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Started by upstream project "BIOFORMATS-test-repo" build number 110 originally caused by: Started by upstream project "Trigger" build number 123 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/jenkins5919039477358532652.sh + '[' samples = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_17059_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] 01:25:59,608 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:25:59,610 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:25:59,610 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:25:59,611 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:25:59,612 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:25:59,612 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:25:59,613 |-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] 01:25:59,613 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:25:59,613 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:25:59,614 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:25:59,615 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:25:59,615 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:25:59,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:25:59,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:25:59,835 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:25:59,835 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:25:59,841 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:25:59,841 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:25:59,841 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:25:59,841 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:25:59,841 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:25:59,842 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:25:59,842 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 229 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-03 01:25:59,851] [main] java.version = 17.0.2 [testng] 01:25:59,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:25:59,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:59,896 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-03_01-25-59.log] [testng] 01:25:59,898 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-07-03 01:25:59,900] [main] testng.directory = /data [testng] [2024-07-03 01:25:59,900] [main] testng.configDirectory = /config [testng] [2024-07-03 01:25:59,909] [main] testng.multiplier = 1.0 [testng] [2024-07-03 01:25:59,910] [main] testng.in-memory = false [testng] [2024-07-03 01:25:59,910] [main] testng.allow-missing = false [testng] [2024-07-03 01:25:59,910] [main] user.language = en [testng] [2024-07-03 01:25:59,910] [main] user.country = ${user.country} [testng] [2024-07-03 01:25:59,910] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-03 01:26:18,885] [main] ---------------------------------------- [testng] [2024-07-03 01:26:18,886] [main] Total files: 164 [testng] [2024-07-03 01:26:18,886] [main] Scan time: 18.974 s (115 ms/file) [testng] [2024-07-03 01:26:18,886] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-03 01:26:26,706] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:26:26,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:26:26,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:26,708 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-03_01-26-26.log] [testng] 01:26:26,708 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7933389c - End of configuration. [testng] [2024-07-03 01:26:26,755] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 01:26:26,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:26:26,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:26,756 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-03_01-26-26.log] [testng] 01:26:26,757 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56ee7015 - End of configuration. [testng] [2024-07-03 01:26:26,806] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:26:26,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:26:26,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:26,807 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-03_01-26-26.log] [testng] 01:26:26,807 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e1a1e58 - End of configuration. [testng] [2024-07-03 01:26:26,813] [pool-1-thread-10] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:26:26,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:26:26,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:26,814 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-03_01-26-26.log] [testng] 01:26:26,814 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d5e1c72 - End of configuration. [testng] [2024-07-03 01:26:26,845] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 01:26:26,845 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:26:26,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:26,846 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-03_01-26-26.log] [testng] 01:26:26,847 |-INFO in ch.qos.logback.core.sift.SiftProcessor@582a7cc7 - End of configuration. [testng] [2024-07-03 01:26:26,855] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:26:26,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:26:26,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:26,856 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-03_01-26-26.log] [testng] 01:26:26,856 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a4aa8c5 - End of configuration. [testng] [2024-07-03 01:26:26,870] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:26:26,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:26:26,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:26,871 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-03_01-26-26.log] [testng] 01:26:26,871 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b459db6 - End of configuration. [testng] [2024-07-03 01:26:26,955] [pool-1-thread-6] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 01:26:26,955 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:26:26,955 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:26,956 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-03_01-26-26.log] [testng] 01:26:26,956 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19469044 - End of configuration. [testng] [2024-07-03 01:26:27,039] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 01:26:27,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:26:27,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:27,040 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-03_01-26-27.log] [testng] 01:26:27,040 |-INFO in ch.qos.logback.core.sift.SiftProcessor@721be608 - End of configuration. [testng] [2024-07-03 01:26:27,047] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] 01:26:27,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:26:27,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:27,048 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-03_01-26-27.log] [testng] 01:26:27,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bee7c5e - End of configuration. [testng] [2024-07-03 01:26:27,089] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 01:26:27,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:26:27,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:27,091 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-03_01-26-27.log] [testng] 01:26:27,091 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bbebeb1 - End of configuration. [testng] [2024-07-03 01:26:27,108] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 01:26:27,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:26:27,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:27,109 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-03_01-26-27.log] [testng] 01:26:27,110 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6456fe3e - End of configuration. [testng] [2024-07-03 01:26:28,303] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-07-03 01:26:28,513] [pool-1-thread-2] Initializing /data/sdub/sdub.pattern: [testng] [2024-07-03 01:26:28,665] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-07-03 01:26:28,874] [pool-1-thread-9] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-07-03 01:26:29,045] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-07-03 01:26:29,052] [pool-1-thread-4] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-07-03 01:26:29,204] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-07-03 01:26:29,210] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-07-03 01:26:29,216] [pool-1-thread-7] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-07-03 01:26:29,348] [pool-1-thread-4] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-07-03 01:26:29,559] [pool-1-thread-5] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-07-03 01:26:29,567] [pool-1-thread-11] Initializing /data/ome/worm.tiff: [testng] [2024-07-03 01:26:29,617] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-07-03 01:26:29,686] [pool-1-thread-10] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-07-03 01:26:29,730] [pool-1-thread-8] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-07-03 01:26:29,940] [pool-1-thread-12] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-07-03 01:26:30,080] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-07-03 01:26:30,275] [pool-1-thread-8] Initializing /data/ome/654Atemp.stk: [testng] [2024-07-03 01:26:30,489] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2024-07-03 01:26:30,693] [pool-1-thread-2] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-07-03 01:26:30,849] [pool-1-thread-4] Initializing /data/ome/C1.lsm: [testng] [2024-07-03 01:26:31,082] [pool-1-thread-6] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-07-03 01:26:32,183] [pool-1-thread-9] Initializing /data/ome/cb_1.r3d: [testng] [2024-07-03 01:26:32,297] [pool-1-thread-12] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-07-03 01:26:32,442] [pool-1-thread-10] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-07-03 01:26:33,052] [pool-1-thread-4] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-07-03 01:26:33,076] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-07-03 01:26:33,117] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-07-03 01:26:33,459] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-07-03 01:26:33,588] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-07-03 01:26:33,606] [pool-1-thread-4] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-07-03 01:26:33,678] [pool-1-thread-1] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-07-03 01:26:33,846] [pool-1-thread-9] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-07-03 01:26:33,867] [pool-1-thread-8] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-07-03 01:26:33,872] [pool-1-thread-3] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-07-03 01:26:33,898] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-07-03 01:26:33,913] [pool-1-thread-11] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-07-03 01:26:33,987] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-07-03 01:26:34,039] [pool-1-thread-4] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-07-03 01:26:34,127] [pool-1-thread-8] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-07-03 01:26:34,222] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-07-03 01:26:34,310] [pool-1-thread-5] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-07-03 01:26:34,424] [pool-1-thread-9] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-07-03 01:26:34,466] [pool-1-thread-11] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-07-03 01:26:34,524] [pool-1-thread-3] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-07-03 01:26:34,591] [pool-1-thread-8] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-07-03 01:26:34,622] [pool-1-thread-1] 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