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Started by upstream project "BIOFORMATS-test-repo" build number 234 originally caused by: Started by upstream project "Trigger" build number 259 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/jenkins15148761529197452550.sh + '[' samples = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_36722_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] 01:36:03,513 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:36:03,515 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 01:36:03,515 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:36:03,516 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:36:03,516 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:36:03,516 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:36:03,516 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:36:03,516 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:36:03,517 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:36:03,517 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:36:03,517 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:36:03,517 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:36:03,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:36:03,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:36:03,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:36:03,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:36:03,767 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:36:03,768 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:36:03,768 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:36:03,768 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:36:03,768 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 01:36:03,769 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 01:36:03,769 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 252 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-25 01:36:03,779] [main] java.version = 1.8.0_342 [testng] 01:36:03,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:36:03,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:03,826 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-25_01-36-03.log] [testng] 01:36:03,827 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-25 01:36:03,829] [main] testng.directory = /data [testng] [2024-10-25 01:36:03,829] [main] testng.configDirectory = /config [testng] [2024-10-25 01:36:03,841] [main] testng.multiplier = 1.0 [testng] [2024-10-25 01:36:03,841] [main] testng.in-memory = false [testng] [2024-10-25 01:36:03,841] [main] testng.allow-missing = false [testng] [2024-10-25 01:36:03,841] [main] user.language = en [testng] [2024-10-25 01:36:03,841] [main] user.country = ${user.country} [testng] [2024-10-25 01:36:03,841] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-25 01:36:36,947] [main] ---------------------------------------- [testng] [2024-10-25 01:36:36,947] [main] Total files: 164 [testng] [2024-10-25 01:36:36,947] [main] Scan time: 33.106 s (201 ms/file) [testng] [2024-10-25 01:36:36,948] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-25 01:37:11,311] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:37:11,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:37:11,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:11,318 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-25_01-37-11.log] [testng] 01:37:11,319 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67f08917 - End of configuration. [testng] [2024-10-25 01:37:11,617] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 01:37:11,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:37:11,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:11,618 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-25_01-37-11.log] [testng] 01:37:11,619 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e91729c - End of configuration. [testng] [2024-10-25 01:37:11,724] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] 01:37:11,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:37:11,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:11,725 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-25_01-37-11.log] [testng] 01:37:11,726 |-INFO in ch.qos.logback.core.sift.SiftProcessor@334f8613 - End of configuration. [testng] [2024-10-25 01:37:12,126] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:37:12,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:37:12,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:12,127 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-25_01-37-12.log] [testng] 01:37:12,127 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d7c78b0 - End of configuration. [testng] [2024-10-25 01:37:12,520] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk: [testng] 01:37:12,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:37:12,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:12,521 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-25_01-37-12.log] [testng] 01:37:12,521 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a053e3c - End of configuration. [testng] [2024-10-25 01:37:13,357] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp: [testng] 01:37:13,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:37:13,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:13,358 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-25_01-37-13.log] [testng] 01:37:13,358 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1952b94f - End of configuration. [testng] [2024-10-25 01:37:13,404] [pool-1-thread-7] Initializing /data/ome/embryo.lsm: [testng] 01:37:13,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:37:13,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:13,404 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-25_01-37-13.log] [testng] 01:37:13,405 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4149fd68 - End of configuration. [testng] [2024-10-25 01:37:13,607] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 01:37:13,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:37:13,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:13,608 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-25_01-37-13.log] [testng] 01:37:13,608 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7eaa15ca - End of configuration. [testng] [2024-10-25 01:37:13,643] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 01:37:13,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:37:13,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:13,644 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-25_01-37-13.log] [testng] 01:37:13,644 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fb6cba0 - End of configuration. [testng] [2024-10-25 01:37:13,882] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 01:37:13,882 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:37:13,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:13,883 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-25_01-37-13.log] [testng] 01:37:13,883 |-INFO in ch.qos.logback.core.sift.SiftProcessor@343b3632 - End of configuration. [testng] [2024-10-25 01:37:13,929] [pool-1-thread-3] Initializing /data/ome/worm.tiff: [testng] 01:37:13,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:37:13,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:13,930 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-25_01-37-13.log] [testng] 01:37:13,931 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3678757c - End of configuration. [testng] [2024-10-25 01:37:14,390] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:37:14,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:37:14,391 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:14,391 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-25_01-37-14.log] [testng] 01:37:14,392 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73304895 - End of configuration. [testng] [2024-10-25 01:37:16,278] [pool-1-thread-6] Initializing /data/ome/C1.lsm: [testng] [2024-10-25 01:37:16,924] [pool-1-thread-10] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-10-25 01:37:16,979] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-10-25 01:37:17,012] [pool-1-thread-5] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-10-25 01:37:17,136] [pool-1-thread-4] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-10-25 01:37:17,161] [pool-1-thread-1] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-10-25 01:37:17,307] [pool-1-thread-2] Initializing /data/sdub/sdub.pattern: [testng] [2024-10-25 01:37:20,213] [pool-1-thread-12] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-10-25 01:37:20,661] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-10-25 01:37:21,178] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-10-25 01:37:21,522] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-10-25 01:37:22,508] [pool-1-thread-3] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-10-25 01:37:22,544] [pool-1-thread-7] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-10-25 01:37:22,607] [pool-1-thread-6] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-10-25 01:37:23,051] [pool-1-thread-9] Initializing /data/ome/cb_1.r3d: [testng] [2024-10-25 01:37:23,178] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-10-25 01:37:23,345] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-10-25 01:37:23,658] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-10-25 01:37:23,987] [pool-1-thread-7] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-10-25 01:37:24,320] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-10-25 01:37:24,604] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-10-25 01:37:24,690] [pool-1-thread-11] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-10-25 01:37:25,221] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-10-25 01:37:25,513] [pool-1-thread-1] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-10-25 01:37:25,978] [pool-1-thread-10] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-10-25 01:37:26,135] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-10-25 01:37:26,542] [pool-1-thread-4] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-10-25 01:37:27,422] [pool-1-thread-6] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-10-25 01:37:27,567] [pool-1-thread-8] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-10-25 01:37:27,984] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-10-25 01:37:28,091] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-10-25 01:37:28,498] [pool-1-thread-7] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-10-25 01:37:29,500] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-10-25 01:37:29,616] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-10-25 01:37:29,851] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-10-25 01:37:30,480] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-10-25 01:37:30,672] [pool-1-thread-6] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-10-25 01:37:31,431] [pool-1-thread-9] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-10-25 01:37:40,585] [pool-1-thread-12] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-10-25 01:37:40,800] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-10-25 01:37:41,019] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-10-25 01:37:41,182] [pool-1-thread-1] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-10-25 01:37:41,754] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-10-25 01:37:42,448] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-10-25 01:37:42,564] [pool-1-thread-10] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-10-25 01:37:43,291] [pool-1-thread-6] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-10-25 01:37:43,678] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 3 minutes 1 second Finished: SUCCESS