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Started by upstream project "BIOFORMATS-test-repo" build number 38 originally caused by: Started by upstream project "Trigger" build number 44 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins7222499644246118439.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_5250_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 test-automated: [testng] File leak detector installed [testng] 09:09:58,229 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 09:09:58,232 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 09:09:58,232 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:09:58,234 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:09:58,234 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 09:09:58,234 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 09:09:58,235 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 09:09:58,235 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:09:58,235 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:09:58,236 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 09:09:58,236 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 09:09:58,236 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 09:09:58,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 09:09:58,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 09:09:58,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 09:09:58,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 09:09:58,576 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 09:09:58,576 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 09:09:58,576 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 09:09:58,577 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 09:09:58,577 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 09:09:58,579 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 09:09:58,579 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 344 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-19 09:09:58,592] [main] java.version = 1.8.0_342 [testng] 09:09:58,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:09:58,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:09:58,665 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-19_09-09-58.log] [testng] 09:09:58,668 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-19 09:09:58,671] [main] testng.directory = /data [testng] [2024-04-19 09:09:58,671] [main] testng.configDirectory = /config [testng] [2024-04-19 09:09:58,690] [main] testng.multiplier = 1.0 [testng] [2024-04-19 09:09:58,691] [main] testng.in-memory = false [testng] [2024-04-19 09:09:58,691] [main] testng.allow-missing = false [testng] [2024-04-19 09:09:58,691] [main] user.language = en [testng] [2024-04-19 09:09:58,691] [main] user.country = ${user.country} [testng] [2024-04-19 09:09:58,691] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-19 09:10:22,303] [main] ---------------------------------------- [testng] [2024-04-19 09:10:22,303] [main] Total files: 164 [testng] [2024-04-19 09:10:22,304] [main] Scan time: 23.612 s (143 ms/file) [testng] [2024-04-19 09:10:22,304] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-19 09:10:33,698] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 09:10:33,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 09:10:33,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:10:33,700 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-19_09-10-33.log] [testng] 09:10:33,700 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38e1e9ee - End of configuration. [testng] [2024-04-19 09:10:33,747] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 09:10:33,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 09:10:33,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:10:33,749 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-19_09-10-33.log] [testng] 09:10:33,749 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f80ffc7 - End of configuration. [testng] [2024-04-19 09:10:33,769] [pool-1-thread-11] Initializing /data/ome/arwen0205_raw00201.pic: [testng] 09:10:33,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 09:10:33,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:10:33,771 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-19_09-10-33.log] [testng] 09:10:33,772 |-INFO in ch.qos.logback.core.sift.SiftProcessor@378e65dd - End of configuration. [testng] [2024-04-19 09:10:33,855] [pool-1-thread-10] Initializing /data/ome/anusgfpzs.lsm: [testng] 09:10:33,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 09:10:33,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:10:33,856 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-19_09-10-33.log] [testng] 09:10:33,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@450a4c43 - End of configuration. [testng] [2024-04-19 09:10:33,913] [pool-1-thread-9] Initializing /data/openjpeg/Rome.jp2: [testng] 09:10:33,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 09:10:33,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:10:33,915 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-19_09-10-33.log] [testng] 09:10:33,915 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bb97311 - End of configuration. [testng] [2024-04-19 09:10:33,938] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 09:10:33,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 09:10:33,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:10:33,939 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-19_09-10-33.log] [testng] 09:10:33,939 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50a75359 - End of configuration. [testng] [2024-04-19 09:10:33,952] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 09:10:33,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 09:10:33,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:10:33,953 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-19_09-10-33.log] [testng] 09:10:33,953 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d121c01 - End of configuration. [testng] [2024-04-19 09:10:34,002] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 09:10:34,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 09:10:34,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:10:34,004 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-19_09-10-34.log] [testng] 09:10:34,005 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5515520c - End of configuration. [testng] [2024-04-19 09:10:34,013] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 09:10:34,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 09:10:34,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:10:34,014 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-19_09-10-34.log] [testng] 09:10:34,014 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a5704a1 - End of configuration. [testng] [2024-04-19 09:10:34,024] [pool-1-thread-4] Initializing /data/ome/C1lowmusgfp.lsm: [testng] 09:10:34,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 09:10:34,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:10:34,025 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-19_09-10-34.log] [testng] 09:10:34,026 |-INFO in ch.qos.logback.core.sift.SiftProcessor@701ba33c - End of configuration. [testng] [2024-04-19 09:10:34,050] [pool-1-thread-3] Initializing /data/ome/C1.lsm: [testng] 09:10:34,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 09:10:34,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:10:34,051 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-19_09-10-34.log] [testng] 09:10:34,052 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ce55c50 - End of configuration. [testng] [2024-04-19 09:10:34,080] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 09:10:34,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 09:10:34,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:10:34,081 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-19_09-10-34.log] [testng] 09:10:34,081 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f4355b7 - End of configuration. [testng] [2024-04-19 09:10:36,581] [pool-1-thread-6] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-04-19 09:10:36,592] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-04-19 09:10:36,635] [pool-1-thread-3] Initializing /data/ome/654Atemp.stk: [testng] [2024-04-19 09:10:36,724] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-04-19 09:10:36,733] [pool-1-thread-7] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-04-19 09:10:36,743] [pool-1-thread-1] Initializing /data/ome/cb_1.r3d: [testng] [2024-04-19 09:10:36,816] [pool-1-thread-5] Initializing /data/ome/embryo.lsm: [testng] [2024-04-19 09:10:37,090] [pool-1-thread-10] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-04-19 09:10:37,178] [pool-1-thread-6] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-04-19 09:10:37,287] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-04-19 09:10:37,301] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-04-19 09:10:37,513] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-04-19 09:10:37,643] [pool-1-thread-2] Initializing /data/sdub/sdub.pattern: [testng] [2024-04-19 09:10:37,824] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-04-19 09:10:37,920] [pool-1-thread-4] Initializing /data/ome/worm.tiff: [testng] [2024-04-19 09:10:38,263] [pool-1-thread-7] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-04-19 09:10:38,277] [pool-1-thread-1] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-04-19 09:10:38,339] [pool-1-thread-5] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-04-19 09:10:38,394] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-04-19 09:10:38,444] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-04-19 09:10:38,602] [pool-1-thread-11] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-04-19 09:10:38,815] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-04-19 09:10:38,859] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-04-19 09:10:38,876] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-04-19 09:10:38,987] [pool-1-thread-12] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-04-19 09:10:39,010] [pool-1-thread-5] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-04-19 09:10:39,716] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-04-19 09:10:39,797] [pool-1-thread-10] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-04-19 09:10:39,824] [pool-1-thread-3] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-04-19 09:10:39,913] [pool-1-thread-11] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-04-19 09:10:40,268] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-04-19 09:10:40,326] [pool-1-thread-12] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-04-19 09:10:40,363] [pool-1-thread-8] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-04-19 09:10:40,387] [pool-1-thread-2] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-04-19 09:10:41,882] [pool-1-thread-1] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-04-19 09:10:41,997] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-04-19 09:10:42,145] [pool-1-thread-7] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-04-19 09:10:42,316] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-04-19 09:10:42,460] [pool-1-thread-1] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-04-19 09:10:42,530] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-04-19 09:10:42,566] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-04-19 09:10:42,572] [pool-1-thread-4] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-04-19 09:10:42,705] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-04-19 09:10:42,773] [pool-1-thread-9] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-04-19 09:10:42,967] [pool-1-thread-1] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-04-19 09:10:43,014] [pool-1-thread-12] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-04-19 09:10:43,285] [pool-1-thread-4] Initializing /data/ome/t1_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: 2 minutes 40 seconds Finished: SUCCESS