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Started by upstream project "BIOFORMATS-test-repo" build number 259 originally caused by: Started by upstream project "Trigger" build number 283 originally caused by: Started by timer 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/jenkins13128156900347328862.sh + '[' samples = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_40822_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 -Duser.language=fr -Duser.country=FR 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] 00:33:55,235 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:33:55,237 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:33:55,237 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:33:55,238 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:33:55,238 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:33:55,238 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:33:55,239 |-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] 00:33:55,239 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:33:55,239 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:33:55,240 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:33:55,240 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:33:55,240 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:33:55,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:33:55,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:33:55,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:33:55,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:33:55,507 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:33:55,508 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:33:55,508 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:33:55,508 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:33:55,508 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:33:55,509 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:33:55,509 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 270 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-18 00:33:55,519] [main] java.version = 1.8.0_342 [testng] 00:33:55,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:33:55,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:55,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-18_00-33-55.log] [testng] 00:33:55,570 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-18 00:33:55,572] [main] testng.directory = /data [testng] [2024-11-18 00:33:55,573] [main] testng.configDirectory = /config [testng] [2024-11-18 00:33:55,585] [main] testng.multiplier = 1.0 [testng] [2024-11-18 00:33:55,585] [main] testng.in-memory = false [testng] [2024-11-18 00:33:55,585] [main] testng.allow-missing = false [testng] [2024-11-18 00:33:55,585] [main] user.language = fr [testng] [2024-11-18 00:33:55,585] [main] user.country = FR [testng] [2024-11-18 00:33:55,585] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-18 00:34:32,920] [main] ---------------------------------------- [testng] [2024-11-18 00:34:32,920] [main] Total files: 164 [testng] [2024-11-18 00:34:32,920] [main] Scan time: 37.335 s (227 ms/file) [testng] [2024-11-18 00:34:32,920] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-18 00:35:37,104] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 00:35:37,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:35:37,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:37,106 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-18_00-35-37.log] [testng] 00:35:37,106 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a083856 - End of configuration. [testng] [2024-11-18 00:35:37,427] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 00:35:37,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:35:37,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:37,428 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-18_00-35-37.log] [testng] 00:35:37,428 |-INFO in ch.qos.logback.core.sift.SiftProcessor@712d9486 - End of configuration. [testng] [2024-11-18 00:35:37,955] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 00:35:37,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:35:37,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:37,958 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-18_00-35-37.log] [testng] 00:35:37,958 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33115bd8 - End of configuration. [testng] [2024-11-18 00:35:38,445] [pool-1-thread-10] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] 00:35:38,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:35:38,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:38,446 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-18_00-35-38.log] [testng] 00:35:38,446 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a7d56ce - End of configuration. [testng] [2024-11-18 00:35:39,497] [pool-1-thread-9] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 00:35:39,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:35:39,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:39,498 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-18_00-35-39.log] [testng] 00:35:39,498 |-INFO in ch.qos.logback.core.sift.SiftProcessor@578fe242 - End of configuration. [testng] [2024-11-18 00:35:40,224] [pool-1-thread-8] Initializing /data/ome/C1midmusnorm.lsm: [testng] 00:35:40,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:35:40,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:40,224 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-18_00-35-40.log] [testng] 00:35:40,225 |-INFO in ch.qos.logback.core.sift.SiftProcessor@611b04e7 - End of configuration. [testng] [2024-11-18 00:35:40,759] [pool-1-thread-7] Initializing /data/openjpeg/Facade.bmp: [testng] 00:35:40,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:35:40,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:40,760 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-18_00-35-40.log] [testng] 00:35:40,761 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26509d2a - End of configuration. [testng] [2024-11-18 00:35:40,844] [pool-1-thread-6] Initializing /data/TAABA/TAABA.pattern: [testng] 00:35:40,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:35:40,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:40,845 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-18_00-35-40.log] [testng] 00:35:40,846 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b6403c9 - End of configuration. [testng] [2024-11-18 00:36:07,042] [pool-1-thread-5] Initializing /data/ome/tiffany.color.tiff: [testng] 00:36:07,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:36:07,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:07,043 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-18_00-36-07.log] [testng] 00:36:07,044 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55fa4c03 - End of configuration. [testng] [2024-11-18 00:36:08,192] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] 00:36:08,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:36:08,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:08,193 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-18_00-36-08.log] [testng] 00:36:08,194 |-INFO in ch.qos.logback.core.sift.SiftProcessor@748dcef0 - End of configuration. [testng] [2024-11-18 00:36:08,491] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 00:36:08,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:36:08,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:08,492 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-18_00-36-08.log] [testng] 00:36:08,511 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ec50b50 - End of configuration. [testng] [2024-11-18 00:36:08,658] [pool-1-thread-2] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:36:08,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:36:08,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:08,659 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-18_00-36-08.log] [testng] 00:36:08,659 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6be217d - End of configuration. [testng] [2024-11-18 00:36:12,980] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-11-18 00:36:13,459] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-11-18 00:36:13,562] [pool-1-thread-3] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-11-18 00:36:14,287] [pool-1-thread-7] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-11-18 00:36:14,695] [pool-1-thread-8] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-11-18 00:36:15,109] [pool-1-thread-12] Initializing /data/ome/654Atemp.stk: [testng] [2024-11-18 00:36:16,914] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-11-18 00:36:17,444] [pool-1-thread-9] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-11-18 00:36:19,164] [pool-1-thread-7] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-11-18 00:36:19,869] [pool-1-thread-1] Initializing /data/ome/worm.tiff: [testng] [2024-11-18 00:36:21,080] [pool-1-thread-10] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-11-18 00:36:21,636] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-11-18 00:36:21,785] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-11-18 00:36:22,501] [pool-1-thread-2] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-11-18 00:36:23,637] [pool-1-thread-8] Initializing /data/ome/C1.lsm: [testng] [2024-11-18 00:36:24,369] [pool-1-thread-3] Initializing /data/ome/embryo.lsm: [testng] [2024-11-18 00:36:25,356] [pool-1-thread-5] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-11-18 00:36:28,596] [pool-1-thread-7] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-11-18 00:36:30,387] [pool-1-thread-10] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-11-18 00:36:31,749] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-11-18 00:36:32,126] [pool-1-thread-8] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-11-18 00:36:32,642] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-11-18 00:36:33,934] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-11-18 00:36:34,402] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-11-18 00:36:34,710] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-11-18 00:36:35,624] [pool-1-thread-5] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-11-18 00:36:36,713] [pool-1-thread-7] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-11-18 00:36:37,754] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-11-18 00:36:38,106] [pool-1-thread-3] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-11-18 00:36:38,212] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-11-18 00:36:39,555] [pool-1-thread-4] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-11-18 00:36:39,796] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-11-18 00:36:40,594] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-11-18 00:36:41,490] [pool-1-thread-10] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-11-18 00:36:42,366] [pool-1-thread-2] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-11-18 00:36:42,928] [pool-1-thread-3] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-11-18 00:36:44,213] [pool-1-thread-7] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-11-18 00:36:44,658] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-11-18 00:36:45,155] [pool-1-thread-12] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-11-18 00:36:46,167] [pool-1-thread-5] Initializing /data/sdub/sdub.pattern: [testng] [2024-11-18 00:36:53,136] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-11-18 00:36:54,606] [pool-1-thread-7] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-11-18 00:36:54,721] [pool-1-thread-4] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-11-18 00:36:56,063] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-11-18 00:36:56,428] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-11-18 00:36:58,257] [pool-1-thread-7] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-11-18 00:36:58,874] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJ.bmp: [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 13 seconds Finished: SUCCESS