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Started by upstream project "BIOFORMATS-test-repo" build number 273 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins13321753512213950470.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42989_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] 07:08:55,800 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 07:08:55,802 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 07:08:55,802 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:08:55,803 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:08:55,803 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 07:08:55,803 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 07:08:55,804 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 07:08:55,804 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:08:55,804 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:08:55,805 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 07:08:55,805 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 07:08:55,805 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 07:08:56,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 07:08:56,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 07:08:56,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 07:08:56,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 07:08:56,087 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 07:08:56,088 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 07:08:56,088 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 07:08:56,088 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 07:08:56,088 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 07:08:56,089 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 07:08:56,089 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 285 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-29 07:08:56,100] [main] java.version = 1.8.0_342 [testng] 07:08:56,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:08:56,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:08:56,150 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-29_07-08-56.log] [testng] 07:08:56,151 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-29 07:08:56,153] [main] testng.directory = /data [testng] [2024-11-29 07:08:56,154] [main] testng.configDirectory = /config [testng] [2024-11-29 07:08:56,167] [main] testng.multiplier = 1.0 [testng] [2024-11-29 07:08:56,167] [main] testng.in-memory = false [testng] [2024-11-29 07:08:56,167] [main] testng.allow-missing = false [testng] [2024-11-29 07:08:56,167] [main] user.language = en [testng] [2024-11-29 07:08:56,167] [main] user.country = ${user.country} [testng] [2024-11-29 07:08:56,167] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-29 07:09:51,510] [main] ---------------------------------------- [testng] [2024-11-29 07:09:51,511] [main] Total files: 164 [testng] [2024-11-29 07:09:51,511] [main] Scan time: 55.343 s (337 ms/file) [testng] [2024-11-29 07:09:51,511] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-29 07:11:20,182] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 07:11:20,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 07:11:20,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:20,183 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-29_07-11-20.log] [testng] 07:11:20,184 |-INFO in ch.qos.logback.core.sift.SiftProcessor@334fc3bf - End of configuration. [testng] [2024-11-29 07:11:20,969] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 07:11:20,969 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 07:11:20,969 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:20,970 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-29_07-11-20.log] [testng] 07:11:20,970 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59913e18 - End of configuration. [testng] [2024-11-29 07:11:21,067] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 07:11:21,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 07:11:21,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:21,068 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-29_07-11-21.log] [testng] 07:11:21,068 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62eb200f - End of configuration. [testng] [2024-11-29 07:11:21,602] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm: [testng] 07:11:21,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 07:11:21,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:21,603 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-29_07-11-21.log] [testng] 07:11:21,603 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48731cf6 - End of configuration. [testng] [2024-11-29 07:11:22,184] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk: [testng] 07:11:22,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 07:11:22,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:22,185 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-29_07-11-22.log] [testng] 07:11:22,186 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4de4edb - End of configuration. [testng] [2024-11-29 07:11:23,598] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 07:11:23,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 07:11:23,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:23,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-29_07-11-23.log] [testng] 07:11:23,600 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14cabfda - End of configuration. [testng] [2024-11-29 07:11:23,714] [pool-1-thread-7] Initializing /data/ome/embryo.lsm: [testng] 07:11:23,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 07:11:23,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:23,715 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-29_07-11-23.log] [testng] 07:11:23,716 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4afd03a4 - End of configuration. [testng] [2024-11-29 07:11:24,357] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 07:11:24,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 07:11:24,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:24,358 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-29_07-11-24.log] [testng] 07:11:24,359 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ee4b36e - End of configuration. [testng] [2024-11-29 07:11:24,490] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 07:11:24,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 07:11:24,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:24,491 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-29_07-11-24.log] [testng] 07:11:24,491 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53da0cd0 - End of configuration. [testng] [2024-11-29 07:11:25,124] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 07:11:25,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 07:11:25,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:25,125 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-29_07-11-25.log] [testng] 07:11:25,125 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8539a6f - End of configuration. [testng] [2024-11-29 07:11:25,221] [pool-1-thread-3] Initializing /data/ome/worm.tiff: [testng] 07:11:25,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 07:11:25,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:25,222 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-29_07-11-25.log] [testng] 07:11:25,222 |-INFO in ch.qos.logback.core.sift.SiftProcessor@249fd3ac - End of configuration. [testng] [2024-11-29 07:11:26,709] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 07:11:26,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 07:11:26,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:26,710 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-29_07-11-26.log] [testng] 07:11:26,711 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bf506d1 - End of configuration. [testng] [2024-11-29 07:11:31,814] [pool-1-thread-4] Initializing /data/ome/C1.lsm: [testng] [2024-11-29 07:11:33,149] [pool-1-thread-8] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-11-29 07:11:33,351] [pool-1-thread-12] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-11-29 07:11:33,651] [pool-1-thread-6] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-11-29 07:11:35,536] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-11-29 07:11:35,835] [pool-1-thread-5] Initializing /data/sdub/sdub.pattern: [testng] [2024-11-29 07:11:43,514] [pool-1-thread-10] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-11-29 07:11:44,316] [pool-1-thread-7] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-11-29 07:11:45,022] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-11-29 07:11:46,186] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-11-29 07:11:46,350] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-11-29 07:11:48,316] [pool-1-thread-12] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-11-29 07:11:49,179] [pool-1-thread-8] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-11-29 07:11:49,387] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-11-29 07:11:51,183] [pool-1-thread-2] Initializing /data/ome/cb_1.r3d: [testng] [2024-11-29 07:11:52,373] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-11-29 07:11:53,631] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-11-29 07:11:53,803] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-11-29 07:11:54,948] [pool-1-thread-7] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-11-29 07:11:55,656] [pool-1-thread-9] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-11-29 07:11:55,916] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-11-29 07:11:56,461] [pool-1-thread-11] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-11-29 07:11:56,692] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-11-29 07:11:57,314] [pool-1-thread-2] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-11-29 07:11:58,278] [pool-1-thread-6] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-11-29 07:11:58,731] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-11-29 07:11:59,538] [pool-1-thread-9] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-11-29 07:12:01,327] [pool-1-thread-12] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-11-29 07:12:02,602] [pool-1-thread-6] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-11-29 07:12:03,259] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-11-29 07:12:03,410] [pool-1-thread-2] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-11-29 07:12:04,984] [pool-1-thread-11] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-11-29 07:12:05,912] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-11-29 07:12:06,275] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-11-29 07:12:06,493] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-11-29 07:12:07,808] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-11-29 07:12:08,651] [pool-1-thread-12] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-11-29 07:12:10,285] [pool-1-thread-3] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-11-29 07:12:40,426] [pool-1-thread-4] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-11-29 07:12:41,443] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-11-29 07:12:42,566] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-11-29 07:12:43,817] [pool-1-thread-11] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-11-29 07:12:45,712] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-11-29 07:12:46,016] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-11-29 07:12:46,389] [pool-1-thread-7] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-11-29 07:12:49,174] [pool-1-thread-10] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-11-29 07:12:50,564] [pool-1-thread-12] 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: 5 minutes 20 seconds Finished: SUCCESS