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Started by upstream project "BIOFORMATS-test-repo" build number 252 originally caused by: Started by upstream project "Trigger" build number 276 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins12329256452698265192.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_39674_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] 00:37:50,281 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:37:50,282 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:37:50,282 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:50,283 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:50,283 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:37:50,284 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:37:50,284 |-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] 00:37:50,284 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:50,284 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:50,285 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:37:50,285 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:37:50,285 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:37:50,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:37:50,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:37:50,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:37:50,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:37:50,548 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:37:50,548 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:37:50,548 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:37:50,549 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:37:50,549 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:37:50,550 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:37:50,550 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 266 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-11 00:37:50,561] [main] java.version = 1.8.0_342 [testng] 00:37:50,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:37:50,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:50,609 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-11_00-37-50.log] [testng] 00:37:50,611 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-11 00:37:50,613] [main] testng.directory = /data [testng] [2024-11-11 00:37:50,613] [main] testng.configDirectory = /config [testng] [2024-11-11 00:37:50,624] [main] testng.multiplier = 1.0 [testng] [2024-11-11 00:37:50,625] [main] testng.in-memory = false [testng] [2024-11-11 00:37:50,625] [main] testng.allow-missing = false [testng] [2024-11-11 00:37:50,625] [main] user.language = fr [testng] [2024-11-11 00:37:50,625] [main] user.country = FR [testng] [2024-11-11 00:37:50,625] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-11 00:38:26,151] [main] ---------------------------------------- [testng] [2024-11-11 00:38:26,237] [main] Total files: 164 [testng] [2024-11-11 00:38:26,237] [main] Scan time: 35.526 s (216 ms/file) [testng] [2024-11-11 00:38:26,238] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-11 00:39:12,308] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 00:39:12,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:39:12,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:12,309 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-11_00-39-12.log] [testng] 00:39:12,310 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65d956fa - End of configuration. [testng] [2024-11-11 00:39:12,502] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 00:39:12,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:39:12,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:12,503 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-11_00-39-12.log] [testng] 00:39:12,504 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a4e3a69 - End of configuration. [testng] [2024-11-11 00:39:12,816] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 00:39:12,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:39:12,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:12,817 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-11_00-39-12.log] [testng] 00:39:12,817 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1eca327d - End of configuration. [testng] [2024-11-11 00:39:13,162] [pool-1-thread-10] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] 00:39:13,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:39:13,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:13,163 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-11_00-39-13.log] [testng] 00:39:13,163 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e6d6bee - End of configuration. [testng] [2024-11-11 00:39:13,761] [pool-1-thread-9] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 00:39:13,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:39:13,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:13,762 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-11_00-39-13.log] [testng] 00:39:13,762 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ec10838 - End of configuration. [testng] [2024-11-11 00:39:14,215] [pool-1-thread-8] Initializing /data/ome/C1midmusnorm.lsm: [testng] 00:39:14,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:39:14,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:14,215 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-11_00-39-14.log] [testng] 00:39:14,216 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d699ec2 - End of configuration. [testng] [2024-11-11 00:39:14,819] [pool-1-thread-7] Initializing /data/openjpeg/Facade.bmp: [testng] 00:39:14,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:39:14,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:14,820 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-11_00-39-14.log] [testng] 00:39:14,820 |-INFO in ch.qos.logback.core.sift.SiftProcessor@554e131 - End of configuration. [testng] [2024-11-11 00:39:14,933] [pool-1-thread-6] Initializing /data/TAABA/TAABA.pattern: [testng] 00:39:14,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:39:14,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:14,933 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-11_00-39-14.log] [testng] 00:39:14,934 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43f4bd6 - End of configuration. [testng] [2024-11-11 00:39:34,942] [pool-1-thread-5] Initializing /data/ome/tiffany.color.tiff: [testng] 00:39:34,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:39:34,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:34,943 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-11_00-39-34.log] [testng] 00:39:34,944 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d61b583 - End of configuration. [testng] [2024-11-11 00:39:35,881] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] 00:39:35,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:39:35,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:35,881 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-11_00-39-35.log] [testng] 00:39:35,882 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67e93ae0 - End of configuration. [testng] [2024-11-11 00:39:36,083] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 00:39:36,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:39:36,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:36,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-11_00-39-36.log] [testng] 00:39:36,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4339c142 - End of configuration. [testng] [2024-11-11 00:39:36,206] [pool-1-thread-2] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:39:36,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:39:36,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:39:36,207 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-11_00-39-36.log] [testng] 00:39:36,207 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6faa9e82 - End of configuration. [testng] [2024-11-11 00:39:40,183] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-11-11 00:39:40,720] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-11-11 00:39:41,307] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-11-11 00:39:41,481] [pool-1-thread-7] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-11-11 00:39:42,122] [pool-1-thread-8] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-11-11 00:39:43,042] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk: [testng] [2024-11-11 00:39:44,480] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-11-11 00:39:44,764] [pool-1-thread-3] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-11-11 00:39:46,166] [pool-1-thread-2] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-11-11 00:39:47,148] [pool-1-thread-10] Initializing /data/ome/worm.tiff: [testng] [2024-11-11 00:39:49,401] [pool-1-thread-7] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-11-11 00:39:50,483] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-11-11 00:39:51,128] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-11-11 00:39:51,631] [pool-1-thread-12] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-11-11 00:39:53,138] [pool-1-thread-1] Initializing /data/ome/C1.lsm: [testng] [2024-11-11 00:39:54,167] [pool-1-thread-5] Initializing /data/ome/embryo.lsm: [testng] [2024-11-11 00:39:55,961] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-11-11 00:40:00,600] [pool-1-thread-2] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-11-11 00:40:02,422] [pool-1-thread-7] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-11-11 00:40:03,570] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-11-11 00:40:03,934] [pool-1-thread-9] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-11-11 00:40:05,212] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-11-11 00:40:05,516] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-11-11 00:40:05,774] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-11-11 00:40:07,517] [pool-1-thread-4] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-11-11 00:40:10,059] [pool-1-thread-5] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-11-11 00:40:11,608] [pool-1-thread-12] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-11-11 00:40:12,534] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-11-11 00:40:12,721] [pool-1-thread-2] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-11-11 00:40:12,908] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-11-11 00:40:13,185] [pool-1-thread-7] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-11-11 00:40:13,537] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-11-11 00:40:14,827] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-11-11 00:40:15,866] [pool-1-thread-10] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-11-11 00:40:16,687] [pool-1-thread-7] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-11-11 00:40:17,074] [pool-1-thread-8] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-11-11 00:40:18,765] [pool-1-thread-4] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-11-11 00:40:18,949] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-11-11 00:40:19,449] [pool-1-thread-12] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-11-11 00:40:20,476] [pool-1-thread-7] Initializing /data/sdub/sdub.pattern: [testng] [2024-11-11 00:40:25,885] [pool-1-thread-5] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-11-11 00:40:26,788] [pool-1-thread-2] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-11-11 00:40:26,946] [pool-1-thread-1] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-11-11 00:40:28,244] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-11-11 00:40:28,367] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-11-11 00:40:30,662] [pool-1-thread-2] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-11-11 00:40:31,254] [pool-1-thread-10] 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: 3 minutes 43 seconds Finished: SUCCESS