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Started by upstream project "BIOFORMATS-test-repo" build number 23 originally caused by: Started by upstream project "Trigger" build number 26 originally caused by: Started by timer 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/jenkins15429638062419807175.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_2790_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] 01:25:14,435 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:25:14,437 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:25:14,437 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:25:14,439 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:25:14,439 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:25:14,439 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:25:14,440 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:25:14,440 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:25:14,440 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:25:14,441 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:25:14,441 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:25:14,441 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:25:14,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:25:14,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:25:14,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:25:14,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:25:14,825 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:25:14,826 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:25:14,826 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:25:14,826 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:25:14,827 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:25:14,828 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:25:14,828 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 388 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-05 01:25:14,842] [main] java.version = 1.8.0_342 [testng] 01:25:14,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:25:14,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:14,916 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-05_01-25-14.log] [testng] 01:25:14,918 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-05 01:25:14,920] [main] testng.directory = /data [testng] [2024-04-05 01:25:14,921] [main] testng.configDirectory = /config [testng] [2024-04-05 01:25:14,941] [main] testng.multiplier = 1.0 [testng] [2024-04-05 01:25:14,942] [main] testng.in-memory = false [testng] [2024-04-05 01:25:14,942] [main] testng.allow-missing = false [testng] [2024-04-05 01:25:14,942] [main] user.language = en [testng] [2024-04-05 01:25:14,942] [main] user.country = ${user.country} [testng] [2024-04-05 01:25:14,942] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-05 01:25:40,801] [main] ---------------------------------------- [testng] [2024-04-05 01:25:40,801] [main] Total files: 164 [testng] [2024-04-05 01:25:40,801] [main] Scan time: 25.859 s (157 ms/file) [testng] [2024-04-05 01:25:40,801] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-05 01:25:56,324] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:25:56,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:25:56,325 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:56,326 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-05_01-25-56.log] [testng] 01:25:56,326 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ad4561 - End of configuration. [testng] [2024-04-05 01:25:56,404] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 01:25:56,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:25:56,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:56,414 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-05_01-25-56.log] [testng] 01:25:56,414 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48953763 - End of configuration. [testng] [2024-04-05 01:25:56,440] [pool-1-thread-11] Initializing /data/ome/arwen0205_raw00201.pic: [testng] 01:25:56,441 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:25:56,441 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:56,442 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-05_01-25-56.log] [testng] 01:25:56,442 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e73a0d0 - End of configuration. [testng] [2024-04-05 01:25:56,491] [pool-1-thread-10] Initializing /data/ome/anusgfpzs.lsm: [testng] 01:25:56,492 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:25:56,492 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:56,493 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-05_01-25-56.log] [testng] 01:25:56,493 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73f9d9ed - End of configuration. [testng] [2024-04-05 01:25:56,541] [pool-1-thread-9] Initializing /data/openjpeg/Rome.jp2: [testng] 01:25:56,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:25:56,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:56,542 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-05_01-25-56.log] [testng] 01:25:56,543 |-INFO in ch.qos.logback.core.sift.SiftProcessor@538aad0d - End of configuration. [testng] [2024-04-05 01:25:56,560] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:25:56,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:25:56,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:56,560 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-05_01-25-56.log] [testng] 01:25:56,561 |-INFO in ch.qos.logback.core.sift.SiftProcessor@132cc529 - End of configuration. [testng] [2024-04-05 01:25:56,575] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 01:25:56,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:25:56,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:56,576 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-05_01-25-56.log] [testng] 01:25:56,577 |-INFO in ch.qos.logback.core.sift.SiftProcessor@408c3fa4 - End of configuration. [testng] [2024-04-05 01:25:56,623] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 01:25:56,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:25:56,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:56,625 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-05_01-25-56.log] [testng] 01:25:56,625 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13ab171d - End of configuration. [testng] [2024-04-05 01:25:56,634] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 01:25:56,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:25:56,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:56,635 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-05_01-25-56.log] [testng] 01:25:56,636 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2db0fed - End of configuration. [testng] [2024-04-05 01:25:56,648] [pool-1-thread-4] Initializing /data/ome/C1lowmusgfp.lsm: [testng] 01:25:56,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:25:56,649 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:56,649 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-05_01-25-56.log] [testng] 01:25:56,650 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30cedecb - End of configuration. [testng] [2024-04-05 01:25:56,675] [pool-1-thread-3] Initializing /data/ome/C1.lsm: [testng] 01:25:56,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:25:56,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:56,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-05_01-25-56.log] [testng] 01:25:56,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ec6cc5a - End of configuration. [testng] [2024-04-05 01:25:56,700] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:25:56,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:25:56,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:56,701 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-05_01-25-56.log] [testng] 01:25:56,702 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a6c8f36 - End of configuration. [testng] [2024-04-05 01:25:58,751] [pool-1-thread-6] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-04-05 01:25:58,761] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-04-05 01:25:58,809] [pool-1-thread-3] Initializing /data/ome/654Atemp.stk: [testng] [2024-04-05 01:25:58,915] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-04-05 01:25:58,925] [pool-1-thread-7] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-04-05 01:25:58,939] [pool-1-thread-1] Initializing /data/ome/cb_1.r3d: [testng] [2024-04-05 01:25:59,250] [pool-1-thread-10] Initializing /data/ome/embryo.lsm: [testng] [2024-04-05 01:25:59,408] [pool-1-thread-5] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-04-05 01:25:59,458] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-04-05 01:25:59,466] [pool-1-thread-7] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-04-05 01:25:59,608] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-04-05 01:25:59,800] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-04-05 01:25:59,851] [pool-1-thread-8] Initializing /data/sdub/sdub.pattern: [testng] [2024-04-05 01:26:00,133] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-04-05 01:26:00,222] [pool-1-thread-4] Initializing /data/ome/worm.tiff: [testng] [2024-04-05 01:26:00,488] [pool-1-thread-11] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-04-05 01:26:00,499] [pool-1-thread-10] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-04-05 01:26:00,510] [pool-1-thread-1] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-04-05 01:26:00,710] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-04-05 01:26:01,009] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-04-05 01:26:01,138] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-04-05 01:26:01,298] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-04-05 01:26:01,582] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-04-05 01:26:01,682] [pool-1-thread-7] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-04-05 01:26:01,977] [pool-1-thread-12] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-04-05 01:26:01,999] [pool-1-thread-9] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-04-05 01:26:02,026] [pool-1-thread-11] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-04-05 01:26:02,744] [pool-1-thread-5] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-04-05 01:26:02,904] [pool-1-thread-1] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-04-05 01:26:03,026] [pool-1-thread-3] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-04-05 01:26:03,279] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-04-05 01:26:03,415] [pool-1-thread-6] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-04-05 01:26:03,426] [pool-1-thread-8] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-04-05 01:26:03,473] [pool-1-thread-12] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-04-05 01:26:04,931] [pool-1-thread-9] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-04-05 01:26:05,033] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-04-05 01:26:05,116] [pool-1-thread-4] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-04-05 01:26:05,341] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-04-05 01:26:05,390] [pool-1-thread-1] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-04-05 01:26:05,483] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-04-05 01:26:05,524] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-04-05 01:26:05,705] [pool-1-thread-10] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-04-05 01:26:05,997] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-04-05 01:26:06,030] [pool-1-thread-1] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-04-05 01:26:06,496] [pool-1-thread-2] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-04-05 01:26:06,705] [pool-1-thread-6] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-04-05 01:26:06,894] [pool-1-thread-7] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 2 minutes 47 seconds Finished: SUCCESS