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Started by upstream project "BIOFORMATS-test-repo" build number 8 originally caused by: Started by upstream project "Trigger" build number 11 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins16928217544566867124.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_1148_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] 00:26:55,261 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:26:55,263 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 00:26:55,263 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:26:55,264 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:26:55,264 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:26:55,264 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:26:55,264 |-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] 00:26:55,264 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:26:55,265 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:26:55,265 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:26:55,265 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:26:55,265 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:26:55,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:26:55,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:26:55,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:26:55,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:26:55,630 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:26:55,630 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:26:55,631 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:26:55,631 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:26:55,631 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 00:26:55,632 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 00:26:55,632 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 367 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-22 00:26:55,643] [main] java.version = 1.8.0_342 [testng] 00:26:55,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:26:55,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:55,701 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-22_00-26-55.log] [testng] 00:26:55,704 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-03-22 00:26:55,706] [main] testng.directory = /data [testng] [2024-03-22 00:26:55,706] [main] testng.configDirectory = /config [testng] [2024-03-22 00:26:55,722] [main] testng.multiplier = 1.0 [testng] [2024-03-22 00:26:55,722] [main] testng.in-memory = false [testng] [2024-03-22 00:26:55,722] [main] testng.allow-missing = false [testng] [2024-03-22 00:26:55,723] [main] user.language = en [testng] [2024-03-22 00:26:55,723] [main] user.country = ${user.country} [testng] [2024-03-22 00:26:55,723] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-03-22 00:27:19,951] [main] ---------------------------------------- [testng] [2024-03-22 00:27:19,951] [main] Total files: 164 [testng] [2024-03-22 00:27:19,952] [main] Scan time: 24.228 s (147 ms/file) [testng] [2024-03-22 00:27:19,952] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-22 00:27:37,190] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:27:37,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:27:37,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:37,191 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-22_00-27-37.log] [testng] 00:27:37,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ed3a155 - End of configuration. [testng] [2024-03-22 00:27:37,485] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 00:27:37,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:27:37,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:37,490 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-22_00-27-37.log] [testng] 00:27:37,491 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49af32fd - End of configuration. [testng] [2024-03-22 00:27:37,538] [pool-1-thread-11] Initializing /data/ome/arwen0205_raw00201.pic: [testng] 00:27:37,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:27:37,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:37,539 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-22_00-27-37.log] [testng] 00:27:37,540 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cba730c - End of configuration. [testng] [2024-03-22 00:27:37,678] [pool-1-thread-10] Initializing /data/ome/anusgfpzs.lsm: [testng] 00:27:37,678 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:27:37,678 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:37,679 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-22_00-27-37.log] [testng] 00:27:37,679 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b78376c - End of configuration. [testng] [2024-03-22 00:27:37,768] [pool-1-thread-9] Initializing /data/openjpeg/Rome.jp2: [testng] 00:27:37,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:27:37,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:37,770 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-22_00-27-37.log] [testng] 00:27:37,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50b559d8 - End of configuration. [testng] [2024-03-22 00:27:37,847] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 00:27:37,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:27:37,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:37,849 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-22_00-27-37.log] [testng] 00:27:37,849 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f52616a - End of configuration. [testng] [2024-03-22 00:27:37,883] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 00:27:37,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:27:37,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:37,884 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-22_00-27-37.log] [testng] 00:27:37,886 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c15e4c2 - End of configuration. [testng] [2024-03-22 00:27:38,007] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 00:27:38,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:27:38,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:38,008 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-22_00-27-38.log] [testng] 00:27:38,009 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d7e4675 - End of configuration. [testng] [2024-03-22 00:27:38,025] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:27:38,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:27:38,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:38,026 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-22_00-27-38.log] [testng] 00:27:38,027 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dcb15cf - End of configuration. [testng] [2024-03-22 00:27:38,121] [pool-1-thread-4] Initializing /data/ome/C1lowmusgfp.lsm: [testng] 00:27:38,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:27:38,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:38,122 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-22_00-27-38.log] [testng] 00:27:38,123 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4aca881f - End of configuration. [testng] [2024-03-22 00:27:38,254] [pool-1-thread-3] Initializing /data/ome/C1.lsm: [testng] 00:27:38,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:27:38,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:38,255 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-22_00-27-38.log] [testng] 00:27:38,256 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15cf7140 - End of configuration. [testng] [2024-03-22 00:27:38,326] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 00:27:38,326 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:27:38,326 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:38,327 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-22_00-27-38.log] [testng] 00:27:38,327 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60398b32 - End of configuration. [testng] [2024-03-22 00:27:40,789] [pool-1-thread-6] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-03-22 00:27:40,804] [pool-1-thread-3] Initializing /data/ome/654Atemp.stk: [testng] [2024-03-22 00:27:41,121] [pool-1-thread-4] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-03-22 00:27:41,144] [pool-1-thread-10] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-03-22 00:27:41,168] [pool-1-thread-5] Initializing /data/ome/cb_1.r3d: [testng] [2024-03-22 00:27:41,265] [pool-1-thread-8] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-03-22 00:27:41,400] [pool-1-thread-1] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-03-22 00:27:41,489] [pool-1-thread-7] Initializing /data/ome/embryo.lsm: [testng] [2024-03-22 00:27:41,848] [pool-1-thread-2] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-03-22 00:27:42,136] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-03-22 00:27:42,167] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-03-22 00:27:42,512] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-03-22 00:27:42,554] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern: [testng] [2024-03-22 00:27:43,751] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-03-22 00:27:44,141] [pool-1-thread-12] Initializing /data/ome/worm.tiff: [testng] [2024-03-22 00:27:44,448] [pool-1-thread-5] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-03-22 00:27:44,519] [pool-1-thread-4] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-03-22 00:27:44,828] [pool-1-thread-7] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-03-22 00:27:45,187] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-03-22 00:27:45,282] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-03-22 00:27:45,616] [pool-1-thread-8] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-03-22 00:27:46,261] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-03-22 00:27:46,452] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-03-22 00:27:46,533] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-03-22 00:27:46,803] [pool-1-thread-3] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-03-22 00:27:46,896] [pool-1-thread-4] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-03-22 00:27:47,705] [pool-1-thread-11] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-03-22 00:27:47,792] [pool-1-thread-8] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-03-22 00:27:47,894] [pool-1-thread-1] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-03-22 00:27:47,940] [pool-1-thread-9] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-03-22 00:27:48,435] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-03-22 00:27:48,594] [pool-1-thread-5] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-03-22 00:27:48,677] [pool-1-thread-7] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-03-22 00:27:48,804] [pool-1-thread-3] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-03-22 00:27:52,059] [pool-1-thread-12] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-03-22 00:27:52,282] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-03-22 00:27:52,450] [pool-1-thread-2] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-03-22 00:27:52,816] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-03-22 00:27:52,836] [pool-1-thread-8] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-03-22 00:27:52,942] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-03-22 00:27:53,124] [pool-1-thread-5] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-03-22 00:27:53,305] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-03-22 00:27:53,543] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-03-22 00:27:53,937] [pool-1-thread-11] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-03-22 00:27:54,650] [pool-1-thread-2] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-03-22 00:27:54,742] [pool-1-thread-10] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-03-22 00:27:54,949] [pool-1-thread-12] 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 41 seconds Finished: SUCCESS