Started by upstream project "BIOFORMATS-test-repo" build number 38
originally caused by:
Started by upstream project "Trigger" build number 44
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/jenkins7222499644246118439.sh
+ '[' samples = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_5250_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] 09:09:58,229 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 09:09:58,232 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service.
[testng] 09:09:58,232 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 09:09:58,234 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 09:09:58,234 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 09:09:58,234 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 09:09:58,235 |-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] 09:09:58,235 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 09:09:58,235 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 09:09:58,236 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 09:09:58,236 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 09:09:58,236 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 09:09:58,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 09:09:58,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 09:09:58,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 09:09:58,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 09:09:58,576 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 09:09:58,576 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 09:09:58,576 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 09:09:58,577 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 09:09:58,577 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration.
[testng] 09:09:58,579 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point
[testng] 09:09:58,579 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 344 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-04-19 09:09:58,592] [main] java.version = 1.8.0_342
[testng] 09:09:58,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 09:09:58,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:09:58,665 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-19_09-09-58.log]
[testng] 09:09:58,668 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration.
[testng] [2024-04-19 09:09:58,671] [main] testng.directory = /data
[testng] [2024-04-19 09:09:58,671] [main] testng.configDirectory = /config
[testng] [2024-04-19 09:09:58,690] [main] testng.multiplier = 1.0
[testng] [2024-04-19 09:09:58,691] [main] testng.in-memory = false
[testng] [2024-04-19 09:09:58,691] [main] testng.allow-missing = false
[testng] [2024-04-19 09:09:58,691] [main] user.language = en
[testng] [2024-04-19 09:09:58,691] [main] user.country = ${user.country}
[testng] [2024-04-19 09:09:58,691] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-04-19 09:10:22,303] [main] ----------------------------------------
[testng] [2024-04-19 09:10:22,303] [main] Total files: 164
[testng] [2024-04-19 09:10:22,304] [main] Scan time: 23.612 s (143 ms/file)
[testng] [2024-04-19 09:10:22,304] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 59 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-04-19 09:10:33,698] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF:
[testng] 09:10:33,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 09:10:33,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:10:33,700 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-19_09-10-33.log]
[testng] 09:10:33,700 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38e1e9ee - End of configuration.
[testng] [2024-04-19 09:10:33,747] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.bmp:
[testng] 09:10:33,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 09:10:33,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:10:33,749 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-19_09-10-33.log]
[testng] 09:10:33,749 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f80ffc7 - End of configuration.
[testng] [2024-04-19 09:10:33,769] [pool-1-thread-11] Initializing /data/ome/arwen0205_raw00201.pic:
[testng] 09:10:33,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 09:10:33,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:10:33,771 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-19_09-10-33.log]
[testng] 09:10:33,772 |-INFO in ch.qos.logback.core.sift.SiftProcessor@378e65dd - End of configuration.
[testng] [2024-04-19 09:10:33,855] [pool-1-thread-10] Initializing /data/ome/anusgfpzs.lsm:
[testng] 09:10:33,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 09:10:33,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:10:33,856 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-19_09-10-33.log]
[testng] 09:10:33,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@450a4c43 - End of configuration.
[testng] [2024-04-19 09:10:33,913] [pool-1-thread-9] Initializing /data/openjpeg/Rome.jp2:
[testng] 09:10:33,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 09:10:33,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:10:33,915 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-19_09-10-33.log]
[testng] 09:10:33,915 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bb97311 - End of configuration.
[testng] [2024-04-19 09:10:33,938] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k:
[testng] 09:10:33,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 09:10:33,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:10:33,939 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-19_09-10-33.log]
[testng] 09:10:33,939 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50a75359 - End of configuration.
[testng] [2024-04-19 09:10:33,952] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF:
[testng] 09:10:33,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 09:10:33,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:10:33,953 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-19_09-10-33.log]
[testng] 09:10:33,953 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d121c01 - End of configuration.
[testng] [2024-04-19 09:10:34,002] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Bretagne1.jpg:
[testng] 09:10:34,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 09:10:34,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:10:34,004 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-19_09-10-34.log]
[testng] 09:10:34,005 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5515520c - End of configuration.
[testng] [2024-04-19 09:10:34,013] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.jp2:
[testng] 09:10:34,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 09:10:34,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:10:34,014 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-19_09-10-34.log]
[testng] 09:10:34,014 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a5704a1 - End of configuration.
[testng] [2024-04-19 09:10:34,024] [pool-1-thread-4] Initializing /data/ome/C1lowmusgfp.lsm:
[testng] 09:10:34,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 09:10:34,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:10:34,025 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-19_09-10-34.log]
[testng] 09:10:34,026 |-INFO in ch.qos.logback.core.sift.SiftProcessor@701ba33c - End of configuration.
[testng] [2024-04-19 09:10:34,050] [pool-1-thread-3] Initializing /data/ome/C1.lsm:
[testng] 09:10:34,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 09:10:34,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:10:34,051 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-19_09-10-34.log]
[testng] 09:10:34,052 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ce55c50 - End of configuration.
[testng] [2024-04-19 09:10:34,080] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.ppm:
[testng] 09:10:34,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 09:10:34,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 09:10:34,081 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-19_09-10-34.log]
[testng] 09:10:34,081 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f4355b7 - End of configuration.
[testng] [2024-04-19 09:10:36,581] [pool-1-thread-6] Initializing /data/openjpeg/thumb_facade.jpg:
[testng] [2024-04-19 09:10:36,592] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff:
[testng] [2024-04-19 09:10:36,635] [pool-1-thread-3] Initializing /data/ome/654Atemp.stk:
[testng] [2024-04-19 09:10:36,724] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv:
[testng] [2024-04-19 09:10:36,733] [pool-1-thread-7] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg:
[testng] [2024-04-19 09:10:36,743] [pool-1-thread-1] Initializing /data/ome/cb_1.r3d:
[testng] [2024-04-19 09:10:36,816] [pool-1-thread-5] Initializing /data/ome/embryo.lsm:
[testng] [2024-04-19 09:10:37,090] [pool-1-thread-10] Initializing /data/ome/t0_pos1-0_5x.lsm:
[testng] [2024-04-19 09:10:37,178] [pool-1-thread-6] Initializing /data/ome/Adultmidsection.lsm:
[testng] [2024-04-19 09:10:37,287] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.ppm:
[testng] [2024-04-19 09:10:37,301] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes1.jpg:
[testng] [2024-04-19 09:10:37,513] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Rome.jpg:
[testng] [2024-04-19 09:10:37,643] [pool-1-thread-2] Initializing /data/sdub/sdub.pattern:
[testng] [2024-04-19 09:10:37,824] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.ppm:
[testng] [2024-04-19 09:10:37,920] [pool-1-thread-4] Initializing /data/ome/worm.tiff:
[testng] [2024-04-19 09:10:38,263] [pool-1-thread-7] Initializing /data/openjpeg/Facade.bmp:
[testng] [2024-04-19 09:10:38,277] [pool-1-thread-1] Initializing /data/kidney_TFl/kidney_TFl.pattern:
[testng] [2024-04-19 09:10:38,339] [pool-1-thread-5] Initializing /data/openjpeg/Rome.bmp:
[testng] [2024-04-19 09:10:38,394] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.bmp:
[testng] [2024-04-19 09:10:38,444] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne1.bmp:
[testng] [2024-04-19 09:10:38,602] [pool-1-thread-11] Initializing /data/mouse-kidney/mouse-kidney.lif:
[testng] [2024-04-19 09:10:38,815] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes2.bmp:
[testng] [2024-04-19 09:10:38,859] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Cevennes2.jpg:
[testng] [2024-04-19 09:10:38,876] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJ.bmp:
[testng] [2024-04-19 09:10:38,987] [pool-1-thread-12] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK:
[testng] [2024-04-19 09:10:39,010] [pool-1-thread-5] Initializing /data/ome/011B1_Morph.HTD:
[testng] [2024-04-19 09:10:39,716] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif:
[testng] [2024-04-19 09:10:39,797] [pool-1-thread-10] Initializing /data/openjpeg/Rome.ppm:
[testng] [2024-04-19 09:10:39,824] [pool-1-thread-3] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk:
[testng] [2024-04-19 09:10:39,913] [pool-1-thread-11] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK:
[testng] [2024-04-19 09:10:40,268] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne2.jpg:
[testng] [2024-04-19 09:10:40,326] [pool-1-thread-12] Initializing /data/ome/210502-0min-NFKB-4.r3d:
[testng] [2024-04-19 09:10:40,363] [pool-1-thread-8] Initializing /data/ome/compressed2ChZ.lsm:
[testng] [2024-04-19 09:10:40,387] [pool-1-thread-2] Initializing /data/TAABA/TAABA.pattern:
[testng] [2024-04-19 09:10:41,882] [pool-1-thread-1] Initializing /data/ome/Cpharynxzs1.lsm:
[testng] [2024-04-19 09:10:41,997] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.j2k:
[testng] [2024-04-19 09:10:42,145] [pool-1-thread-7] Initializing /data/openjpeg/Facade.pnm:
[testng] [2024-04-19 09:10:42,316] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.ppm:
[testng] [2024-04-19 09:10:42,460] [pool-1-thread-1] Initializing /data/ome/Cmidmusgfp1.lsm:
[testng] [2024-04-19 09:10:42,530] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.j2k:
[testng] [2024-04-19 09:10:42,566] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJW.bmp:
[testng] [2024-04-19 09:10:42,572] [pool-1-thread-4] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF:
[testng] [2024-04-19 09:10:42,705] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Speedway.jpg:
[testng] [2024-04-19 09:10:42,773] [pool-1-thread-9] Initializing /data/10-31 E1/10-31 E1.tif:
[testng] [2024-04-19 09:10:42,967] [pool-1-thread-1] Initializing /data/ome/C1midmusnorm.lsm:
[testng] [2024-04-19 09:10:43,014] [pool-1-thread-12] Initializing /data/ome/CHOBI_d3d.dv:
[testng] [2024-04-19 09:10:43,285] [pool-1-thread-4] 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 40 seconds
Finished: SUCCESS