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Started by upstream project "BIOFORMATS-test-repo" build number 2 originally caused by: Started by upstream project "Trigger" build number 3 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins12737428593969034597.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_164_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] 00:27:53,320 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:27:53,322 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 00:27:53,322 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:27:53,323 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:27:53,323 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:27:53,323 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:27:53,323 |-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] 00:27:53,323 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:27:53,324 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:27:53,324 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:27:53,324 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:27:53,324 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:27:53,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:27:53,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:27:53,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:27:53,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:27:53,667 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:27:53,667 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:27:53,667 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:27:53,668 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:27:53,668 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 00:27:53,669 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 00:27:53,670 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 346 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-15 00:27:53,682] [main] java.version = 1.8.0_342 [testng] 00:27:53,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:27:53,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:53,758 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-15_00-27-53.log] [testng] 00:27:53,760 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-03-15 00:27:53,763] [main] testng.directory = /data [testng] [2024-03-15 00:27:53,763] [main] testng.configDirectory = /config [testng] [2024-03-15 00:27:53,782] [main] testng.multiplier = 1.0 [testng] [2024-03-15 00:27:53,782] [main] testng.in-memory = false [testng] [2024-03-15 00:27:53,783] [main] testng.allow-missing = false [testng] [2024-03-15 00:27:53,783] [main] user.language = en [testng] [2024-03-15 00:27:53,783] [main] user.country = ${user.country} [testng] [2024-03-15 00:27:53,783] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-03-15 00:28:19,097] [main] ---------------------------------------- [testng] [2024-03-15 00:28:19,097] [main] Total files: 164 [testng] [2024-03-15 00:28:19,097] [main] Scan time: 25.314 s (154 ms/file) [testng] [2024-03-15 00:28:19,097] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-15 00:28:42,434] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:28:42,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:28:42,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:42,445 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-15_00-28-42.log] [testng] 00:28:42,446 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30acdd2c - End of configuration. [testng] [2024-03-15 00:28:42,632] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 00:28:42,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:28:42,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:42,633 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-15_00-28-42.log] [testng] 00:28:42,634 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d9f00d - End of configuration. [testng] [2024-03-15 00:28:42,658] [pool-1-thread-11] Initializing /data/ome/arwen0205_raw00201.pic: [testng] 00:28:42,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:28:42,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:42,660 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-15_00-28-42.log] [testng] 00:28:42,660 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d5625c3 - End of configuration. [testng] [2024-03-15 00:28:42,725] [pool-1-thread-10] Initializing /data/ome/anusgfpzs.lsm: [testng] 00:28:42,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:28:42,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:42,726 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-15_00-28-42.log] [testng] 00:28:42,726 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d4d094e - End of configuration. [testng] [2024-03-15 00:28:42,814] [pool-1-thread-9] Initializing /data/openjpeg/Rome.jp2: [testng] 00:28:42,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:28:42,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:42,815 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-15_00-28-42.log] [testng] 00:28:42,815 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59e080c9 - End of configuration. [testng] [2024-03-15 00:28:42,859] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 00:28:42,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:28:42,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:42,860 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-15_00-28-42.log] [testng] 00:28:42,860 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3582ca55 - End of configuration. [testng] [2024-03-15 00:28:42,899] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 00:28:42,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:28:42,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:42,900 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-15_00-28-42.log] [testng] 00:28:42,900 |-INFO in ch.qos.logback.core.sift.SiftProcessor@415b1e5b - End of configuration. [testng] [2024-03-15 00:28:43,015] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 00:28:43,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:28:43,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:43,017 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-15_00-28-43.log] [testng] 00:28:43,017 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69edda6c - End of configuration. [testng] [2024-03-15 00:28:43,082] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:28:43,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:28:43,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:43,083 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-15_00-28-43.log] [testng] 00:28:43,084 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e2368ea - End of configuration. [testng] [2024-03-15 00:28:43,165] [pool-1-thread-4] Initializing /data/ome/C1lowmusgfp.lsm: [testng] 00:28:43,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:28:43,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:43,165 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-15_00-28-43.log] [testng] 00:28:43,166 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b75fbdf - End of configuration. [testng] [2024-03-15 00:28:43,249] [pool-1-thread-3] Initializing /data/ome/C1.lsm: [testng] 00:28:43,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:28:43,250 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:43,250 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-15_00-28-43.log] [testng] 00:28:43,251 |-INFO in ch.qos.logback.core.sift.SiftProcessor@97f7ca4 - End of configuration. [testng] [2024-03-15 00:28:43,372] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 00:28:43,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:28:43,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:43,373 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-15_00-28-43.log] [testng] 00:28:43,374 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bbedc02 - End of configuration. [testng] [2024-03-15 00:28:45,970] [pool-1-thread-6] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-03-15 00:28:46,277] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] [2024-03-15 00:28:46,399] [pool-1-thread-3] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-03-15 00:28:46,437] [pool-1-thread-10] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-03-15 00:28:46,730] [pool-1-thread-1] Initializing /data/ome/654Atemp.stk: [testng] [2024-03-15 00:28:47,221] [pool-1-thread-7] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-03-15 00:28:47,615] [pool-1-thread-5] Initializing /data/ome/embryo.lsm: [testng] [2024-03-15 00:28:47,798] [pool-1-thread-8] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-03-15 00:28:48,031] [pool-1-thread-2] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-03-15 00:28:48,147] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-03-15 00:28:48,414] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-03-15 00:28:48,527] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-03-15 00:28:48,641] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern: [testng] [2024-03-15 00:28:49,949] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-03-15 00:28:50,189] [pool-1-thread-4] Initializing /data/ome/worm.tiff: [testng] [2024-03-15 00:28:50,487] [pool-1-thread-6] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-03-15 00:28:50,769] [pool-1-thread-12] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-03-15 00:28:50,989] [pool-1-thread-3] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-03-15 00:28:51,414] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-03-15 00:28:51,502] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-03-15 00:28:51,877] [pool-1-thread-2] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-03-15 00:28:52,211] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-03-15 00:28:52,318] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-03-15 00:28:52,377] [pool-1-thread-5] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-03-15 00:28:52,405] [pool-1-thread-8] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-03-15 00:28:52,793] [pool-1-thread-1] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-03-15 00:28:53,470] [pool-1-thread-9] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-03-15 00:28:53,756] [pool-1-thread-12] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-03-15 00:28:53,823] [pool-1-thread-7] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-03-15 00:28:54,236] [pool-1-thread-2] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-03-15 00:28:54,556] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-03-15 00:28:54,651] [pool-1-thread-6] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-03-15 00:28:54,986] [pool-1-thread-11] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-03-15 00:28:55,264] [pool-1-thread-8] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-03-15 00:28:59,498] [pool-1-thread-4] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-03-15 00:28:59,599] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-03-15 00:28:59,709] [pool-1-thread-5] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-03-15 00:28:59,731] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-03-15 00:28:59,860] [pool-1-thread-12] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-03-15 00:29:00,115] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-03-15 00:29:00,296] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-03-15 00:29:00,372] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-03-15 00:29:00,582] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-03-15 00:29:00,617] [pool-1-thread-4] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-03-15 00:29:00,957] [pool-1-thread-12] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-03-15 00:29:01,115] [pool-1-thread-11] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-03-15 00:29:01,293] [pool-1-thread-5] 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 49 seconds Finished: SUCCESS