Started by upstream project "BIOFORMATS-test-repo" build number 272
originally caused by:
Started by upstream project "Trigger" build number 294
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7
[BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins5053259298922021203.sh
+ '[' samples = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_42825_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] 00:34:21,155 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 00:34:21,157 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service.
[testng] 00:34:21,157 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:34:21,158 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:34:21,158 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:34:21,158 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:34:21,158 |-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] 00:34:21,158 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:34:21,159 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:34:21,159 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:34:21,159 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:34:21,159 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:34:21,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:34:21,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:34:21,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:34:21,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:34:21,443 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:34:21,443 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:34:21,444 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:34:21,444 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:34:21,444 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration.
[testng] 00:34:21,445 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point
[testng] 00:34:21,445 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 286 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-29 00:34:21,457] [main] java.version = 1.8.0_342
[testng] 00:34:21,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:34:21,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:34:21,511 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-29_00-34-21.log]
[testng] 00:34:21,513 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration.
[testng] [2024-11-29 00:34:21,515] [main] testng.directory = /data
[testng] [2024-11-29 00:34:21,515] [main] testng.configDirectory = /config
[testng] [2024-11-29 00:34:21,529] [main] testng.multiplier = 1.0
[testng] [2024-11-29 00:34:21,530] [main] testng.in-memory = false
[testng] [2024-11-29 00:34:21,530] [main] testng.allow-missing = false
[testng] [2024-11-29 00:34:21,530] [main] user.language = en
[testng] [2024-11-29 00:34:21,530] [main] user.country = ${user.country}
[testng] [2024-11-29 00:34:21,530] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-11-29 00:35:09,227] [main] ----------------------------------------
[testng] [2024-11-29 00:35:09,227] [main] Total files: 164
[testng] [2024-11-29 00:35:09,228] [main] Scan time: 47.697 s (290 ms/file)
[testng] [2024-11-29 00:35:09,228] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 59 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-29 00:36:19,430] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK:
[testng] 00:36:19,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:36:19,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:36:19,432 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-29_00-36-19.log]
[testng] 00:36:19,432 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d251121 - End of configuration.
[testng] [2024-11-29 00:36:20,473] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJW.bmp:
[testng] 00:36:20,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:36:20,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:36:20,474 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-29_00-36-20.log]
[testng] 00:36:20,474 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34b8064a - End of configuration.
[testng] [2024-11-29 00:36:20,611] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm:
[testng] 00:36:20,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:36:20,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:36:20,612 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-29_00-36-20.log]
[testng] 00:36:20,612 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a3c1a53 - End of configuration.
[testng] [2024-11-29 00:36:21,383] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm:
[testng] 00:36:21,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:36:21,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:36:21,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-29_00-36-21.log]
[testng] 00:36:21,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20096708 - End of configuration.
[testng] [2024-11-29 00:36:21,837] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk:
[testng] 00:36:21,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:36:21,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:36:21,838 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-29_00-36-21.log]
[testng] 00:36:21,838 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dc0c17c - End of configuration.
[testng] [2024-11-29 00:36:22,925] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp:
[testng] 00:36:22,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:36:22,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:36:22,926 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-29_00-36-22.log]
[testng] 00:36:22,926 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5827d8bd - End of configuration.
[testng] [2024-11-29 00:36:23,019] [pool-1-thread-7] Initializing /data/ome/embryo.lsm:
[testng] 00:36:23,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:36:23,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:36:23,020 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-29_00-36-23.log]
[testng] 00:36:23,020 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ce261a1 - End of configuration.
[testng] [2024-11-29 00:36:23,569] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg:
[testng] 00:36:23,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:36:23,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:36:23,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-29_00-36-23.log]
[testng] 00:36:23,570 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d7c78b0 - End of configuration.
[testng] [2024-11-29 00:36:23,691] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm:
[testng] 00:36:23,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:36:23,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:36:23,692 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-29_00-36-23.log]
[testng] 00:36:23,692 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29c08edb - End of configuration.
[testng] [2024-11-29 00:36:24,050] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm:
[testng] 00:36:24,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:36:24,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:36:24,051 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-29_00-36-24.log]
[testng] 00:36:24,051 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61bef709 - End of configuration.
[testng] [2024-11-29 00:36:24,107] [pool-1-thread-3] Initializing /data/ome/worm.tiff:
[testng] 00:36:24,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:36:24,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:36:24,108 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-29_00-36-24.log]
[testng] 00:36:24,108 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75186d06 - End of configuration.
[testng] [2024-11-29 00:36:25,182] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF:
[testng] 00:36:25,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:36:25,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:36:25,183 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-29_00-36-25.log]
[testng] 00:36:25,183 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66a1d392 - End of configuration.
[testng] [2024-11-29 00:36:28,717] [pool-1-thread-6] Initializing /data/ome/C1.lsm:
[testng] [2024-11-29 00:36:29,077] [pool-1-thread-4] Initializing /data/openjpeg/Facade.bmp:
[testng] [2024-11-29 00:36:29,377] [pool-1-thread-12] Initializing /data/openjpeg/Rome.ppm:
[testng] [2024-11-29 00:36:29,700] [pool-1-thread-8] Initializing /data/ome/arwen0205_raw00201.pic:
[testng] [2024-11-29 00:36:30,179] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne2.jpg:
[testng] [2024-11-29 00:36:30,273] [pool-1-thread-7] Initializing /data/ome/anusgfpzs.lsm:
[testng] [2024-11-29 00:36:30,604] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern:
[testng] [2024-11-29 00:36:33,982] [pool-1-thread-1] Initializing /data/ome/C1midmusnorm.lsm:
[testng] [2024-11-29 00:36:34,416] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk:
[testng] [2024-11-29 00:36:35,180] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.bmp:
[testng] [2024-11-29 00:36:35,664] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.jp2:
[testng] [2024-11-29 00:36:36,925] [pool-1-thread-5] Initializing /data/openjpeg/Facade.pnm:
[testng] [2024-11-29 00:36:37,046] [pool-1-thread-2] Initializing /data/openjpeg/Rome.bmp:
[testng] [2024-11-29 00:36:37,543] [pool-1-thread-9] Initializing /data/ome/tiffany.color.tiff:
[testng] [2024-11-29 00:36:38,739] [pool-1-thread-6] Initializing /data/ome/cb_1.r3d:
[testng] [2024-11-29 00:36:39,001] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.j2k:
[testng] [2024-11-29 00:36:39,483] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.ppm:
[testng] [2024-11-29 00:36:39,871] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF:
[testng] [2024-11-29 00:36:40,771] [pool-1-thread-2] Initializing /data/ome/compressed2ChZ.lsm:
[testng] [2024-11-29 00:36:41,548] [pool-1-thread-5] Initializing /data/ome/tinyTest.d3d.dv:
[testng] [2024-11-29 00:36:41,722] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.ppm:
[testng] [2024-11-29 00:36:42,281] [pool-1-thread-6] Initializing /data/openjpeg/thumb_facade.jpg:
[testng] [2024-11-29 00:36:42,398] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.bmp:
[testng] [2024-11-29 00:36:42,588] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif:
[testng] [2024-11-29 00:36:42,876] [pool-1-thread-12] Initializing /data/ome/CHOBI_d3d.dv:
[testng] [2024-11-29 00:36:43,270] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.j2k:
[testng] [2024-11-29 00:36:43,835] [pool-1-thread-5] Initializing /data/ome/011B1_Morph.HTD:
[testng] [2024-11-29 00:36:45,428] [pool-1-thread-4] Initializing /data/ome/210502-0min-NFKB-4.r3d:
[testng] [2024-11-29 00:36:45,577] [pool-1-thread-6] Initializing /data/openjpeg/Rome.jp2:
[testng] [2024-11-29 00:36:45,908] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.bmp:
[testng] [2024-11-29 00:36:45,977] [pool-1-thread-3] Initializing /data/kidney_TFl/kidney_TFl.pattern:
[testng] [2024-11-29 00:36:46,759] [pool-1-thread-9] Initializing /data/ome/C1lowmusgfp.lsm:
[testng] [2024-11-29 00:36:47,104] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes2.jpg:
[testng] [2024-11-29 00:36:47,189] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Cevennes1.jpg:
[testng] [2024-11-29 00:36:47,627] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF:
[testng] [2024-11-29 00:36:49,511] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.ppm:
[testng] [2024-11-29 00:36:49,801] [pool-1-thread-4] Initializing /data/ome/n2_plate18_P24_w1.tif:
[testng] [2024-11-29 00:36:51,039] [pool-1-thread-7] Initializing /data/TAABA/TAABA.pattern:
[testng] [2024-11-29 00:37:09,427] [pool-1-thread-2] Initializing /data/ome/t1_pos1-0_5x.lsm:
[testng] [2024-11-29 00:37:09,751] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.j2k:
[testng] [2024-11-29 00:37:10,714] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Rome.jpg:
[testng] [2024-11-29 00:37:12,047] [pool-1-thread-9] Initializing /data/ome/Cpharynxzs1.lsm:
[testng] [2024-11-29 00:37:13,068] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJ.bmp:
[testng] [2024-11-29 00:37:13,794] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Bretagne1.jpg:
[testng] [2024-11-29 00:37:14,391] [pool-1-thread-11] Initializing /data/10-31 E1/10-31 E1.tif:
[testng] [2024-11-29 00:37:15,890] [pool-1-thread-2] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK:
[testng] [2024-11-29 00:37:16,776] [pool-1-thread-4] 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: 4 minutes 13 seconds
Finished: SUCCESS