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Started by upstream project "BIOFORMATS-test-repo" build number 107 originally caused by: Started by upstream project "Trigger" build number 119 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins676199467301161023.sh + '[' samples = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_16567_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] 01:26:07,620 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:26:07,622 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:26:07,622 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:26:07,623 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:26:07,624 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:26:07,625 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:26:07,625 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:26:07,625 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:26:07,626 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:26:07,626 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:26:07,627 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:26:07,627 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:26:07,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:26:07,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:26:07,888 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:26:07,888 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:26:07,896 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:26:07,896 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:26:07,897 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:26:07,897 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:26:07,897 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:26:07,898 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:26:07,898 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 272 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-30 01:26:07,912] [main] java.version = 17.0.2 [testng] 01:26:07,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:26:07,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:07,977 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-30_01-26-07.log] [testng] 01:26:07,979 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-30 01:26:07,982] [main] testng.directory = /data [testng] [2024-06-30 01:26:07,982] [main] testng.configDirectory = /config [testng] [2024-06-30 01:26:07,995] [main] testng.multiplier = 1.0 [testng] [2024-06-30 01:26:07,996] [main] testng.in-memory = false [testng] [2024-06-30 01:26:07,997] [main] testng.allow-missing = false [testng] [2024-06-30 01:26:07,997] [main] user.language = en [testng] [2024-06-30 01:26:07,997] [main] user.country = ${user.country} [testng] [2024-06-30 01:26:07,997] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-30 01:26:26,682] [main] ---------------------------------------- [testng] [2024-06-30 01:26:26,682] [main] Total files: 164 [testng] [2024-06-30 01:26:26,682] [main] Scan time: 18.685 s (113 ms/file) [testng] [2024-06-30 01:26:26,682] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-30 01:26:34,857] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:26:34,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:26:34,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:34,858 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-30_01-26-34.log] [testng] 01:26:34,859 |-INFO in ch.qos.logback.core.sift.SiftProcessor@291ae4af - End of configuration. [testng] [2024-06-30 01:26:34,907] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 01:26:34,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:26:34,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:34,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-30_01-26-34.log] [testng] 01:26:34,909 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25904576 - End of configuration. [testng] [2024-06-30 01:26:34,962] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:26:34,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:26:34,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:34,964 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-30_01-26-34.log] [testng] 01:26:34,964 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6732c8bc - End of configuration. [testng] [2024-06-30 01:26:34,975] [pool-1-thread-10] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:26:34,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:26:34,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:34,976 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-30_01-26-34.log] [testng] 01:26:34,977 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76063626 - End of configuration. [testng] [2024-06-30 01:26:35,032] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 01:26:35,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:26:35,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:35,033 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-30_01-26-35.log] [testng] 01:26:35,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@af8b938 - End of configuration. [testng] [2024-06-30 01:26:35,044] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:26:35,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:26:35,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:35,045 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-30_01-26-35.log] [testng] 01:26:35,046 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20634cc8 - End of configuration. [testng] [2024-06-30 01:26:35,060] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:26:35,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:26:35,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:35,061 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-30_01-26-35.log] [testng] 01:26:35,061 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d69277a - End of configuration. [testng] [2024-06-30 01:26:35,115] [pool-1-thread-6] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 01:26:35,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:26:35,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:35,116 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-30_01-26-35.log] [testng] 01:26:35,117 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f84bd30 - End of configuration. [testng] [2024-06-30 01:26:35,226] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 01:26:35,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:26:35,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:35,227 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-30_01-26-35.log] [testng] 01:26:35,228 |-INFO in ch.qos.logback.core.sift.SiftProcessor@721be608 - End of configuration. [testng] [2024-06-30 01:26:35,235] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] 01:26:35,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:26:35,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:35,236 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-30_01-26-35.log] [testng] 01:26:35,237 |-INFO in ch.qos.logback.core.sift.SiftProcessor@643c14e4 - End of configuration. [testng] [2024-06-30 01:26:35,277] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 01:26:35,277 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:26:35,277 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:35,278 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-30_01-26-35.log] [testng] 01:26:35,279 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fd6dd35 - End of configuration. [testng] [2024-06-30 01:26:35,295] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 01:26:35,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:26:35,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:35,296 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-30_01-26-35.log] [testng] 01:26:35,296 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50380ee1 - End of configuration. [testng] [2024-06-30 01:26:37,170] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-06-30 01:26:37,178] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-06-30 01:26:37,184] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-06-30 01:26:37,192] [pool-1-thread-1] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-06-30 01:26:37,202] [pool-1-thread-4] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-06-30 01:26:37,368] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-06-30 01:26:37,374] [pool-1-thread-7] Initializing /data/sdub/sdub.pattern: [testng] [2024-06-30 01:26:37,686] [pool-1-thread-3] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-06-30 01:26:37,805] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-06-30 01:26:37,810] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-06-30 01:26:37,818] [pool-1-thread-9] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-06-30 01:26:37,985] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-06-30 01:26:37,997] [pool-1-thread-8] Initializing /data/ome/worm.tiff: [testng] [2024-06-30 01:26:38,139] [pool-1-thread-5] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-06-30 01:26:38,230] [pool-1-thread-12] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-06-30 01:26:38,279] [pool-1-thread-2] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-06-30 01:26:38,473] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-06-30 01:26:38,519] [pool-1-thread-12] Initializing /data/ome/654Atemp.stk: [testng] [2024-06-30 01:26:38,719] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2024-06-30 01:26:38,918] [pool-1-thread-9] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-06-30 01:26:39,120] [pool-1-thread-7] Initializing /data/ome/C1.lsm: [testng] [2024-06-30 01:26:39,251] [pool-1-thread-2] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-06-30 01:26:40,180] [pool-1-thread-6] Initializing /data/ome/cb_1.r3d: [testng] [2024-06-30 01:26:40,249] [pool-1-thread-4] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-06-30 01:26:40,436] [pool-1-thread-12] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-06-30 01:26:41,063] [pool-1-thread-5] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-06-30 01:26:41,095] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-06-30 01:26:41,139] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-06-30 01:26:41,375] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-06-30 01:26:41,479] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-06-30 01:26:41,724] [pool-1-thread-8] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-06-30 01:26:41,734] [pool-1-thread-6] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-06-30 01:26:41,811] [pool-1-thread-7] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-06-30 01:26:41,847] [pool-1-thread-10] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-06-30 01:26:41,938] [pool-1-thread-9] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-06-30 01:26:41,984] [pool-1-thread-5] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-06-30 01:26:42,136] [pool-1-thread-8] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-06-30 01:26:42,171] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-06-30 01:26:42,217] [pool-1-thread-4] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-06-30 01:26:42,293] [pool-1-thread-8] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-06-30 01:26:42,377] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-06-30 01:26:42,427] [pool-1-thread-7] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-06-30 01:26:42,491] [pool-1-thread-10] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-06-30 01:26:42,574] [pool-1-thread-6] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-06-30 01:26:42,671] [pool-1-thread-11] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-06-30 01:26:42,678] [pool-1-thread-5] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-06-30 01:26:42,757] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJW.bmp: [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 10 seconds Finished: SUCCESS