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Started by upstream project "BIOFORMATS-test-repo" build number 42 originally caused by: Started by upstream project "Trigger" build number 49 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins17339519532731338103.sh + '[' samples = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_5906_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 [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 06:11:45,148 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 06:11:45,151 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 06:11:45,151 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:11:45,152 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:11:45,153 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 06:11:45,154 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 06:11:45,155 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 3 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 06:11:45,155 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:11:45,155 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:11:45,156 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 06:11:45,157 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 06:11:45,157 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 06:11:45,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 06:11:45,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 06:11:45,407 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 06:11:45,407 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 06:11:45,414 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 06:11:45,414 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 06:11:45,414 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 06:11:45,415 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 06:11:45,415 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 06:11:45,416 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 06:11:45,416 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 261 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-23 06:11:45,427] [main] java.version = 11.0.16 [testng] 06:11:45,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:11:45,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:11:45,495 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-23_06-11-45.log] [testng] 06:11:45,499 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-04-23 06:11:45,503] [main] testng.directory = /data [testng] [2024-04-23 06:11:45,503] [main] testng.configDirectory = /config [testng] [2024-04-23 06:11:45,520] [main] testng.multiplier = 1.0 [testng] [2024-04-23 06:11:45,523] [main] testng.in-memory = false [testng] [2024-04-23 06:11:45,523] [main] testng.allow-missing = false [testng] [2024-04-23 06:11:45,523] [main] user.language = en [testng] [2024-04-23 06:11:45,523] [main] user.country = ${user.country} [testng] [2024-04-23 06:11:45,523] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-23 06:12:04,096] [main] ---------------------------------------- [testng] [2024-04-23 06:12:04,096] [main] Total files: 164 [testng] [2024-04-23 06:12:04,097] [main] Scan time: 18.572 s (113 ms/file) [testng] [2024-04-23 06:12:04,097] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-23 06:12:13,154] [pool-1-thread-1] Initializing /data/ome/C1.lsm: [testng] 06:12:13,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 06:12:13,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:12:13,158 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-23_06-12-13.log] [testng] 06:12:13,159 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76ae52ae - End of configuration. [testng] [2024-04-23 06:12:13,192] [pool-1-thread-12] Initializing /data/openjpeg/Facade.bmp: [testng] 06:12:13,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 06:12:13,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:12:13,193 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-23_06-12-13.log] [testng] 06:12:13,194 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e7a8091 - End of configuration. [testng] [2024-04-23 06:12:13,208] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 06:12:13,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 06:12:13,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:12:13,209 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-23_06-12-13.log] [testng] 06:12:13,210 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36373d13 - End of configuration. [testng] [2024-04-23 06:12:13,217] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] 06:12:13,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 06:12:13,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:12:13,219 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-23_06-12-13.log] [testng] 06:12:13,219 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c66e407 - End of configuration. [testng] [2024-04-23 06:12:13,242] [pool-1-thread-9] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] 06:12:13,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 06:12:13,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:12:13,243 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-23_06-12-13.log] [testng] 06:12:13,243 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5450adc - End of configuration. [testng] [2024-04-23 06:12:13,285] [pool-1-thread-8] Initializing /data/ome/Adultmidsection.lsm: [testng] 06:12:13,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 06:12:13,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:12:13,286 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-23_06-12-13.log] [testng] 06:12:13,286 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50b62f96 - End of configuration. [testng] [2024-04-23 06:12:13,317] [pool-1-thread-7] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 06:12:13,318 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 06:12:13,318 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:12:13,318 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-23_06-12-13.log] [testng] 06:12:13,319 |-INFO in ch.qos.logback.core.sift.SiftProcessor@679df212 - End of configuration. [testng] [2024-04-23 06:12:13,527] [pool-1-thread-6] Initializing /data/openjpeg/Rome.ppm: [testng] 06:12:13,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:12:13,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:12:13,528 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-23_06-12-13.log] [testng] 06:12:13,528 |-INFO in ch.qos.logback.core.sift.SiftProcessor@525bc4bc - End of configuration. [testng] [2024-04-23 06:12:13,539] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 06:12:13,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 06:12:13,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:12:13,540 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-23_06-12-13.log] [testng] 06:12:13,541 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e8bdcf8 - End of configuration. [testng] [2024-04-23 06:12:13,591] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 06:12:13,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 06:12:13,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:12:13,592 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-23_06-12-13.log] [testng] 06:12:13,593 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28b342dd - End of configuration. [testng] [2024-04-23 06:12:13,601] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 06:12:13,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 06:12:13,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:12:13,602 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-23_06-12-13.log] [testng] 06:12:13,602 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34977e1a - End of configuration. [testng] [2024-04-23 06:12:13,670] [pool-1-thread-2] Initializing /data/sdub/sdub.pattern: [testng] 06:12:13,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 06:12:13,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:12:13,671 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-23_06-12-13.log] [testng] 06:12:13,672 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cb56543 - End of configuration. [testng] [2024-04-23 06:12:15,878] [pool-1-thread-4] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-04-23 06:12:15,898] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-04-23 06:12:15,905] [pool-1-thread-6] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-04-23 06:12:15,941] [pool-1-thread-1] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-04-23 06:12:15,950] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-04-23 06:12:16,059] [pool-1-thread-8] Initializing /data/ome/654Atemp.stk: [testng] [2024-04-23 06:12:16,574] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-04-23 06:12:16,599] [pool-1-thread-9] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-04-23 06:12:16,637] [pool-1-thread-5] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-04-23 06:12:16,660] [pool-1-thread-1] Initializing /data/ome/worm.tiff: [testng] [2024-04-23 06:12:16,714] [pool-1-thread-2] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-04-23 06:12:16,845] [pool-1-thread-10] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-04-23 06:12:16,987] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-04-23 06:12:17,051] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-04-23 06:12:17,239] [pool-1-thread-7] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-04-23 06:12:17,253] [pool-1-thread-2] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-04-23 06:12:18,224] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-04-23 06:12:18,252] [pool-1-thread-6] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-04-23 06:12:18,371] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-04-23 06:12:18,380] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-04-23 06:12:18,584] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-04-23 06:12:18,678] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-04-23 06:12:18,943] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-04-23 06:12:18,973] [pool-1-thread-6] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-04-23 06:12:19,014] [pool-1-thread-12] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-04-23 06:12:19,169] [pool-1-thread-7] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-04-23 06:12:19,345] [pool-1-thread-10] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-04-23 06:12:19,567] [pool-1-thread-6] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-04-23 06:12:19,679] [pool-1-thread-7] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-04-23 06:12:20,096] [pool-1-thread-12] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-04-23 06:12:20,147] [pool-1-thread-3] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-04-23 06:12:20,371] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-04-23 06:12:20,397] [pool-1-thread-3] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-04-23 06:12:21,029] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-04-23 06:12:21,196] [pool-1-thread-1] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-04-23 06:12:21,389] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-04-23 06:12:21,407] [pool-1-thread-10] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-04-23 06:12:21,482] [pool-1-thread-11] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-04-23 06:12:21,496] [pool-1-thread-7] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-04-23 06:12:21,570] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] [2024-04-23 06:12:21,978] [pool-1-thread-11] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-04-23 06:12:22,303] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-04-23 06:12:22,535] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-04-23 06:12:22,848] [pool-1-thread-4] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-04-23 06:12:22,979] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-04-23 06:12:23,123] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2024-04-23 06:12:23,614] [pool-1-thread-4] 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: 2 minutes 19 seconds Finished: SUCCESS