Started by upstream project "BIOFORMATS-test-repo" build number 6
originally caused by:
Started by upstream project "Trigger" build number 9
originally caused by:
Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9
[BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins11407892135793880784.sh
+ '[' bruker = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_925_merge_ci -v /uod/idr/repos/curated/bruker:/data -v /uod/idr-scratch/merge-ci/curated/bruker:/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] 11:29:20,164 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 11:29:20,165 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 11:29:20,165 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 11:29:20,166 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 11:29:20,167 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 11:29:20,167 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 11:29:20,167 |-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] 11:29:20,167 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 11:29:20,168 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 11:29:20,168 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 11:29:20,168 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 11:29:20,169 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 11:29:20,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 11:29:20,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 11:29:20,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 11:29:20,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 11:29:20,364 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 11:29:20,365 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 11:29:20,365 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 11:29:20,365 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 11:29:20,365 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 11:29:20,366 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 11:29:20,366 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 198 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-03-20 11:29:20,375] [main] java.version = 17.0.2
[testng] 11:29:20,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 11:29:20,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:29:20,419 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-20_11-29-20.log]
[testng] 11:29:20,420 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-03-20 11:29:20,422] [main] testng.directory = /data
[testng] [2024-03-20 11:29:20,422] [main] testng.configDirectory = /config
[testng] [2024-03-20 11:29:20,431] [main] testng.multiplier = 1.0
[testng] [2024-03-20 11:29:20,432] [main] testng.in-memory = false
[testng] [2024-03-20 11:29:20,432] [main] testng.allow-missing = false
[testng] [2024-03-20 11:29:20,432] [main] user.language = en
[testng] [2024-03-20 11:29:20,432] [main] user.country = ${user.country}
[testng] [2024-03-20 11:29:20,432] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-03-20 11:36:13,851] [main] ----------------------------------------
[testng] [2024-03-20 11:36:13,851] [main] Total files: 826
[testng] [2024-03-20 11:36:13,851] [main] Scan time: 413.419 s (500 ms/file)
[testng] [2024-03-20 11:36:13,852] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 17 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-03-20 11:36:28,714] [pool-1-thread-1] Initializing /data/wis/RA_240912_m1.g71/1/acqp:
[testng] 11:36:28,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 11:36:28,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:36:28,715 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-20_11-36-28.log]
[testng] 11:36:28,716 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66f49960 - End of configuration.
[testng] [2024-03-20 11:36:29,686] [pool-1-thread-12] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif:
[testng] 11:36:29,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 11:36:29,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:36:29,687 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-20_11-36-29.log]
[testng] 11:36:29,688 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4eec66e8 - End of configuration.
[testng] [2024-03-20 11:36:29,985] [pool-1-thread-11] Initializing /data/wis/RA_060110.051/1/acqp:
[testng] 11:36:29,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 11:36:29,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:36:29,986 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-20_11-36-29.log]
[testng] 11:36:29,986 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c31bd20 - End of configuration.
[testng] [2024-03-20 11:36:30,702] [pool-1-thread-10] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif:
[testng] 11:36:30,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 11:36:30,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:36:30,703 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-20_11-36-30.log]
[testng] 11:36:30,703 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43ee698f - End of configuration.
[testng] [2024-03-20 11:36:31,013] [pool-1-thread-9] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif:
[testng] 11:36:31,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 11:36:31,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:36:31,013 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-20_11-36-31.log]
[testng] 11:36:31,014 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22c27c61 - End of configuration.
[testng] [2024-03-20 11:36:31,295] [pool-1-thread-8] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif:
[testng] 11:36:31,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 11:36:31,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:36:31,296 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-20_11-36-31.log]
[testng] 11:36:31,296 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14905b4d - End of configuration.
[testng] [2024-03-20 11:36:31,573] [pool-1-thread-7] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif:
[testng] 11:36:31,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 11:36:31,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:36:31,574 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-20_11-36-31.log]
[testng] 11:36:31,575 |-INFO in ch.qos.logback.core.sift.SiftProcessor@612dbea7 - End of configuration.
[testng] [2024-03-20 11:36:31,875] [pool-1-thread-6] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif:
[testng] 11:36:31,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 11:36:31,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:36:31,876 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-20_11-36-31.log]
[testng] 11:36:31,877 |-INFO in ch.qos.logback.core.sift.SiftProcessor@443e61b1 - End of configuration.
[testng] [2024-03-20 11:36:32,141] [pool-1-thread-5] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif:
[testng] 11:36:32,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 11:36:32,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:36:32,142 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-20_11-36-32.log]
[testng] 11:36:32,142 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40fc9a9e - End of configuration.
[testng] [2024-03-20 11:36:32,469] [pool-1-thread-4] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif:
[testng] 11:36:32,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 11:36:32,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:36:32,470 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-20_11-36-32.log]
[testng] 11:36:32,470 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32bfee9e - End of configuration.
[testng] [2024-03-20 11:36:32,758] [pool-1-thread-3] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif:
[testng] 11:36:32,758 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 11:36:32,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:36:32,759 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-20_11-36-32.log]
[testng] 11:36:32,759 |-INFO in ch.qos.logback.core.sift.SiftProcessor@324ed183 - End of configuration.
[testng] [2024-03-20 11:36:33,049] [pool-1-thread-2] Initializing /data/samples/dimension-mismatch/1/acqp:
[testng] 11:36:33,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 11:36:33,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:36:33,050 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-20_11-36-33.log]
[testng] 11:36:33,050 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49b5e6bb - End of configuration.
[testng] [2024-03-20 11:36:37,764] [pool-1-thread-4] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif:
[testng] [2024-03-20 11:36:38,127] [pool-1-thread-5] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif:
[testng] [2024-03-20 11:36:38,521] [pool-1-thread-6] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif:
[testng] [2024-03-20 11:36:38,887] [pool-1-thread-3] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif:
[testng] [2024-03-20 11:36:39,250] [pool-1-thread-9] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 901, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 9 minutes 42 seconds
Finished: SUCCESS