Started by upstream project "BIOFORMATS-test-repo" build number 209
originally caused by:
Started by upstream project "Trigger" build number 235
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4
[BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins1780067951009507801.sh
+ '[' samples = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_33138_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] 01:32:24,764 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:32:24,765 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service.
[testng] 01:32:24,765 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:32:24,766 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:32:24,766 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:32:24,766 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:32:24,767 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:32:24,767 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:32:24,767 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:32:24,768 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:32:24,768 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:32:24,768 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:32:25,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:32:25,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:32:25,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:32:25,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:32:25,068 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:32:25,069 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:32:25,069 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:32:25,069 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:32:25,069 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration.
[testng] 01:32:25,070 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point
[testng] 01:32:25,070 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 303 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-04 01:32:25,081] [main] java.version = 1.8.0_342
[testng] 01:32:25,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:32:25,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:32:25,134 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-04_01-32-25.log]
[testng] 01:32:25,135 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration.
[testng] [2024-10-04 01:32:25,138] [main] testng.directory = /data
[testng] [2024-10-04 01:32:25,138] [main] testng.configDirectory = /config
[testng] [2024-10-04 01:32:25,151] [main] testng.multiplier = 1.0
[testng] [2024-10-04 01:32:25,151] [main] testng.in-memory = false
[testng] [2024-10-04 01:32:25,151] [main] testng.allow-missing = false
[testng] [2024-10-04 01:32:25,151] [main] user.language = en
[testng] [2024-10-04 01:32:25,151] [main] user.country = ${user.country}
[testng] [2024-10-04 01:32:25,151] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-10-04 01:33:05,071] [main] ----------------------------------------
[testng] [2024-10-04 01:33:05,072] [main] Total files: 164
[testng] [2024-10-04 01:33:05,072] [main] Scan time: 39.919 s (243 ms/file)
[testng] [2024-10-04 01:33:05,072] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 59 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-04 01:33:43,434] [pool-1-thread-1] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK:
[testng] 01:33:43,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:33:43,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:33:43,435 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-04_01-33-43.log]
[testng] 01:33:43,436 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b79098f - End of configuration.
[testng] [2024-10-04 01:33:43,847] [pool-1-thread-12] Initializing /data/ome/tiffany.color.tiff:
[testng] 01:33:43,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:33:43,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:33:43,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-04_01-33-43.log]
[testng] 01:33:43,848 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20862982 - End of configuration.
[testng] [2024-10-04 01:33:44,324] [pool-1-thread-11] Initializing /data/ome/C1lowmusgfp.lsm:
[testng] 01:33:44,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:33:44,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:33:44,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-04_01-33-44.log]
[testng] 01:33:44,326 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dc0c17c - End of configuration.
[testng] [2024-10-04 01:33:44,598] [pool-1-thread-10] Initializing /data/ome/C1.lsm:
[testng] 01:33:44,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:33:44,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:33:44,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-04_01-33-44.log]
[testng] 01:33:44,599 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2331ee1 - End of configuration.
[testng] [2024-10-04 01:33:44,738] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.ppm:
[testng] 01:33:44,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:33:44,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:33:44,739 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-04_01-33-44.log]
[testng] 01:33:44,739 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a148311 - End of configuration.
[testng] [2024-10-04 01:33:44,770] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF:
[testng] 01:33:44,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:33:44,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:33:44,771 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-04_01-33-44.log]
[testng] 01:33:44,771 |-INFO in ch.qos.logback.core.sift.SiftProcessor@716ea815 - End of configuration.
[testng] [2024-10-04 01:33:45,059] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Speedway.jpg:
[testng] 01:33:45,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:33:45,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:33:45,060 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-04_01-33-45.log]
[testng] 01:33:45,061 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22c10d98 - End of configuration.
[testng] [2024-10-04 01:33:45,092] [pool-1-thread-6] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK:
[testng] 01:33:45,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:33:45,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:33:45,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-04_01-33-45.log]
[testng] 01:33:45,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@588cc7d2 - End of configuration.
[testng] [2024-10-04 01:33:45,296] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.jp2:
[testng] 01:33:45,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:33:45,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:33:45,297 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-04_01-33-45.log]
[testng] 01:33:45,298 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44deeb35 - End of configuration.
[testng] [2024-10-04 01:33:45,405] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.j2k:
[testng] 01:33:45,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:33:45,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:33:45,406 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-04_01-33-45.log]
[testng] 01:33:45,406 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51b5eb98 - End of configuration.
[testng] [2024-10-04 01:33:45,573] [pool-1-thread-3] Initializing /data/10-31 E1/10-31 E1.tif:
[testng] 01:33:45,573 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:33:45,573 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:33:45,574 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-04_01-33-45.log]
[testng] 01:33:45,574 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6db7869e - End of configuration.
[testng] [2024-10-04 01:33:45,924] [pool-1-thread-2] Initializing /data/ome/t1_pos1-0_5x.lsm:
[testng] 01:33:45,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:33:45,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:33:45,925 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-04_01-33-45.log]
[testng] 01:33:45,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63d5a684 - End of configuration.
[testng] [2024-10-04 01:33:48,162] [pool-1-thread-7] Initializing /data/openjpeg/Rome.jp2:
[testng] [2024-10-04 01:33:48,965] [pool-1-thread-9] Initializing /data/ome/C1midmusnorm.lsm:
[testng] [2024-10-04 01:33:49,271] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne2.jpg:
[testng] [2024-10-04 01:33:49,358] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJ.bmp:
[testng] [2024-10-04 01:33:49,668] [pool-1-thread-5] Initializing /data/ome/compressed2ChZ.lsm:
[testng] [2024-10-04 01:33:50,090] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Cevennes2.jpg:
[testng] [2024-10-04 01:33:50,132] [pool-1-thread-6] Initializing /data/ome/Cmidmusgfp1.lsm:
[testng] [2024-10-04 01:33:50,286] [pool-1-thread-2] Initializing /data/ome/cb_1.r3d:
[testng] [2024-10-04 01:33:50,424] [pool-1-thread-8] Initializing /data/ome/anusgfpzs.lsm:
[testng] [2024-10-04 01:33:50,564] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.ppm:
[testng] [2024-10-04 01:33:50,811] [pool-1-thread-3] Initializing /data/openjpeg/Facade.bmp:
[testng] [2024-10-04 01:33:51,120] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJW.bmp:
[testng] [2024-10-04 01:33:51,470] [pool-1-thread-12] Initializing /data/openjpeg/Rome.ppm:
[testng] [2024-10-04 01:33:51,620] [pool-1-thread-4] Initializing /data/ome/worm.tiff:
[testng] [2024-10-04 01:33:52,119] [pool-1-thread-9] Initializing /data/ome/embryo.lsm:
[testng] [2024-10-04 01:33:52,334] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.bmp:
[testng] [2024-10-04 01:33:52,387] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.j2k:
[testng] [2024-10-04 01:33:52,551] [pool-1-thread-6] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF:
[testng] [2024-10-04 01:33:52,755] [pool-1-thread-8] Initializing /data/ome/n2_plate18_P24_w1.tif:
[testng] [2024-10-04 01:33:53,122] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.bmp:
[testng] [2024-10-04 01:33:53,446] [pool-1-thread-7] Initializing /data/openjpeg/Facade.pnm:
[testng] [2024-10-04 01:33:53,549] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm:
[testng] [2024-10-04 01:33:53,628] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d:
[testng] [2024-10-04 01:33:54,230] [pool-1-thread-5] Initializing /data/ome/Cpharynxzs1.lsm:
[testng] [2024-10-04 01:33:54,510] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes2.bmp:
[testng] [2024-10-04 01:33:54,631] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk:
[testng] [2024-10-04 01:33:55,861] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm:
[testng] [2024-10-04 01:33:56,155] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Bretagne1.jpg:
[testng] [2024-10-04 01:33:56,291] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.ppm:
[testng] [2024-10-04 01:33:56,349] [pool-1-thread-6] Initializing /data/ome/CHOBI_d3d.dv:
[testng] [2024-10-04 01:33:56,534] [pool-1-thread-2] Initializing /data/ome/011B1_Morph.HTD:
[testng] [2024-10-04 01:33:57,373] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Rome.jpg:
[testng] [2024-10-04 01:33:57,498] [pool-1-thread-5] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg:
[testng] [2024-10-04 01:33:57,627] [pool-1-thread-8] Initializing /data/ome/t0_pos1-0_5x.lsm:
[testng] [2024-10-04 01:33:57,867] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne2.j2k:
[testng] [2024-10-04 01:33:58,138] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF:
[testng] [2024-10-04 01:33:58,539] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif:
[testng] [2024-10-04 01:33:58,690] [pool-1-thread-6] Initializing /data/ome/tinyTest.d3d.dv:
[testng] [2024-10-04 01:33:58,942] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.bmp:
[testng] [2024-10-04 01:33:59,016] [pool-1-thread-10] Initializing /data/openjpeg/thumb_facade.jpg:
[testng] [2024-10-04 01:33:59,096] [pool-1-thread-5] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk:
[testng] [2024-10-04 01:34:00,035] [pool-1-thread-6] Initializing /data/openjpeg/Rome.bmp:
[testng] [2024-10-04 01:34:00,631] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Cevennes1.jpg:
[testng] [2024-10-04 01:34:00,853] [pool-1-thread-9] Initializing /data/TAABA/TAABA.pattern:
[testng] [2024-10-04 01:34:08,746] [pool-1-thread-8] Initializing /data/kidney_TFl/kidney_TFl.pattern:
[testng] [2024-10-04 01:34:09,098] [pool-1-thread-10] Initializing /data/ome/arwen0205_raw00201.pic:
[testng] [2024-10-04 01:34:09,314] [pool-1-thread-7] Initializing /data/sdub/sdub.pattern:
[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 12 seconds
Finished: SUCCESS