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Started by upstream project "BIOFORMATS-test-repo" build number 106 originally caused by: Started by upstream project "Trigger" build number 118 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/jenkins9925525212724587317.sh + '[' samples = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_16403_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] 01:25:52,983 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:25:52,985 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:25:52,986 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:25:52,987 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:25:52,988 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:25:52,988 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:25:52,989 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:25:52,989 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:25:52,989 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:25:52,990 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:25:52,991 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:25:52,991 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:25:53,207 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:25:53,207 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:25:53,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:25:53,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:25:53,235 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:25:53,235 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:25:53,235 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:25:53,235 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:25:53,235 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:25:53,237 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:25:53,237 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 248 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-29 01:25:53,246] [main] java.version = 11.0.16 [testng] 01:25:53,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:25:53,250 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:53,293 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-29_01-25-53.log] [testng] 01:25:53,294 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-06-29 01:25:53,297] [main] testng.directory = /data [testng] [2024-06-29 01:25:53,297] [main] testng.configDirectory = /config [testng] [2024-06-29 01:25:53,307] [main] testng.multiplier = 1.0 [testng] [2024-06-29 01:25:53,308] [main] testng.in-memory = false [testng] [2024-06-29 01:25:53,308] [main] testng.allow-missing = false [testng] [2024-06-29 01:25:53,308] [main] user.language = en [testng] [2024-06-29 01:25:53,308] [main] user.country = ${user.country} [testng] [2024-06-29 01:25:53,308] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-29 01:26:11,458] [main] ---------------------------------------- [testng] [2024-06-29 01:26:11,458] [main] Total files: 164 [testng] [2024-06-29 01:26:11,458] [main] Scan time: 18.15 s (110 ms/file) [testng] [2024-06-29 01:26:11,459] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-29 01:26:20,040] [pool-1-thread-1] Initializing /data/ome/C1.lsm: [testng] 01:26:20,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:26:20,043 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:20,046 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-29_01-26-20.log] [testng] 01:26:20,047 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c89b3e6 - End of configuration. [testng] [2024-06-29 01:26:20,112] [pool-1-thread-12] Initializing /data/openjpeg/Facade.bmp: [testng] 01:26:20,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:26:20,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:20,113 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-29_01-26-20.log] [testng] 01:26:20,114 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ff55c5e - End of configuration. [testng] [2024-06-29 01:26:20,136] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:26:20,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:26:20,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:20,138 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-29_01-26-20.log] [testng] 01:26:20,138 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4702ad24 - End of configuration. [testng] [2024-06-29 01:26:20,150] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] 01:26:20,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:26:20,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:20,152 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-29_01-26-20.log] [testng] 01:26:20,153 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72d7feb9 - End of configuration. [testng] [2024-06-29 01:26:20,195] [pool-1-thread-9] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] 01:26:20,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:26:20,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:20,197 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-29_01-26-20.log] [testng] 01:26:20,197 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a90c1a3 - End of configuration. [testng] [2024-06-29 01:26:20,301] [pool-1-thread-8] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:26:20,302 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:26:20,302 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:20,303 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-29_01-26-20.log] [testng] 01:26:20,304 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48291505 - End of configuration. [testng] [2024-06-29 01:26:20,400] [pool-1-thread-7] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 01:26:20,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:26:20,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:20,401 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-29_01-26-20.log] [testng] 01:26:20,401 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31b78629 - End of configuration. [testng] [2024-06-29 01:26:20,763] [pool-1-thread-6] Initializing /data/openjpeg/Rome.ppm: [testng] 01:26:20,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:26:20,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:20,764 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-29_01-26-20.log] [testng] 01:26:20,765 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a9894c1 - End of configuration. [testng] [2024-06-29 01:26:20,778] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:26:20,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:26:20,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:20,779 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-29_01-26-20.log] [testng] 01:26:20,780 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7926de0f - End of configuration. [testng] [2024-06-29 01:26:20,832] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 01:26:20,833 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:26:20,833 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:20,834 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-29_01-26-20.log] [testng] 01:26:20,834 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46204784 - End of configuration. [testng] [2024-06-29 01:26:20,846] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 01:26:20,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:26:20,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:20,847 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-29_01-26-20.log] [testng] 01:26:20,847 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41e84a53 - End of configuration. [testng] [2024-06-29 01:26:20,923] [pool-1-thread-2] Initializing /data/sdub/sdub.pattern: [testng] 01:26:20,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:26:20,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:20,925 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-29_01-26-20.log] [testng] 01:26:20,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54c7ad64 - End of configuration. [testng] [2024-06-29 01:26:22,933] [pool-1-thread-4] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-06-29 01:26:22,947] [pool-1-thread-10] Initializing /data/ome/654Atemp.stk: [testng] [2024-06-29 01:26:23,023] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-06-29 01:26:23,030] [pool-1-thread-6] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-06-29 01:26:23,072] [pool-1-thread-1] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-06-29 01:26:23,085] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-06-29 01:26:23,498] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-06-29 01:26:23,682] [pool-1-thread-3] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-06-29 01:26:23,704] [pool-1-thread-5] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-06-29 01:26:23,720] [pool-1-thread-1] Initializing /data/ome/worm.tiff: [testng] [2024-06-29 01:26:23,988] [pool-1-thread-9] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-06-29 01:26:24,014] [pool-1-thread-4] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-06-29 01:26:24,312] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-06-29 01:26:24,330] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-06-29 01:26:24,499] [pool-1-thread-7] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-06-29 01:26:24,568] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-06-29 01:26:24,582] [pool-1-thread-5] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-06-29 01:26:26,034] [pool-1-thread-3] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-06-29 01:26:26,163] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-06-29 01:26:26,336] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-06-29 01:26:26,343] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-06-29 01:26:26,685] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-06-29 01:26:27,045] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-06-29 01:26:27,144] [pool-1-thread-10] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-06-29 01:26:27,366] [pool-1-thread-3] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-06-29 01:26:27,554] [pool-1-thread-7] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-06-29 01:26:27,584] [pool-1-thread-4] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-06-29 01:26:27,743] [pool-1-thread-8] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-06-29 01:26:28,111] [pool-1-thread-10] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-06-29 01:26:28,276] [pool-1-thread-7] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-06-29 01:26:28,399] [pool-1-thread-8] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-06-29 01:26:28,495] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-06-29 01:26:28,537] [pool-1-thread-3] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-06-29 01:26:29,406] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-06-29 01:26:29,497] [pool-1-thread-1] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-06-29 01:26:29,676] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-06-29 01:26:29,713] [pool-1-thread-2] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-06-29 01:26:29,932] [pool-1-thread-11] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-06-29 01:26:30,167] [pool-1-thread-10] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-06-29 01:26:30,317] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] [2024-06-29 01:26:30,674] [pool-1-thread-11] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-06-29 01:26:30,935] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-06-29 01:26:31,113] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-06-29 01:26:31,225] [pool-1-thread-8] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-06-29 01:26:31,568] [pool-1-thread-4] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-06-29 01:26:31,622] [pool-1-thread-9] Initializing /data/ome/embryo.lsm: [testng] [2024-06-29 01:26:31,914] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.ppm: [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 23 seconds Finished: SUCCESS