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Started by upstream project "BIOFORMATS-test-repo" build number 129 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins10195563540367386596.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_20175_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] 13:54:27,729 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 13:54:27,731 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 13:54:27,731 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:54:27,732 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:54:27,732 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 13:54:27,732 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 13:54:27,732 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 13:54:27,732 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:54:27,733 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:54:27,733 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 13:54:27,733 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 13:54:27,733 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 13:54:28,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 13:54:28,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 13:54:28,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 13:54:28,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 13:54:28,051 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 13:54:28,052 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 13:54:28,052 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 13:54:28,053 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 13:54:28,053 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 13:54:28,054 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 13:54:28,054 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 321 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-22 13:54:28,068] [main] java.version = 1.8.0_342 [testng] 13:54:28,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 13:54:28,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:28,124 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-22_13-54-28.log] [testng] 13:54:28,126 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-22 13:54:28,128] [main] testng.directory = /data [testng] [2024-07-22 13:54:28,129] [main] testng.configDirectory = /config [testng] [2024-07-22 13:54:28,142] [main] testng.multiplier = 1.0 [testng] [2024-07-22 13:54:28,142] [main] testng.in-memory = false [testng] [2024-07-22 13:54:28,142] [main] testng.allow-missing = false [testng] [2024-07-22 13:54:28,142] [main] user.language = fr [testng] [2024-07-22 13:54:28,143] [main] user.country = FR [testng] [2024-07-22 13:54:28,143] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-22 13:54:47,627] [main] ---------------------------------------- [testng] [2024-07-22 13:54:47,627] [main] Total files: 164 [testng] [2024-07-22 13:54:47,628] [main] Scan time: 19.484 s (118 ms/file) [testng] [2024-07-22 13:54:47,628] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-22 13:54:58,132] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 13:54:58,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 13:54:58,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:58,134 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-22_13-54-58.log] [testng] 13:54:58,134 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15824469 - End of configuration. [testng] [2024-07-22 13:54:58,175] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 13:54:58,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 13:54:58,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:58,177 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-22_13-54-58.log] [testng] 13:54:58,177 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f43e980 - End of configuration. [testng] [2024-07-22 13:54:58,197] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 13:54:58,198 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 13:54:58,198 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:58,199 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-22_13-54-58.log] [testng] 13:54:58,200 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b6403c9 - End of configuration. [testng] [2024-07-22 13:54:58,262] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm: [testng] 13:54:58,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 13:54:58,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:58,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-22_13-54-58.log] [testng] 13:54:58,264 |-INFO in ch.qos.logback.core.sift.SiftProcessor@243d8f2a - End of configuration. [testng] [2024-07-22 13:54:58,300] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk: [testng] 13:54:58,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 13:54:58,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:58,302 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-22_13-54-58.log] [testng] 13:54:58,302 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cc17576 - End of configuration. [testng] [2024-07-22 13:54:58,437] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 13:54:58,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 13:54:58,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:58,438 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-22_13-54-58.log] [testng] 13:54:58,438 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ed3807 - End of configuration. [testng] [2024-07-22 13:54:58,448] [pool-1-thread-7] Initializing /data/ome/embryo.lsm: [testng] 13:54:58,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 13:54:58,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:58,450 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-22_13-54-58.log] [testng] 13:54:58,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ba042c - End of configuration. [testng] [2024-07-22 13:54:58,489] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 13:54:58,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 13:54:58,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:58,490 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-22_13-54-58.log] [testng] 13:54:58,490 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3dea7c27 - End of configuration. [testng] [2024-07-22 13:54:58,506] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 13:54:58,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 13:54:58,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:58,507 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-22_13-54-58.log] [testng] 13:54:58,507 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3680c314 - End of configuration. [testng] [2024-07-22 13:54:58,532] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 13:54:58,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 13:54:58,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:58,533 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-22_13-54-58.log] [testng] 13:54:58,534 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f095bdf - End of configuration. [testng] [2024-07-22 13:54:58,543] [pool-1-thread-3] Initializing /data/ome/worm.tiff: [testng] 13:54:58,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 13:54:58,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:58,544 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-22_13-54-58.log] [testng] 13:54:58,545 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4269d9ea - End of configuration. [testng] [2024-07-22 13:54:58,625] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 13:54:58,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 13:54:58,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:58,627 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-22_13-54-58.log] [testng] 13:54:58,628 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4931f7a5 - End of configuration. [testng] [2024-07-22 13:55:01,662] [pool-1-thread-6] Initializing /data/ome/C1.lsm: [testng] [2024-07-22 13:55:01,684] [pool-1-thread-5] Initializing /data/sdub/sdub.pattern: [testng] [2024-07-22 13:55:01,918] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-07-22 13:55:01,926] [pool-1-thread-10] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-07-22 13:55:01,975] [pool-1-thread-7] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-07-22 13:55:01,982] [pool-1-thread-2] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-07-22 13:55:02,295] [pool-1-thread-11] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-07-22 13:55:02,424] [pool-1-thread-4] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-07-22 13:55:02,510] [pool-1-thread-1] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-07-22 13:55:02,868] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-07-22 13:55:02,881] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-07-22 13:55:03,386] [pool-1-thread-12] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-07-22 13:55:03,415] [pool-1-thread-6] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-07-22 13:55:03,513] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-07-22 13:55:03,977] [pool-1-thread-3] Initializing /data/ome/cb_1.r3d: [testng] [2024-07-22 13:55:04,092] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-07-22 13:55:04,112] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-07-22 13:55:04,212] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-07-22 13:55:04,559] [pool-1-thread-6] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-07-22 13:55:04,780] [pool-1-thread-1] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-07-22 13:55:04,965] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-07-22 13:55:05,009] [pool-1-thread-4] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-07-22 13:55:05,041] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-07-22 13:55:05,288] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-07-22 13:55:05,344] [pool-1-thread-10] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-07-22 13:55:05,356] [pool-1-thread-11] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-07-22 13:55:05,995] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-07-22 13:55:06,041] [pool-1-thread-1] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-07-22 13:55:06,057] [pool-1-thread-7] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-07-22 13:55:06,182] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-07-22 13:55:06,260] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-07-22 13:55:06,520] [pool-1-thread-2] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-07-22 13:55:06,576] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-07-22 13:55:06,828] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-07-22 13:55:06,839] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-07-22 13:55:06,893] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-07-22 13:55:06,903] [pool-1-thread-8] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-07-22 13:55:06,975] [pool-1-thread-9] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-07-22 13:55:08,619] [pool-1-thread-6] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-07-22 13:55:08,667] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-07-22 13:55:08,756] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-07-22 13:55:08,847] [pool-1-thread-1] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-07-22 13:55:08,963] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-07-22 13:55:09,143] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-07-22 13:55:09,225] [pool-1-thread-8] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-07-22 13:55:09,546] [pool-1-thread-12] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-07-22 13:55:09,768] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-07-22 13:55:11,326] [pool-1-thread-12] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 1, Skips: 0 [testng] =============================================== [testng] [testng] The tests failed. BUILD FAILED /bio-formats-build/bioformats/components/test-suite/build.xml:270: if=failedTest Total time: 2 minutes 41 seconds Build step 'Execute shell' marked build as failure Finished: FAILURE