Started by upstream project "BIOFORMATS-test-repo" build number 120
originally caused by:
Started by upstream project "Trigger" build number 137
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder
[BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins792408513789430398.sh
+ '[' samples = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_18699_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
[javac] warning: [options] bootstrap class path not set in conjunction with -source 8
[javac] 1 warning
test-automated:
[testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket
[testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket
[testng] File leak detector installed
[testng] 01:23:40,991 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:23:40,992 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 01:23:40,992 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:23:40,993 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:23:40,994 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:23:40,994 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:23:40,994 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:23:40,994 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:23:40,995 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:23:40,995 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:23:40,996 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:23:40,996 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:23:41,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:23:41,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:23:41,198 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:23:41,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:23:41,204 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:23:41,204 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:23:41,204 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:23:41,205 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:23:41,205 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 01:23:41,205 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 01:23:41,205 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 210 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-07-14 01:23:41,215] [main] java.version = 17.0.2
[testng] 01:23:41,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:23:41,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:23:41,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-14_01-23-41.log]
[testng] 01:23:41,266 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-07-14 01:23:41,268] [main] testng.directory = /data
[testng] [2024-07-14 01:23:41,268] [main] testng.configDirectory = /config
[testng] [2024-07-14 01:23:41,277] [main] testng.multiplier = 1.0
[testng] [2024-07-14 01:23:41,278] [main] testng.in-memory = false
[testng] [2024-07-14 01:23:41,278] [main] testng.allow-missing = false
[testng] [2024-07-14 01:23:41,278] [main] user.language = en
[testng] [2024-07-14 01:23:41,278] [main] user.country = ${user.country}
[testng] [2024-07-14 01:23:41,278] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-07-14 01:24:01,882] [main] ----------------------------------------
[testng] [2024-07-14 01:24:01,882] [main] Total files: 164
[testng] [2024-07-14 01:24:01,882] [main] Scan time: 20.604 s (125 ms/file)
[testng] [2024-07-14 01:24:01,882] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 59 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-07-14 01:24:09,643] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm:
[testng] 01:24:09,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:24:09,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:09,645 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-14_01-24-09.log]
[testng] 01:24:09,645 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b1e9265 - End of configuration.
[testng] [2024-07-14 01:24:09,687] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF:
[testng] 01:24:09,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:24:09,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:09,688 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-14_01-24-09.log]
[testng] 01:24:09,689 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1694f3db - End of configuration.
[testng] [2024-07-14 01:24:09,738] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm:
[testng] 01:24:09,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:24:09,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:09,740 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-14_01-24-09.log]
[testng] 01:24:09,740 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5fc115a9 - End of configuration.
[testng] [2024-07-14 01:24:09,753] [pool-1-thread-10] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK:
[testng] 01:24:09,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:24:09,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:09,754 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-14_01-24-09.log]
[testng] 01:24:09,754 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38b75c39 - End of configuration.
[testng] [2024-07-14 01:24:09,793] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes1.jpg:
[testng] 01:24:09,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:24:09,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:09,794 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-14_01-24-09.log]
[testng] 01:24:09,794 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2179e7cf - End of configuration.
[testng] [2024-07-14 01:24:09,801] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k:
[testng] 01:24:09,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:24:09,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:09,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-14_01-24-09.log]
[testng] 01:24:09,802 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20634cc8 - End of configuration.
[testng] [2024-07-14 01:24:09,813] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF:
[testng] 01:24:09,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:24:09,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:09,814 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-14_01-24-09.log]
[testng] 01:24:09,814 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12dbf165 - End of configuration.
[testng] [2024-07-14 01:24:09,869] [pool-1-thread-6] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK:
[testng] 01:24:09,869 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:24:09,869 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:09,870 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-14_01-24-09.log]
[testng] 01:24:09,870 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e53f8d0 - End of configuration.
[testng] [2024-07-14 01:24:09,947] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm:
[testng] 01:24:09,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:24:09,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:09,949 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-14_01-24-09.log]
[testng] 01:24:09,949 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68e16d1e - End of configuration.
[testng] [2024-07-14 01:24:09,957] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff:
[testng] 01:24:09,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:24:09,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:09,958 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-14_01-24-09.log]
[testng] 01:24:09,958 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50380ee1 - End of configuration.
[testng] [2024-07-14 01:24:09,997] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d:
[testng] 01:24:09,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:24:09,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:09,998 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-14_01-24-09.log]
[testng] 01:24:09,998 |-INFO in ch.qos.logback.core.sift.SiftProcessor@496f76af - End of configuration.
[testng] [2024-07-14 01:24:10,014] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm:
[testng] 01:24:10,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:24:10,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:10,015 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-14_01-24-10.log]
[testng] 01:24:10,016 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12bbba09 - End of configuration.
[testng] [2024-07-14 01:24:11,958] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne1.jpg:
[testng] [2024-07-14 01:24:11,965] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.bmp:
[testng] [2024-07-14 01:24:11,973] [pool-1-thread-10] Initializing /data/openjpeg/thumb_facade.jpg:
[testng] [2024-07-14 01:24:11,982] [pool-1-thread-2] Initializing /data/10-31 E1/10-31 E1.tif:
[testng] [2024-07-14 01:24:12,157] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.bmp:
[testng] [2024-07-14 01:24:12,163] [pool-1-thread-12] Initializing /data/sdub/sdub.pattern:
[testng] [2024-07-14 01:24:12,392] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Rome.jpg:
[testng] [2024-07-14 01:24:12,504] [pool-1-thread-3] Initializing /data/ome/arwen0205_raw00201.pic:
[testng] [2024-07-14 01:24:12,638] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.bmp:
[testng] [2024-07-14 01:24:12,645] [pool-1-thread-9] Initializing /data/mouse-kidney/mouse-kidney.lif:
[testng] [2024-07-14 01:24:12,890] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJ.bmp:
[testng] [2024-07-14 01:24:12,896] [pool-1-thread-5] Initializing /data/ome/t0_pos1-0_5x.lsm:
[testng] [2024-07-14 01:24:12,951] [pool-1-thread-11] Initializing /data/ome/worm.tiff:
[testng] [2024-07-14 01:24:13,025] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Bretagne2.jpg:
[testng] [2024-07-14 01:24:13,242] [pool-1-thread-1] Initializing /data/openjpeg/Rome.ppm:
[testng] [2024-07-14 01:24:13,265] [pool-1-thread-7] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk:
[testng] [2024-07-14 01:24:13,502] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Speedway.jpg:
[testng] [2024-07-14 01:24:13,608] [pool-1-thread-1] Initializing /data/ome/654Atemp.stk:
[testng] [2024-07-14 01:24:13,800] [pool-1-thread-6] Initializing /data/ome/embryo.lsm:
[testng] [2024-07-14 01:24:13,960] [pool-1-thread-9] Initializing /data/ome/compressed2ChZ.lsm:
[testng] [2024-07-14 01:24:14,037] [pool-1-thread-12] Initializing /data/ome/C1.lsm:
[testng] [2024-07-14 01:24:14,242] [pool-1-thread-7] Initializing /data/TAABA/TAABA.pattern:
[testng] [2024-07-14 01:24:15,223] [pool-1-thread-2] Initializing /data/ome/cb_1.r3d:
[testng] [2024-07-14 01:24:15,323] [pool-1-thread-6] Initializing /data/ome/t1_pos1-0_5x.lsm:
[testng] [2024-07-14 01:24:15,411] [pool-1-thread-5] Initializing /data/ome/011B1_Morph.HTD:
[testng] [2024-07-14 01:24:15,950] [pool-1-thread-12] Initializing /data/ome/C1midmusnorm.lsm:
[testng] [2024-07-14 01:24:16,090] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.j2k:
[testng] [2024-07-14 01:24:16,108] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.bmp:
[testng] [2024-07-14 01:24:16,358] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.ppm:
[testng] [2024-07-14 01:24:16,486] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes2.jpg:
[testng] [2024-07-14 01:24:16,584] [pool-1-thread-12] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg:
[testng] [2024-07-14 01:24:16,596] [pool-1-thread-1] Initializing /data/kidney_TFl/kidney_TFl.pattern:
[testng] [2024-07-14 01:24:16,738] [pool-1-thread-2] Initializing /data/ome/Cpharynxzs1.lsm:
[testng] [2024-07-14 01:24:16,762] [pool-1-thread-9] Initializing /data/ome/anusgfpzs.lsm:
[testng] [2024-07-14 01:24:16,882] [pool-1-thread-12] Initializing /data/ome/Cmidmusgfp1.lsm:
[testng] [2024-07-14 01:24:16,921] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF:
[testng] [2024-07-14 01:24:16,980] [pool-1-thread-4] Initializing /data/ome/tinyTest.d3d.dv:
[testng] [2024-07-14 01:24:17,035] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.jp2:
[testng] [2024-07-14 01:24:17,123] [pool-1-thread-4] Initializing /data/openjpeg/Facade.bmp:
[testng] [2024-07-14 01:24:17,201] [pool-1-thread-10] Initializing /data/ome/CHOBI_d3d.dv:
[testng] [2024-07-14 01:24:17,227] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.j2k:
[testng] [2024-07-14 01:24:17,247] [pool-1-thread-8] Initializing /data/openjpeg/Facade.pnm:
[testng] [2024-07-14 01:24:17,311] [pool-1-thread-2] Initializing /data/ome/C1lowmusgfp.lsm:
[testng] [2024-07-14 01:24:17,331] [pool-1-thread-9] Initializing /data/ome/n2_plate18_P24_w1.tif:
[testng] [2024-07-14 01:24:17,433] [pool-1-thread-1] Initializing /data/openjpeg/Rome.bmp:
[testng] [2024-07-14 01:24:17,539] [pool-1-thread-11] Initializing /data/openjpeg/Rome.jp2:
[testng] [2024-07-14 01:24:17,603] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJW.bmp:
[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 19 seconds
Finished: SUCCESS