Started by upstream project "BIOFORMATS-test-repo" build number 192
originally caused by:
Started by upstream project "Trigger" build number 214
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3
[BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins7473697409182679623.sh
+ '[' samples = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_30350_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] 01:27:31,380 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:27:31,381 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 01:27:31,381 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:27:31,382 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:27:31,382 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:27:31,382 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:27:31,383 |-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] 01:27:31,383 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:27:31,383 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:27:31,384 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:27:31,384 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:27:31,384 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:27:31,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:27:31,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:27:31,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:27:31,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:27:31,610 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:27:31,610 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:27:31,610 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:27:31,611 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:27:31,611 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 01:27:31,612 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 01:27:31,613 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 230 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-09-18 01:27:31,627] [main] java.version = 17.0.2
[testng] 01:27:31,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:27:31,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:31,693 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-18_01-27-31.log]
[testng] 01:27:31,695 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-09-18 01:27:31,699] [main] testng.directory = /data
[testng] [2024-09-18 01:27:31,699] [main] testng.configDirectory = /config
[testng] [2024-09-18 01:27:31,715] [main] testng.multiplier = 1.0
[testng] [2024-09-18 01:27:31,717] [main] testng.in-memory = false
[testng] [2024-09-18 01:27:31,717] [main] testng.allow-missing = false
[testng] [2024-09-18 01:27:31,717] [main] user.language = en
[testng] [2024-09-18 01:27:31,717] [main] user.country = ${user.country}
[testng] [2024-09-18 01:27:31,717] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-09-18 01:27:51,991] [main] ----------------------------------------
[testng] [2024-09-18 01:27:51,991] [main] Total files: 164
[testng] [2024-09-18 01:27:51,991] [main] Scan time: 20.273 s (123 ms/file)
[testng] [2024-09-18 01:27:51,991] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 59 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-09-18 01:28:09,016] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF:
[testng] 01:28:09,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:28:09,017 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:09,018 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-18_01-28-09.log]
[testng] 01:28:09,018 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69c33288 - End of configuration.
[testng] [2024-09-18 01:28:09,078] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.jp2:
[testng] 01:28:09,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:28:09,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:09,079 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-18_01-28-09.log]
[testng] 01:28:09,080 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f24812e - End of configuration.
[testng] [2024-09-18 01:28:09,100] [pool-1-thread-11] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK:
[testng] 01:28:09,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:28:09,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:09,101 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-18_01-28-09.log]
[testng] 01:28:09,101 |-INFO in ch.qos.logback.core.sift.SiftProcessor@146172ae - End of configuration.
[testng] [2024-09-18 01:28:09,169] [pool-1-thread-10] Initializing /data/ome/t1_pos1-0_5x.lsm:
[testng] 01:28:09,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:28:09,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:09,171 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-18_01-28-09.log]
[testng] 01:28:09,171 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62b3fb32 - End of configuration.
[testng] [2024-09-18 01:28:09,228] [pool-1-thread-9] Initializing /data/ome/210502-0min-NFKB-4.r3d:
[testng] 01:28:09,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:28:09,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:09,229 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-18_01-28-09.log]
[testng] 01:28:09,229 |-INFO in ch.qos.logback.core.sift.SiftProcessor@980f9fe - End of configuration.
[testng] [2024-09-18 01:28:09,254] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes1.jpg:
[testng] 01:28:09,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:28:09,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:09,256 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-18_01-28-09.log]
[testng] 01:28:09,257 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3646ac05 - End of configuration.
[testng] [2024-09-18 01:28:09,274] [pool-1-thread-7] Initializing /data/openjpeg/Facade.bmp:
[testng] 01:28:09,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:28:09,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:09,276 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-18_01-28-09.log]
[testng] 01:28:09,276 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d17ee21 - End of configuration.
[testng] [2024-09-18 01:28:09,289] [pool-1-thread-6] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF:
[testng] 01:28:09,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:28:09,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:09,290 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-18_01-28-09.log]
[testng] 01:28:09,290 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cf72a04 - End of configuration.
[testng] [2024-09-18 01:28:09,367] [pool-1-thread-5] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK:
[testng] 01:28:09,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:28:09,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:09,368 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-18_01-28-09.log]
[testng] 01:28:09,368 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56eaf0e1 - End of configuration.
[testng] [2024-09-18 01:28:09,499] [pool-1-thread-4] Initializing /data/ome/Adultmidsection.lsm:
[testng] 01:28:09,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:28:09,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:09,509 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-18_01-28-09.log]
[testng] 01:28:09,510 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27fd28d2 - End of configuration.
[testng] [2024-09-18 01:28:09,550] [pool-1-thread-3] Initializing /data/ome/worm.tiff:
[testng] 01:28:09,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:28:09,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:09,551 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-18_01-28-09.log]
[testng] 01:28:09,552 |-INFO in ch.qos.logback.core.sift.SiftProcessor@745207ca - End of configuration.
[testng] [2024-09-18 01:28:09,606] [pool-1-thread-2] Initializing /data/ome/cb_1.r3d:
[testng] 01:28:09,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:28:09,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:09,606 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-18_01-28-09.log]
[testng] 01:28:09,607 |-INFO in ch.qos.logback.core.sift.SiftProcessor@121bc3d8 - End of configuration.
[testng] [2024-09-18 01:28:10,906] [pool-1-thread-8] Initializing /data/openjpeg/Rome.ppm:
[testng] [2024-09-18 01:28:11,290] [pool-1-thread-11] Initializing /data/ome/n2_plate18_P24_w1.tif:
[testng] [2024-09-18 01:28:11,385] [pool-1-thread-4] Initializing /data/openjpeg/Rome.jp2:
[testng] [2024-09-18 01:28:11,485] [pool-1-thread-8] Initializing /data/ome/tiffany.color.tiff:
[testng] [2024-09-18 01:28:11,979] [pool-1-thread-2] Initializing /data/openjpeg/FacadeERROPJW.bmp:
[testng] [2024-09-18 01:28:11,994] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.ppm:
[testng] [2024-09-18 01:28:12,002] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.ppm:
[testng] [2024-09-18 01:28:12,013] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF:
[testng] [2024-09-18 01:28:12,112] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm:
[testng] [2024-09-18 01:28:12,222] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Bretagne1.jpg:
[testng] [2024-09-18 01:28:12,490] [pool-1-thread-3] Initializing /data/ome/embryo.lsm:
[testng] [2024-09-18 01:28:12,714] [pool-1-thread-7] Initializing /data/ome/anusgfpzs.lsm:
[testng] [2024-09-18 01:28:12,756] [pool-1-thread-6] Initializing /data/openjpeg/Rome.bmp:
[testng] [2024-09-18 01:28:12,771] [pool-1-thread-10] Initializing /data/ome/654Atemp.stk:
[testng] [2024-09-18 01:28:12,947] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.bmp:
[testng] [2024-09-18 01:28:12,976] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Speedway.jpg:
[testng] [2024-09-18 01:28:13,100] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Rome.jpg:
[testng] [2024-09-18 01:28:13,282] [pool-1-thread-8] Initializing /data/ome/Cmidmusgfp1.lsm:
[testng] [2024-09-18 01:28:13,339] [pool-1-thread-1] Initializing /data/ome/CHOBI_d3d.dv:
[testng] [2024-09-18 01:28:13,464] [pool-1-thread-12] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg:
[testng] [2024-09-18 01:28:13,476] [pool-1-thread-3] Initializing /data/ome/C1midmusnorm.lsm:
[testng] [2024-09-18 01:28:13,546] [pool-1-thread-11] Initializing /data/ome/arwen0205_raw00201.pic:
[testng] [2024-09-18 01:28:13,596] [pool-1-thread-6] Initializing /data/TAABA/TAABA.pattern:
[testng] [2024-09-18 01:28:16,845] [pool-1-thread-7] Initializing /data/ome/t0_pos1-0_5x.lsm:
[testng] [2024-09-18 01:28:17,009] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.bmp:
[testng] [2024-09-18 01:28:17,028] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne1.ppm:
[testng] [2024-09-18 01:28:17,119] [pool-1-thread-8] Initializing /data/openjpeg/Facade.pnm:
[testng] [2024-09-18 01:28:17,128] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJ.bmp:
[testng] [2024-09-18 01:28:17,202] [pool-1-thread-1] Initializing /data/ome/011B1_Morph.HTD:
[testng] [2024-09-18 01:28:17,843] [pool-1-thread-3] Initializing /data/ome/C1.lsm:
[testng] [2024-09-18 01:28:17,964] [pool-1-thread-10] Initializing /data/mouse-kidney/mouse-kidney.lif:
[testng] [2024-09-18 01:28:18,074] [pool-1-thread-5] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk:
[testng] [2024-09-18 01:28:18,240] [pool-1-thread-9] Initializing /data/ome/compressed2ChZ.lsm:
[testng] [2024-09-18 01:28:18,280] [pool-1-thread-2] Initializing /data/openjpeg/thumb_facade.jpg:
[testng] [2024-09-18 01:28:18,510] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.j2k:
[testng] [2024-09-18 01:28:18,572] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Cevennes2.jpg:
[testng] [2024-09-18 01:28:18,642] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.bmp:
[testng] [2024-09-18 01:28:18,742] [pool-1-thread-7] Initializing /data/kidney_TFl/kidney_TFl.pattern:
[testng] [2024-09-18 01:28:18,965] [pool-1-thread-3] Initializing /data/ome/tinyTest.d3d.dv:
[testng] [2024-09-18 01:28:19,024] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne2.j2k:
[testng] [2024-09-18 01:28:19,122] [pool-1-thread-8] Initializing /data/10-31 E1/10-31 E1.tif:
[testng] [2024-09-18 01:28:19,424] [pool-1-thread-11] Initializing /data/ome/Cpharynxzs1.lsm:
[testng] [2024-09-18 01:28:19,505] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Bretagne2.jpg:
[testng] [2024-09-18 01:28:19,611] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.j2k:
[testng] [2024-09-18 01:28:19,677] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.ppm:
[testng] [2024-09-18 01:28:19,820] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.bmp:
[testng] [2024-09-18 01:28:20,407] [pool-1-thread-11] 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: 2 minutes 22 seconds
Finished: SUCCESS