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Started by upstream project "BIOFORMATS-test-repo" build number 217 originally caused by: Started by upstream project "Trigger" build number 244 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins2994579994814575326.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_34397_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] 02:00:35,134 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:00:35,136 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 02:00:35,136 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:00:35,137 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:00:35,138 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:00:35,138 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:00:35,138 |-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] 02:00:35,138 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:00:35,138 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:00:35,139 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:00:35,139 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:00:35,139 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:00:35,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:00:35,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:00:35,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:00:35,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:00:35,394 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:00:35,394 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:00:35,394 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:00:35,395 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:00:35,395 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 02:00:35,396 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 02:00:35,396 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 258 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-11 02:00:35,405] [main] java.version = 1.8.0_342 [testng] 02:00:35,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:00:35,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:00:35,450 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-11_02-00-35.log] [testng] 02:00:35,451 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-11 02:00:35,453] [main] testng.directory = /data [testng] [2024-10-11 02:00:35,453] [main] testng.configDirectory = /config [testng] [2024-10-11 02:00:35,465] [main] testng.multiplier = 1.0 [testng] [2024-10-11 02:00:35,466] [main] testng.in-memory = false [testng] [2024-10-11 02:00:35,466] [main] testng.allow-missing = false [testng] [2024-10-11 02:00:35,466] [main] user.language = en [testng] [2024-10-11 02:00:35,466] [main] user.country = ${user.country} [testng] [2024-10-11 02:00:35,466] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-11 02:02:19,767] [main] ---------------------------------------- [testng] [2024-10-11 02:02:19,877] [main] Total files: 164 [testng] [2024-10-11 02:02:19,877] [main] Scan time: 104.301 s (635 ms/file) [testng] [2024-10-11 02:02:19,877] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-11 02:04:35,972] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 02:04:35,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:04:35,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:35,974 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-11_02-04-35.log] [testng] 02:04:35,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2bfda4d4 - End of configuration. [testng] [2024-10-11 02:04:37,964] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 02:04:37,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:04:37,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:37,966 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-11_02-04-37.log] [testng] 02:04:37,966 |-INFO in ch.qos.logback.core.sift.SiftProcessor@430882be - End of configuration. [testng] [2024-10-11 02:04:38,213] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 02:04:38,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:04:38,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:38,214 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-11_02-04-38.log] [testng] 02:04:38,215 |-INFO in ch.qos.logback.core.sift.SiftProcessor@257a6ebf - End of configuration. [testng] [2024-10-11 02:04:39,871] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm: [testng] 02:04:39,871 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:04:39,871 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:39,872 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-11_02-04-39.log] [testng] 02:04:39,873 |-INFO in ch.qos.logback.core.sift.SiftProcessor@210d1b26 - End of configuration. [testng] [2024-10-11 02:04:40,802] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk: [testng] 02:04:40,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:04:40,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:40,803 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-11_02-04-40.log] [testng] 02:04:40,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79ff09fd - End of configuration. [testng] [2024-10-11 02:04:42,803] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 02:04:42,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:04:42,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:42,804 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-11_02-04-42.log] [testng] 02:04:42,805 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b872a6d - End of configuration. [testng] [2024-10-11 02:04:42,893] [pool-1-thread-7] Initializing /data/ome/embryo.lsm: [testng] 02:04:42,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:04:42,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:42,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-11_02-04-42.log] [testng] 02:04:42,895 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ac48d01 - End of configuration. [testng] [2024-10-11 02:04:43,894] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 02:04:43,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:04:43,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:43,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-11_02-04-43.log] [testng] 02:04:43,895 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1859b8a3 - End of configuration. [testng] [2024-10-11 02:04:44,001] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 02:04:44,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:04:44,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:44,002 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-11_02-04-44.log] [testng] 02:04:44,002 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c81e018 - End of configuration. [testng] [2024-10-11 02:04:44,434] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 02:04:44,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:04:44,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:44,435 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-11_02-04-44.log] [testng] 02:04:44,436 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e42d73a - End of configuration. [testng] [2024-10-11 02:04:44,482] [pool-1-thread-3] Initializing /data/ome/worm.tiff: [testng] 02:04:44,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:04:44,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:44,483 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-11_02-04-44.log] [testng] 02:04:44,483 |-INFO in ch.qos.logback.core.sift.SiftProcessor@edf6df - End of configuration. [testng] [2024-10-11 02:04:45,855] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 02:04:45,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:04:45,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:45,858 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-11_02-04-45.log] [testng] 02:04:45,859 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7dd4dbe3 - End of configuration. [testng] [2024-10-11 02:04:52,507] [pool-1-thread-4] Initializing /data/ome/C1.lsm: [testng] [2024-10-11 02:04:54,294] [pool-1-thread-8] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-10-11 02:04:54,471] [pool-1-thread-12] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-10-11 02:04:55,752] [pool-1-thread-6] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-10-11 02:04:57,970] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-10-11 02:04:58,887] [pool-1-thread-5] Initializing /data/sdub/sdub.pattern: [testng] [2024-10-11 02:05:13,730] [pool-1-thread-10] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-10-11 02:05:14,808] [pool-1-thread-7] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-10-11 02:05:16,147] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-10-11 02:05:16,313] [pool-1-thread-2] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-10-11 02:05:17,950] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-10-11 02:05:19,913] [pool-1-thread-3] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-10-11 02:05:20,209] [pool-1-thread-8] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-10-11 02:05:20,696] [pool-1-thread-12] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-10-11 02:05:23,181] [pool-1-thread-1] Initializing /data/ome/cb_1.r3d: [testng] [2024-10-11 02:05:23,710] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-10-11 02:05:24,900] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-10-11 02:05:25,593] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-10-11 02:05:27,667] [pool-1-thread-3] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-10-11 02:05:28,319] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-10-11 02:05:28,689] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-10-11 02:05:29,357] [pool-1-thread-4] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-10-11 02:05:29,561] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-10-11 02:05:29,945] [pool-1-thread-2] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-10-11 02:05:30,312] [pool-1-thread-11] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-10-11 02:05:31,726] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-10-11 02:05:32,959] [pool-1-thread-10] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-10-11 02:05:35,366] [pool-1-thread-9] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-10-11 02:05:36,166] [pool-1-thread-11] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-10-11 02:05:37,038] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-10-11 02:05:37,146] [pool-1-thread-8] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-10-11 02:05:38,108] [pool-1-thread-12] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-10-11 02:05:41,821] [pool-1-thread-6] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-10-11 02:05:45,161] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-10-11 02:05:45,273] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-10-11 02:05:45,428] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-10-11 02:05:46,709] [pool-1-thread-4] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-10-11 02:05:50,068] [pool-1-thread-9] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-10-11 02:06:26,073] [pool-1-thread-1] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-10-11 02:06:27,653] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-10-11 02:06:28,565] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-10-11 02:06:28,712] [pool-1-thread-8] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-10-11 02:06:30,749] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-10-11 02:06:33,692] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-10-11 02:06:34,208] [pool-1-thread-3] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-10-11 02:06:35,704] [pool-1-thread-1] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-10-11 02:06:37,808] [pool-1-thread-4] 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: 7 minutes 58 seconds Finished: SUCCESS