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Started by upstream project "BIOFORMATS-test-repo" build number 221 originally caused by: Started by upstream project "Trigger" build number 248 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/jenkins1111355772656736273.sh + '[' samples = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35054_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] 01:54:22,312 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:54:22,314 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 01:54:22,314 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:54:22,315 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:54:22,315 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:54:22,315 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:54:22,316 |-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] 01:54:22,316 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:54:22,316 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:54:22,317 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:54:22,317 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:54:22,317 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:54:22,477 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:54:22,477 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:54:22,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:54:22,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:54:22,504 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:54:22,504 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:54:22,504 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:54:22,504 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:54:22,504 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 01:54:22,505 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 01:54:22,505 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 189 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-15 01:54:22,514] [main] java.version = 11.0.16 [testng] 01:54:22,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:54:22,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:22,558 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-15_01-54-22.log] [testng] 01:54:22,559 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-15 01:54:22,561] [main] testng.directory = /data [testng] [2024-10-15 01:54:22,561] [main] testng.configDirectory = /config [testng] [2024-10-15 01:54:22,570] [main] testng.multiplier = 1.0 [testng] [2024-10-15 01:54:22,571] [main] testng.in-memory = false [testng] [2024-10-15 01:54:22,571] [main] testng.allow-missing = false [testng] [2024-10-15 01:54:22,571] [main] user.language = en [testng] [2024-10-15 01:54:22,572] [main] user.country = ${user.country} [testng] [2024-10-15 01:54:22,572] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-15 01:57:15,856] [main] ---------------------------------------- [testng] [2024-10-15 01:57:15,856] [main] Total files: 164 [testng] [2024-10-15 01:57:15,856] [main] Scan time: 173.284 s (1056 ms/file) [testng] [2024-10-15 01:57:15,856] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-15 02:01:38,853] [pool-1-thread-1] Initializing /data/openjpeg/Rome.bmp: [testng] 02:01:38,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:01:38,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:38,855 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-15_02-01-38.log] [testng] 02:01:38,856 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cabaf70 - End of configuration. [testng] [2024-10-15 02:01:39,312] [pool-1-thread-12] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 02:01:39,312 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:01:39,312 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:39,313 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-15_02-01-39.log] [testng] 02:01:39,313 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c2dd770 - End of configuration. [testng] [2024-10-15 02:01:41,890] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 02:01:41,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:01:41,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:41,891 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-15_02-01-41.log] [testng] 02:01:41,891 |-INFO in ch.qos.logback.core.sift.SiftProcessor@489b3e0e - End of configuration. [testng] [2024-10-15 02:01:42,039] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] 02:01:42,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:01:42,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:42,040 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-15_02-01-42.log] [testng] 02:01:42,040 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fec57a0 - End of configuration. [testng] [2024-10-15 02:01:42,923] [pool-1-thread-9] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 02:01:42,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:01:42,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:42,924 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-15_02-01-42.log] [testng] 02:01:42,924 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f76d5d5 - End of configuration. [testng] [2024-10-15 02:01:44,956] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 02:01:44,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:01:44,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:44,957 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-15_02-01-44.log] [testng] 02:01:44,957 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32e28d41 - End of configuration. [testng] [2024-10-15 02:01:46,150] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 02:01:46,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:01:46,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:46,151 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-15_02-01-46.log] [testng] 02:01:46,151 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60a17b4f - End of configuration. [testng] [2024-10-15 02:01:48,584] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 02:01:48,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:01:48,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:48,585 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-15_02-01-48.log] [testng] 02:01:48,585 |-INFO in ch.qos.logback.core.sift.SiftProcessor@89206f - End of configuration. [testng] [2024-10-15 02:01:49,155] [pool-1-thread-5] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 02:01:49,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:01:49,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:49,156 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-15_02-01-49.log] [testng] 02:01:49,156 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f9daf33 - End of configuration. [testng] [2024-10-15 02:01:51,908] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] 02:01:51,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:01:51,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:51,909 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-15_02-01-51.log] [testng] 02:01:51,909 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a8483e5 - End of configuration. [testng] [2024-10-15 02:01:53,519] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 02:01:53,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:01:53,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:53,520 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-15_02-01-53.log] [testng] 02:01:53,521 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d85bf8a - End of configuration. [testng] [2024-10-15 02:01:54,439] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 02:01:54,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:01:54,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:54,440 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-15_02-01-54.log] [testng] 02:01:54,441 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23628b26 - End of configuration. [testng] [2024-10-15 02:02:01,760] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-10-15 02:02:07,031] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2024-10-15 02:02:09,531] [pool-1-thread-10] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-10-15 02:03:33,508] [pool-1-thread-11] Initializing /data/ome/cb_1.r3d: [testng] [2024-10-15 02:03:33,933] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-10-15 02:03:40,071] [pool-1-thread-8] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-10-15 02:03:42,868] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-10-15 02:03:44,367] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-10-15 02:03:44,760] [pool-1-thread-7] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-10-15 02:03:47,691] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-10-15 02:03:48,762] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-10-15 02:03:51,020] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-10-15 02:03:51,596] [pool-1-thread-3] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-10-15 02:03:55,521] [pool-1-thread-2] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-10-15 02:03:58,026] [pool-1-thread-11] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-10-15 02:04:00,238] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-10-15 02:04:00,997] [pool-1-thread-4] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-10-15 02:04:02,552] [pool-1-thread-12] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-10-15 02:04:08,358] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-10-15 02:04:12,187] [pool-1-thread-6] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-10-15 02:04:16,589] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-10-15 02:04:16,790] [pool-1-thread-1] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-10-15 02:04:20,074] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk: [testng] [2024-10-15 02:04:26,168] [pool-1-thread-7] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-10-15 02:04:28,111] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-10-15 02:04:30,120] [pool-1-thread-2] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-10-15 02:04:31,612] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-10-15 02:04:33,040] [pool-1-thread-4] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-10-15 02:04:36,389] [pool-1-thread-3] Initializing /data/ome/worm.tiff: [testng] [2024-10-15 02:04:43,817] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-10-15 02:04:44,083] [pool-1-thread-6] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-10-15 02:04:44,670] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-10-15 02:04:47,313] [pool-1-thread-12] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-10-15 02:04:49,469] [pool-1-thread-7] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-10-15 02:04:53,674] [pool-1-thread-4] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-10-15 02:04:58,137] [pool-1-thread-6] Initializing /data/ome/C1.lsm: [testng] [2024-10-15 02:05:00,374] [pool-1-thread-5] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-10-15 02:05:04,046] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-10-15 02:05:05,416] [pool-1-thread-5] Initializing /data/sdub/sdub.pattern: [testng] [2024-10-15 02:05:28,613] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-10-15 02:05:29,608] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-10-15 02:05:32,448] [pool-1-thread-11] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-10-15 02:05:33,137] [pool-1-thread-7] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-10-15 02:05:34,686] [pool-1-thread-9] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-10-15 02:05:35,124] [pool-1-thread-3] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-10-15 02:05:38,574] [pool-1-thread-6] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-10-15 02:05:42,834] [pool-1-thread-11] 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: 16 minutes 52 seconds Finished: SUCCESS