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Started by upstream project "BIOFORMATS-test-repo" build number 264 originally caused by: Started by upstream project "Trigger" build number 287 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins17456211608347146119.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41642_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] 00:37:47,884 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:37:47,886 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:37:47,886 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:47,887 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:47,887 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:37:47,887 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:37:47,887 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:37:47,887 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:47,888 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:47,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:37:47,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:37:47,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:37:48,106 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:37:48,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:37:48,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:37:48,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:37:48,141 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:37:48,141 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:37:48,141 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:37:48,142 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:37:48,142 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:37:48,143 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:37:48,143 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 255 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-22 00:37:48,152] [main] java.version = 1.8.0_342 [testng] 00:37:48,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:37:48,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:48,200 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-22_00-37-48.log] [testng] 00:37:48,202 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-22 00:37:48,204] [main] testng.directory = /data [testng] [2024-11-22 00:37:48,204] [main] testng.configDirectory = /config [testng] [2024-11-22 00:37:48,216] [main] testng.multiplier = 1.0 [testng] [2024-11-22 00:37:48,216] [main] testng.in-memory = false [testng] [2024-11-22 00:37:48,216] [main] testng.allow-missing = false [testng] [2024-11-22 00:37:48,216] [main] user.language = en [testng] [2024-11-22 00:37:48,216] [main] user.country = ${user.country} [testng] [2024-11-22 00:37:48,216] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-22 00:38:29,649] [main] ---------------------------------------- [testng] [2024-11-22 00:38:29,649] [main] Total files: 164 [testng] [2024-11-22 00:38:29,649] [main] Scan time: 41.432 s (252 ms/file) [testng] [2024-11-22 00:38:29,649] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-22 00:39:02,580] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:39:02,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:39:02,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:02,582 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-22_00-39-02.log] [testng] 00:39:02,582 |-INFO in ch.qos.logback.core.sift.SiftProcessor@540a7ba8 - End of configuration. [testng] [2024-11-22 00:39:02,772] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 00:39:02,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:39:02,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:02,773 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-22_00-39-02.log] [testng] 00:39:02,774 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72910e37 - End of configuration. [testng] [2024-11-22 00:39:02,848] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 00:39:02,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:39:02,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:02,849 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-22_00-39-02.log] [testng] 00:39:02,849 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f444476 - End of configuration. [testng] [2024-11-22 00:39:03,320] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm: [testng] 00:39:03,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:39:03,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:03,321 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-22_00-39-03.log] [testng] 00:39:03,322 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5eb1b740 - End of configuration. [testng] [2024-11-22 00:39:03,751] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk: [testng] 00:39:03,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:39:03,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:03,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-22_00-39-03.log] [testng] 00:39:03,752 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22c10d98 - End of configuration. [testng] [2024-11-22 00:39:04,704] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 00:39:04,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:39:04,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:04,705 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-22_00-39-04.log] [testng] 00:39:04,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@588cc7d2 - End of configuration. [testng] [2024-11-22 00:39:04,775] [pool-1-thread-7] Initializing /data/ome/embryo.lsm: [testng] 00:39:04,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:39:04,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:04,776 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-22_00-39-04.log] [testng] 00:39:04,776 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44deeb35 - End of configuration. [testng] [2024-11-22 00:39:05,146] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 00:39:05,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:39:05,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:05,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-22_00-39-05.log] [testng] 00:39:05,148 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51b5eb98 - End of configuration. [testng] [2024-11-22 00:39:05,238] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 00:39:05,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:39:05,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:05,238 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-22_00-39-05.log] [testng] 00:39:05,239 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5790e2a5 - End of configuration. [testng] [2024-11-22 00:39:05,649] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 00:39:05,649 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:39:05,649 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:05,650 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-22_00-39-05.log] [testng] 00:39:05,650 |-INFO in ch.qos.logback.core.sift.SiftProcessor@143a13e8 - End of configuration. [testng] [2024-11-22 00:39:05,712] [pool-1-thread-3] Initializing /data/ome/worm.tiff: [testng] 00:39:05,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:39:05,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:05,713 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-22_00-39-05.log] [testng] 00:39:05,713 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18e5776c - End of configuration. [testng] [2024-11-22 00:39:06,439] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:39:06,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:39:06,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:06,440 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-22_00-39-06.log] [testng] 00:39:06,441 |-INFO in ch.qos.logback.core.sift.SiftProcessor@265d8ad1 - End of configuration. [testng] [2024-11-22 00:39:09,969] [pool-1-thread-6] Initializing /data/ome/C1.lsm: [testng] [2024-11-22 00:39:10,209] [pool-1-thread-4] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-11-22 00:39:10,439] [pool-1-thread-12] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-11-22 00:39:10,847] [pool-1-thread-8] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-11-22 00:39:11,366] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern: [testng] [2024-11-22 00:39:15,628] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-11-22 00:39:15,774] [pool-1-thread-5] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-11-22 00:39:16,443] [pool-1-thread-1] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-11-22 00:39:17,100] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-11-22 00:39:17,763] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-11-22 00:39:18,416] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-11-22 00:39:19,530] [pool-1-thread-7] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-11-22 00:39:19,878] [pool-1-thread-2] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-11-22 00:39:20,010] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-11-22 00:39:21,631] [pool-1-thread-6] Initializing /data/ome/cb_1.r3d: [testng] [2024-11-22 00:39:22,078] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-11-22 00:39:22,527] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-11-22 00:39:22,588] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-11-22 00:39:23,828] [pool-1-thread-2] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-11-22 00:39:24,268] [pool-1-thread-1] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-11-22 00:39:24,898] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-11-22 00:39:24,990] [pool-1-thread-6] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-11-22 00:39:25,146] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-11-22 00:39:25,340] [pool-1-thread-11] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-11-22 00:39:26,084] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-11-22 00:39:26,848] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-11-22 00:39:27,389] [pool-1-thread-1] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-11-22 00:39:29,232] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-11-22 00:39:29,465] [pool-1-thread-9] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-11-22 00:39:29,938] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-11-22 00:39:30,055] [pool-1-thread-5] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-11-22 00:39:30,496] [pool-1-thread-6] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-11-22 00:39:31,471] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-11-22 00:39:31,555] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-11-22 00:39:32,145] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-11-22 00:39:33,245] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-11-22 00:39:33,447] [pool-1-thread-4] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-11-22 00:39:35,327] [pool-1-thread-2] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-11-22 00:39:55,173] [pool-1-thread-11] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-11-22 00:39:56,304] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-11-22 00:39:56,953] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-11-22 00:39:58,981] [pool-1-thread-5] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-11-22 00:40:01,446] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-11-22 00:40:02,074] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-11-22 00:40:02,640] [pool-1-thread-12] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-11-22 00:40:03,727] [pool-1-thread-11] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-11-22 00:40:05,124] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 4 minutes 5 seconds Finished: SUCCESS