Started by upstream project "BIOFORMATS-test-repo" build number 303 originally caused by: Started by upstream project "Trigger" build number 325 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/jenkins11759003991880767099.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_47923_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] 00:40:54,549 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:40:54,551 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:40:54,551 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:40:54,552 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:40:54,552 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:40:54,552 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:40:54,552 |-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] 00:40:54,552 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:40:54,553 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:40:54,553 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:40:54,553 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:40:54,553 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:40:54,790 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:40:54,790 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:40:54,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:40:54,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:40:54,827 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:40:54,827 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:40:54,827 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:40:54,828 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:40:54,828 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:40:54,829 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:40:54,829 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 276 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-30 00:40:54,839] [main] java.version = 1.8.0_342 [testng] 00:40:54,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:40:54,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:54,886 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-30_00-40-54.log] [testng] 00:40:54,887 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-30 00:40:54,889] [main] testng.directory = /data [testng] [2024-12-30 00:40:54,889] [main] testng.configDirectory = /config [testng] [2024-12-30 00:40:54,902] [main] testng.multiplier = 1.0 [testng] [2024-12-30 00:40:54,902] [main] testng.in-memory = false [testng] [2024-12-30 00:40:54,902] [main] testng.allow-missing = false [testng] [2024-12-30 00:40:54,902] [main] user.language = fr [testng] [2024-12-30 00:40:54,902] [main] user.country = FR [testng] [2024-12-30 00:40:54,902] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-30 00:41:32,514] [main] ---------------------------------------- [testng] [2024-12-30 00:41:32,514] [main] Total files: 164 [testng] [2024-12-30 00:41:32,514] [main] Scan time: 37.612 s (229 ms/file) [testng] [2024-12-30 00:41:32,514] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-30 00:42:15,966] [pool-1-thread-1] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 00:42:15,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:42:15,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:15,968 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-30_00-42-15.log] [testng] 00:42:15,968 |-INFO in ch.qos.logback.core.sift.SiftProcessor@255ce7d9 - End of configuration. [testng] [2024-12-30 00:42:16,643] [pool-1-thread-12] Initializing /data/ome/tinyTest.d3d.dv: [testng] 00:42:16,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:42:16,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:16,645 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-30_00-42-16.log] [testng] 00:42:16,645 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10628999 - End of configuration. [testng] [2024-12-30 00:42:16,769] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 00:42:16,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:42:16,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:16,770 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-30_00-42-16.log] [testng] 00:42:16,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38d6fa78 - End of configuration. [testng] [2024-12-30 00:42:17,210] [pool-1-thread-10] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 00:42:17,210 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:42:17,210 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:17,211 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-30_00-42-17.log] [testng] 00:42:17,211 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79ccbb72 - End of configuration. [testng] [2024-12-30 00:42:17,669] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 00:42:17,669 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:42:17,669 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:17,670 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-30_00-42-17.log] [testng] 00:42:17,670 |-INFO in ch.qos.logback.core.sift.SiftProcessor@368ec061 - End of configuration. [testng] [2024-12-30 00:42:18,289] [pool-1-thread-8] Initializing /data/ome/Adultmidsection.lsm: [testng] 00:42:18,290 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:42:18,290 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:18,290 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-30_00-42-18.log] [testng] 00:42:18,291 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23254bfb - End of configuration. [testng] [2024-12-30 00:42:18,648] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 00:42:18,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:42:18,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:18,649 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-30_00-42-18.log] [testng] 00:42:18,649 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57d9dbd3 - End of configuration. [testng] [2024-12-30 00:42:18,737] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] 00:42:18,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:42:18,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:18,738 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-30_00-42-18.log] [testng] 00:42:18,739 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55da31d9 - End of configuration. [testng] [2024-12-30 00:42:18,847] [pool-1-thread-5] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:42:18,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:42:18,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:18,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-30_00-42-18.log] [testng] 00:42:18,848 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32ad4035 - End of configuration. [testng] [2024-12-30 00:42:19,632] [pool-1-thread-4] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 00:42:19,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:42:19,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:19,632 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-30_00-42-19.log] [testng] 00:42:19,633 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ddfc088 - End of configuration. [testng] [2024-12-30 00:42:20,836] [pool-1-thread-3] Initializing /data/openjpeg/Rome.bmp: [testng] 00:42:20,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:42:20,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:20,837 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-30_00-42-20.log] [testng] 00:42:20,837 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b6b16b - End of configuration. [testng] [2024-12-30 00:42:20,918] [pool-1-thread-2] Initializing /data/ome/CHOBI_d3d.dv: [testng] 00:42:20,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:42:20,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:20,919 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-30_00-42-20.log] [testng] 00:42:20,919 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1eb674af - End of configuration. [testng] [2024-12-30 00:42:24,042] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-12-30 00:42:24,500] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-12-30 00:42:24,583] [pool-1-thread-3] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-12-30 00:42:25,665] [pool-1-thread-2] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-12-30 00:42:26,401] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-12-30 00:42:28,061] [pool-1-thread-10] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-12-30 00:42:28,323] [pool-1-thread-8] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-12-30 00:42:28,441] [pool-1-thread-11] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-12-30 00:42:29,215] [pool-1-thread-2] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-12-30 00:42:46,211] [pool-1-thread-9] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-12-30 00:42:46,623] [pool-1-thread-5] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-12-30 00:42:46,982] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-12-30 00:42:47,069] [pool-1-thread-12] Initializing /data/ome/worm.tiff: [testng] [2024-12-30 00:42:48,333] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-12-30 00:42:48,467] [pool-1-thread-8] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-12-30 00:42:49,557] [pool-1-thread-10] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-12-30 00:42:49,777] [pool-1-thread-6] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-12-30 00:42:51,978] [pool-1-thread-9] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-12-30 00:42:53,269] [pool-1-thread-1] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-12-30 00:42:54,135] [pool-1-thread-11] Initializing /data/ome/654Atemp.stk: [testng] [2024-12-30 00:42:55,913] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-12-30 00:42:56,273] [pool-1-thread-5] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-12-30 00:42:57,608] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-12-30 00:42:59,164] [pool-1-thread-10] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-12-30 00:43:00,312] [pool-1-thread-1] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-12-30 00:43:01,505] [pool-1-thread-12] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-12-30 00:43:02,674] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-12-30 00:43:04,213] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-12-30 00:43:05,768] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-12-30 00:43:06,245] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-12-30 00:43:07,722] [pool-1-thread-9] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-12-30 00:43:08,397] [pool-1-thread-12] Initializing /data/sdub/sdub.pattern: [testng] [2024-12-30 00:43:16,135] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-12-30 00:43:16,273] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-12-30 00:43:18,770] [pool-1-thread-10] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-12-30 00:43:19,505] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-12-30 00:43:19,926] [pool-1-thread-6] Initializing /data/ome/cb_1.r3d: [testng] [2024-12-30 00:43:20,454] [pool-1-thread-5] Initializing /data/ome/C1.lsm: [testng] [2024-12-30 00:43:21,183] [pool-1-thread-8] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-12-30 00:43:21,897] [pool-1-thread-11] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-12-30 00:43:23,292] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-12-30 00:43:23,500] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2024-12-30 00:43:25,226] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-12-30 00:43:26,868] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-12-30 00:43:27,716] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-12-30 00:43:28,670] [pool-1-thread-8] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-12-30 00:43:30,065] [pool-1-thread-5] 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: 3 minutes 37 seconds Finished: SUCCESS