Started by upstream project "BIOFORMATS-test-repo" build number 263
originally caused by:
Started by user devspace
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/jenkins4119138458148580906.sh
+ '[' analyze = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_41561_merge_ci -v /uod/idr/repos/curated/analyze:/data -v /uod/idr-scratch/merge-ci/curated/analyze:/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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release
[javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
[javac] 4 warnings
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] 18:30:13,190 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 18:30:13,192 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service.
[testng] 18:30:13,192 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 18:30:13,193 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 18:30:13,193 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 18:30:13,194 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 18:30:13,194 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 18:30:13,194 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 18:30:13,194 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 18:30:13,195 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 18:30:13,195 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 18:30:13,196 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 18:30:13,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 18:30:13,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 18:30:13,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 18:30:13,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 18:30:13,392 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 18:30:13,392 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 18:30:13,392 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 18:30:13,393 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 18:30:13,393 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration.
[testng] 18:30:13,393 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point
[testng] 18:30:13,394 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 200 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-21 18:30:13,403] [main] java.version = 21
[testng] 18:30:13,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 18:30:13,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 18:30:13,448 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-21_18-30-13.log]
[testng] 18:30:13,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration.
[testng] [2024-11-21 18:30:13,451] [main] testng.directory = /data
[testng] [2024-11-21 18:30:13,452] [main] testng.configDirectory = /config
[testng] [2024-11-21 18:30:13,461] [main] testng.multiplier = 1.0
[testng] [2024-11-21 18:30:13,461] [main] testng.in-memory = false
[testng] [2024-11-21 18:30:13,461] [main] testng.allow-missing = false
[testng] [2024-11-21 18:30:13,461] [main] user.language = en
[testng] [2024-11-21 18:30:13,461] [main] user.country = ${user.country}
[testng] [2024-11-21 18:30:13,461] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-11-21 18:30:30,766] [main] ----------------------------------------
[testng] [2024-11-21 18:30:30,766] [main] Total files: 21
[testng] [2024-11-21 18:30:30,766] [main] Scan time: 17.305 s (824 ms/file)
[testng] [2024-11-21 18:30:30,766] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 21 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-21 18:30:51,168] [pool-1-thread-1] Initializing /data/frans/CT_CHEST.hdr:
[testng] 18:30:51,168 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 18:30:51,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 18:30:51,170 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-21_18-30-51.log]
[testng] 18:30:51,170 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c7fb67c - End of configuration.
[testng] [2024-11-21 18:30:52,077] [pool-1-thread-12] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr:
[testng] 18:30:52,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 18:30:52,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 18:30:52,079 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-21_18-30-52.log]
[testng] 18:30:52,079 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e1f4f9f - End of configuration.
[testng] [2024-11-21 18:30:52,976] [pool-1-thread-11] Initializing /data/frans/brodmann.hdr:
[testng] 18:30:52,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 18:30:52,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 18:30:52,978 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-21_18-30-52.log]
[testng] 18:30:52,978 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61c5e6fa - End of configuration.
[testng] [2024-11-21 18:30:53,917] [pool-1-thread-10] Initializing /data/frans/CT_HAND.hdr:
[testng] 18:30:53,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 18:30:53,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 18:30:53,918 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-21_18-30-53.log]
[testng] 18:30:53,918 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5300cb8d - End of configuration.
[testng] [2024-11-21 18:30:54,794] [pool-1-thread-9] Initializing /data/frans/CT_WHOLE.hdr:
[testng] 18:30:54,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 18:30:54,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 18:30:54,795 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-21_18-30-54.log]
[testng] 18:30:54,795 |-INFO in ch.qos.logback.core.sift.SiftProcessor@378b64e6 - End of configuration.
[testng] [2024-11-21 18:30:55,643] [pool-1-thread-8] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr:
[testng] 18:30:55,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 18:30:55,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 18:30:55,644 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-21_18-30-55.log]
[testng] 18:30:55,644 |-INFO in ch.qos.logback.core.sift.SiftProcessor@729cf4f9 - End of configuration.
[testng] [2024-11-21 18:30:56,574] [pool-1-thread-7] Initializing /data/frans/CT_KNEE.hdr:
[testng] 18:30:56,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 18:30:56,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 18:30:56,575 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-21_18-30-56.log]
[testng] 18:30:56,575 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54efd25b - End of configuration.
[testng] [2024-11-21 18:30:57,505] [pool-1-thread-6] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr:
[testng] 18:30:57,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 18:30:57,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 18:30:57,506 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-21_18-30-57.log]
[testng] 18:30:57,507 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e1ee04e - End of configuration.
[testng] [2024-11-21 18:30:58,460] [pool-1-thread-5] Initializing /data/frans/CT_CRANI.hdr:
[testng] 18:30:58,460 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 18:30:58,460 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 18:30:58,461 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-21_18-30-58.log]
[testng] 18:30:58,462 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4afc8a22 - End of configuration.
[testng] [2024-11-21 18:30:59,410] [pool-1-thread-4] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr:
[testng] 18:30:59,410 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 18:30:59,410 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 18:30:59,411 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-21_18-30-59.log]
[testng] 18:30:59,411 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4addbd91 - End of configuration.
[testng] [2024-11-21 18:31:00,363] [pool-1-thread-3] Initializing /data/frans/betmask.hdr:
[testng] 18:31:00,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 18:31:00,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 18:31:00,364 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-21_18-31-00.log]
[testng] 18:31:00,364 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e3a70f1 - End of configuration.
[testng] [2024-11-21 18:31:01,325] [pool-1-thread-2] Initializing /data/frans/CT_APERT.hdr:
[testng] 18:31:01,326 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 18:31:01,326 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 18:31:01,326 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-21_18-31-01.log]
[testng] 18:31:01,327 |-INFO in ch.qos.logback.core.sift.SiftProcessor@133cfe97 - End of configuration.
[testng] [2024-11-21 18:31:13,793] [pool-1-thread-3] Initializing /data/frans/ch2.hdr:
[testng] [2024-11-21 18:31:14,761] [pool-1-thread-11] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr:
[testng] [2024-11-21 18:31:15,694] [pool-1-thread-6] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr:
[testng] [2024-11-21 18:31:16,625] [pool-1-thread-12] Initializing /data/frans/MR_SEGBRAIN.hdr:
[testng] [2024-11-21 18:31:17,600] [pool-1-thread-4] Initializing /data/frans/ch2bet.hdr:
[testng] [2024-11-21 18:31:18,533] [pool-1-thread-8] Initializing /data/frans/aal.hdr:
[testng] [2024-11-21 18:31:19,640] [pool-1-thread-9] Initializing /data/frans/m000-MR_CHEST.gif:
[testng] [2024-11-21 18:31:19,889] [pool-1-thread-2] Initializing /data/frans/CT_FOOT.hdr:
[testng] [2024-11-21 18:31:21,066] [pool-1-thread-7] Initializing /data/frans/MR_CHEST.hdr:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1113, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 1 minute 20 seconds
Finished: SUCCESS