01,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:32:01,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:32:01,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:32:01,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:32:01,295 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:32:01,295 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:32:01,295 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:32:01,296 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:32:01,296 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 00:32:01,297 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 00:32:01,297 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 216 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-29 00:32:01,306] [main] java.version = 11.0.16 [testng] 00:32:01,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:32:01,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:01,353 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-29_00-32-01.log] [testng] 00:32:01,355 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-29 00:32:01,357] [main] testng.directory = /data [testng] [2024-10-29 00:32:01,357] [main] testng.configDirectory = /config [testng] [2024-10-29 00:32:01,367] [main] testng.multiplier = 1.0 [testng] [2024-10-29 00:32:01,369] [main] testng.in-memory = false [testng] [2024-10-29 00:32:01,369] [main] testng.allow-missing = false [testng] [2024-10-29 00:32:01,369] [main] user.language = en [testng] [2024-10-29 00:32:01,369] [main] user.country = ${user.country} [testng] [2024-10-29 00:32:01,369] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-29 00:32:24,709] [main] ---------------------------------------- [testng] [2024-10-29 00:32:24,710] [main] Total files: 164 [testng] [2024-10-29 00:32:24,710] [main] Scan time: 23.34 s (142 ms/file) [testng] [2024-10-29 00:32:24,710] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-29 00:32:47,713] [pool-1-thread-1] Initializing /data/openjpeg/Rome.bmp: [testng] 00:32:47,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:32:47,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:47,717 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-29_00-32-47.log] [testng] 00:32:47,717 |-INFO in ch.qos.logback.core.sift.SiftProcessor@591296dc - End of configuration. [testng] [2024-10-29 00:32:47,801] [pool-1-thread-12] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:32:47,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:32:47,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:47,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-29_00-32-47.log] [testng] 00:32:47,802 |-INFO in ch.qos.logback.core.sift.SiftProcessor@181c4ffa - End of configuration. [testng] [2024-10-29 00:32:48,447] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 00:32:48,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:32:48,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:48,448 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-29_00-32-48.log] [testng] 00:32:48,449 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c0d9ced - End of configuration. [testng] [2024-10-29 00:32:48,584] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] 00:32:48,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:32:48,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:48,586 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-29_00-32-48.log] [testng] 00:32:48,586 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55f2e1e4 - End of configuration. [testng] [2024-10-29 00:32:48,732] [pool-1-thread-9] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 00:32:48,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:32:48,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:48,733 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-29_00-32-48.log] [testng] 00:32:48,733 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a529831 - End of configuration. [testng] [2024-10-29 00:32:49,836] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 00:32:49,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:32:49,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:49,838 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-29_00-32-49.log] [testng] 00:32:49,838 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56cbed58 - End of configuration. [testng] [2024-10-29 00:32:50,383] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:32:50,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:32:50,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:50,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-29_00-32-50.log] [testng] 00:32:50,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c343abf - End of configuration. [testng] [2024-10-29 00:32:51,132] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 00:32:51,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:32:51,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:51,133 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-29_00-32-51.log] [testng] 00:32:51,133 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4000063b - End of configuration. [testng] [2024-10-29 00:32:51,258] [pool-1-thread-5] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 00:32:51,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:32:51,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:51,259 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-29_00-32-51.log] [testng] 00:32:51,260 |-INFO in ch.qos.logback.core.sift.SiftProcessor@286adf1b - End of configuration. [testng] [2024-10-29 00:32:52,467] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] 00:32:52,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:32:52,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:52,468 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-29_00-32-52.log] [testng] 00:32:52,469 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17fdd328 - End of configuration. [testng] [2024-10-29 00:32:53,065] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 00:32:53,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:32:53,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:53,066 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-29_00-32-53.log] [testng] 00:32:53,067 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7dc93f0 - End of configuration. [testng] [2024-10-29 00:32:53,451] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:32:53,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:32:53,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:53,452 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-29_00-32-53.log] [testng] 00:32:53,453 |-INFO in ch.qos.logback.core.sift.SiftProcessor@276f289d - End of configuration. [testng] [2024-10-29 00:32:57,687] [pool-1-thread-6] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-10-29 00:32:58,854] [pool-1-thread-1] Initializing /data/ome/embryo.lsm: [testng] [2024-10-29 00:32:59,541] [pool-1-thread-10] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-10-29 00:33:18,496] [pool-1-thread-11] Initializing /data/ome/cb_1.r3d: [testng] [2024-10-29 00:33:18,712] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-10-29 00:33:18,824] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-10-29 00:33:18,927] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-10-29 00:33:19,397] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-10-29 00:33:19,502] [pool-1-thread-3] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-10-29 00:33:20,231] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-10-29 00:33:23,143] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-10-29 00:33:23,806] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-10-29 00:33:24,113] [pool-1-thread-8] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-10-29 00:33:24,710] [pool-1-thread-7] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-10-29 00:33:25,397] [pool-1-thread-2] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-10-29 00:33:26,129] [pool-1-thread-12] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-10-29 00:33:27,104] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-10-29 00:33:27,427] [pool-1-thread-9] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-10-29 00:33:29,000] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-10-29 00:33:29,956] [pool-1-thread-12] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-10-29 00:33:30,752] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-10-29 00:33:30,865] [pool-1-thread-6] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-10-29 00:33:32,196] [pool-1-thread-1] Initializing /data/ome/654Atemp.stk: [testng] [2024-10-29 00:33:33,910] [pool-1-thread-2] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-10-29 00:33:34,564] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-10-29 00:33:35,280] [pool-1-thread-11] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-10-29 00:33:35,913] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-10-29 00:33:37,720] [pool-1-thread-12] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-10-29 00:33:38,314] [pool-1-thread-4] Initializing /data/ome/worm.tiff: [testng] [2024-10-29 00:33:39,482] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-10-29 00:33:39,811] [pool-1-thread-2] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-10-29 00:33:39,993] [pool-1-thread-8] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-10-29 00:33:41,097] [pool-1-thread-7] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-10-29 00:33:41,644] [pool-1-thread-12] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-10-29 00:33:42,706] [pool-1-thread-9] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-10-29 00:33:44,452] [pool-1-thread-1] Initializing /data/ome/C1.lsm: [testng] [2024-10-29 00:33:44,961] [pool-1-thread-5] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-10-29 00:33:45,095] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-10-29 00:33:46,570] [pool-1-thread-5] Initializing /data/sdub/sdub.pattern: [testng] [2024-10-29 00:33:53,590] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-10-29 00:33:53,710] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-10-29 00:33:54,603] [pool-1-thread-12] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-10-29 00:33:55,003] [pool-1-thread-7] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-10-29 00:33:55,350] [pool-1-thread-8] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-10-29 00:33:56,354] [pool-1-thread-1] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-10-29 00:33:57,857] [pool-1-thread-4] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-10-29 00:33:58,427] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.bmp: [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 9 seconds Finished: SUCCESS