Started by upstream project "BIOFORMATS-test-repo" build number 264
originally caused by:
Started by upstream project "Trigger" build number 287
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8
[BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins17456211608347146119.sh
+ '[' samples = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_41642_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] 00:37:47,884 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 00:37:47,886 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service.
[testng] 00:37:47,886 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:37:47,887 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:37:47,887 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:37:47,887 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:37:47,887 |-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] 00:37:47,887 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:37:47,888 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:37:47,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:37:47,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:37:47,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:37:48,106 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:37:48,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:37:48,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:37:48,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:37:48,141 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:37:48,141 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:37:48,141 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:37:48,142 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:37:48,142 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration.
[testng] 00:37:48,143 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point
[testng] 00:37:48,143 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 255 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-22 00:37:48,152] [main] java.version = 1.8.0_342
[testng] 00:37:48,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:37:48,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:48,200 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-22_00-37-48.log]
[testng] 00:37:48,202 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration.
[testng] [2024-11-22 00:37:48,204] [main] testng.directory = /data
[testng] [2024-11-22 00:37:48,204] [main] testng.configDirectory = /config
[testng] [2024-11-22 00:37:48,216] [main] testng.multiplier = 1.0
[testng] [2024-11-22 00:37:48,216] [main] testng.in-memory = false
[testng] [2024-11-22 00:37:48,216] [main] testng.allow-missing = false
[testng] [2024-11-22 00:37:48,216] [main] user.language = en
[testng] [2024-11-22 00:37:48,216] [main] user.country = ${user.country}
[testng] [2024-11-22 00:37:48,216] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-11-22 00:38:29,649] [main] ----------------------------------------
[testng] [2024-11-22 00:38:29,649] [main] Total files: 164
[testng] [2024-11-22 00:38:29,649] [main] Scan time: 41.432 s (252 ms/file)
[testng] [2024-11-22 00:38:29,649] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 59 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-22 00:39:02,580] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK:
[testng] 00:39:02,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:39:02,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:39:02,582 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-22_00-39-02.log]
[testng] 00:39:02,582 |-INFO in ch.qos.logback.core.sift.SiftProcessor@540a7ba8 - End of configuration.
[testng] [2024-11-22 00:39:02,772] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJW.bmp:
[testng] 00:39:02,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:39:02,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:39:02,773 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-22_00-39-02.log]
[testng] 00:39:02,774 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72910e37 - End of configuration.
[testng] [2024-11-22 00:39:02,848] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm:
[testng] 00:39:02,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:39:02,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:39:02,849 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-22_00-39-02.log]
[testng] 00:39:02,849 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f444476 - End of configuration.
[testng] [2024-11-22 00:39:03,320] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm:
[testng] 00:39:03,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:39:03,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:39:03,321 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-22_00-39-03.log]
[testng] 00:39:03,322 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5eb1b740 - End of configuration.
[testng] [2024-11-22 00:39:03,751] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk:
[testng] 00:39:03,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:39:03,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:39:03,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-22_00-39-03.log]
[testng] 00:39:03,752 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22c10d98 - End of configuration.
[testng] [2024-11-22 00:39:04,704] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp:
[testng] 00:39:04,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:39:04,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:39:04,705 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-22_00-39-04.log]
[testng] 00:39:04,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@588cc7d2 - End of configuration.
[testng] [2024-11-22 00:39:04,775] [pool-1-thread-7] Initializing /data/ome/embryo.lsm:
[testng] 00:39:04,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:39:04,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:39:04,776 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-22_00-39-04.log]
[testng] 00:39:04,776 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44deeb35 - End of configuration.
[testng] [2024-11-22 00:39:05,146] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg:
[testng] 00:39:05,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:39:05,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:39:05,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-22_00-39-05.log]
[testng] 00:39:05,148 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51b5eb98 - End of configuration.
[testng] [2024-11-22 00:39:05,238] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm:
[testng] 00:39:05,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:39:05,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:39:05,238 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-22_00-39-05.log]
[testng] 00:39:05,239 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5790e2a5 - End of configuration.
[testng] [2024-11-22 00:39:05,649] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm:
[testng] 00:39:05,649 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:39:05,649 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:39:05,650 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-22_00-39-05.log]
[testng] 00:39:05,650 |-INFO in ch.qos.logback.core.sift.SiftProcessor@143a13e8 - End of configuration.
[testng] [2024-11-22 00:39:05,712] [pool-1-thread-3] Initializing /data/ome/worm.tiff:
[testng] 00:39:05,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:39:05,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:39:05,713 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-22_00-39-05.log]
[testng] 00:39:05,713 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18e5776c - End of configuration.
[testng] [2024-11-22 00:39:06,439] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF:
[testng] 00:39:06,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:39:06,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:39:06,440 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-22_00-39-06.log]
[testng] 00:39:06,441 |-INFO in ch.qos.logback.core.sift.SiftProcessor@265d8ad1 - End of configuration.
[testng] [2024-11-22 00:39:09,969] [pool-1-thread-6] Initializing /data/ome/C1.lsm:
[testng] [2024-11-22 00:39:10,209] [pool-1-thread-4] Initializing /data/openjpeg/Facade.bmp:
[testng] [2024-11-22 00:39:10,439] [pool-1-thread-12] Initializing /data/openjpeg/Rome.ppm:
[testng] [2024-11-22 00:39:10,847] [pool-1-thread-8] Initializing /data/ome/arwen0205_raw00201.pic:
[testng] [2024-11-22 00:39:11,366] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern:
[testng] [2024-11-22 00:39:15,628] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Bretagne2.jpg:
[testng] [2024-11-22 00:39:15,774] [pool-1-thread-5] Initializing /data/ome/anusgfpzs.lsm:
[testng] [2024-11-22 00:39:16,443] [pool-1-thread-1] Initializing /data/ome/C1midmusnorm.lsm:
[testng] [2024-11-22 00:39:17,100] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk:
[testng] [2024-11-22 00:39:17,763] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.bmp:
[testng] [2024-11-22 00:39:18,416] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.jp2:
[testng] [2024-11-22 00:39:19,530] [pool-1-thread-7] Initializing /data/openjpeg/Facade.pnm:
[testng] [2024-11-22 00:39:19,878] [pool-1-thread-2] Initializing /data/openjpeg/Rome.bmp:
[testng] [2024-11-22 00:39:20,010] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff:
[testng] [2024-11-22 00:39:21,631] [pool-1-thread-6] Initializing /data/ome/cb_1.r3d:
[testng] [2024-11-22 00:39:22,078] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.j2k:
[testng] [2024-11-22 00:39:22,527] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.ppm:
[testng] [2024-11-22 00:39:22,588] [pool-1-thread-9] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF:
[testng] [2024-11-22 00:39:23,828] [pool-1-thread-2] Initializing /data/ome/compressed2ChZ.lsm:
[testng] [2024-11-22 00:39:24,268] [pool-1-thread-1] Initializing /data/ome/tinyTest.d3d.dv:
[testng] [2024-11-22 00:39:24,898] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.ppm:
[testng] [2024-11-22 00:39:24,990] [pool-1-thread-6] Initializing /data/openjpeg/thumb_facade.jpg:
[testng] [2024-11-22 00:39:25,146] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.bmp:
[testng] [2024-11-22 00:39:25,340] [pool-1-thread-11] Initializing /data/mouse-kidney/mouse-kidney.lif:
[testng] [2024-11-22 00:39:26,084] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv:
[testng] [2024-11-22 00:39:26,848] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes1.j2k:
[testng] [2024-11-22 00:39:27,389] [pool-1-thread-1] Initializing /data/ome/011B1_Morph.HTD:
[testng] [2024-11-22 00:39:29,232] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d:
[testng] [2024-11-22 00:39:29,465] [pool-1-thread-9] Initializing /data/openjpeg/Rome.jp2:
[testng] [2024-11-22 00:39:29,938] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.bmp:
[testng] [2024-11-22 00:39:30,055] [pool-1-thread-5] Initializing /data/ome/C1lowmusgfp.lsm:
[testng] [2024-11-22 00:39:30,496] [pool-1-thread-6] Initializing /data/kidney_TFl/kidney_TFl.pattern:
[testng] [2024-11-22 00:39:31,471] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Cevennes1.jpg:
[testng] [2024-11-22 00:39:31,555] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Cevennes2.jpg:
[testng] [2024-11-22 00:39:32,145] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF:
[testng] [2024-11-22 00:39:33,245] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.ppm:
[testng] [2024-11-22 00:39:33,447] [pool-1-thread-4] Initializing /data/ome/n2_plate18_P24_w1.tif:
[testng] [2024-11-22 00:39:35,327] [pool-1-thread-2] Initializing /data/TAABA/TAABA.pattern:
[testng] [2024-11-22 00:39:55,173] [pool-1-thread-11] Initializing /data/ome/t1_pos1-0_5x.lsm:
[testng] [2024-11-22 00:39:56,304] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.j2k:
[testng] [2024-11-22 00:39:56,953] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Rome.jpg:
[testng] [2024-11-22 00:39:58,981] [pool-1-thread-5] Initializing /data/ome/Cpharynxzs1.lsm:
[testng] [2024-11-22 00:40:01,446] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJ.bmp:
[testng] [2024-11-22 00:40:02,074] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne1.jpg:
[testng] [2024-11-22 00:40:02,640] [pool-1-thread-12] Initializing /data/10-31 E1/10-31 E1.tif:
[testng] [2024-11-22 00:40:03,727] [pool-1-thread-11] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK:
[testng] [2024-11-22 00:40:05,124] [pool-1-thread-8] 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 5 seconds
Finished: SUCCESS