Started by upstream project "BIOFORMATS-test-repo" build number 255
originally caused by:
Started by upstream project "Trigger" build number 279
originally caused by:
Started by timer
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/jenkins3157738832111806240.sh
+ '[' bruker = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_40271_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 03:23:57,693 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 03:23:57,694 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service.
[testng] 03:23:57,694 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 03:23:57,695 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 03:23:57,695 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 03:23:57,696 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 03:23:57,696 |-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] 03:23:57,696 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 03:23:57,697 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 03:23:57,697 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 03:23:57,697 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 03:23:57,698 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 03:23:57,861 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 03:23:57,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 03:23:57,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 03:23:57,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 03:23:57,894 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 03:23:57,894 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 03:23:57,894 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 03:23:57,894 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 03:23:57,894 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration.
[testng] 03:23:57,895 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point
[testng] 03:23:57,895 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 198 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-14 03:23:57,904] [main] java.version = 21
[testng] 03:23:57,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 03:23:57,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:23:57,949 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-14_03-23-57.log]
[testng] 03:23:57,950 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration.
[testng] [2024-11-14 03:23:57,952] [main] testng.directory = /data
[testng] [2024-11-14 03:23:57,952] [main] testng.configDirectory = /config
[testng] [2024-11-14 03:23:57,961] [main] testng.multiplier = 1.0
[testng] [2024-11-14 03:23:57,961] [main] testng.in-memory = false
[testng] [2024-11-14 03:23:57,961] [main] testng.allow-missing = false
[testng] [2024-11-14 03:23:57,961] [main] user.language = en
[testng] [2024-11-14 03:23:57,961] [main] user.country = ${user.country}
[testng] [2024-11-14 03:23:57,961] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-11-14 03:46:58,224] [main] ----------------------------------------
[testng] [2024-11-14 03:46:58,225] [main] Total files: 826
[testng] [2024-11-14 03:46:58,225] [main] Scan time: 1380.262 s (1671 ms/file)
[testng] [2024-11-14 03:46:58,225] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 17 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-14 03:48:16,706] [pool-1-thread-1] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif:
[testng] 03:48:16,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 03:48:16,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:48:16,708 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-14_03-48-16.log]
[testng] 03:48:16,708 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34e8852 - End of configuration.
[testng] [2024-11-14 03:48:18,571] [pool-1-thread-12] Initializing /data/wis/RA_060110.051/1/acqp:
[testng] 03:48:18,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 03:48:18,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:48:18,572 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-14_03-48-18.log]
[testng] 03:48:18,572 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24fe875f - End of configuration.
[testng] [2024-11-14 03:48:23,128] [pool-1-thread-11] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif:
[testng] 03:48:23,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 03:48:23,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:48:23,129 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-14_03-48-23.log]
[testng] 03:48:23,130 |-INFO in ch.qos.logback.core.sift.SiftProcessor@626501d4 - End of configuration.
[testng] [2024-11-14 03:48:24,980] [pool-1-thread-10] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif:
[testng] 03:48:24,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 03:48:24,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:48:24,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-14_03-48-24.log]
[testng] 03:48:24,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@506be020 - End of configuration.
[testng] [2024-11-14 03:48:26,902] [pool-1-thread-9] Initializing /data/wis/RA_240912_m1.g71/1/acqp:
[testng] 03:48:26,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 03:48:26,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:48:26,903 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-14_03-48-26.log]
[testng] 03:48:26,903 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34cafbb9 - End of configuration.
[testng] [2024-11-14 03:48:32,894] [pool-1-thread-8] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif:
[testng] 03:48:32,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 03:48:32,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:48:32,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-14_03-48-32.log]
[testng] 03:48:32,895 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16b232a9 - End of configuration.
[testng] [2024-11-14 03:48:34,789] [pool-1-thread-7] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif:
[testng] 03:48:34,790 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 03:48:34,790 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:48:34,790 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-14_03-48-34.log]
[testng] 03:48:34,791 |-INFO in ch.qos.logback.core.sift.SiftProcessor@238a7fa3 - End of configuration.
[testng] [2024-11-14 03:48:36,696] [pool-1-thread-6] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif:
[testng] 03:48:36,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 03:48:36,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:48:36,697 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-14_03-48-36.log]
[testng] 03:48:36,698 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b51095e - End of configuration.
[testng] [2024-11-14 03:48:38,542] [pool-1-thread-5] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif:
[testng] 03:48:38,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 03:48:38,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:48:38,543 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-14_03-48-38.log]
[testng] 03:48:38,544 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48e63500 - End of configuration.
[testng] [2024-11-14 03:48:40,316] [pool-1-thread-4] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif:
[testng] 03:48:40,316 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 03:48:40,316 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:48:40,316 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-14_03-48-40.log]
[testng] 03:48:40,317 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d3a9f08 - End of configuration.
[testng] [2024-11-14 03:48:42,103] [pool-1-thread-3] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif:
[testng] 03:48:42,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 03:48:42,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:48:42,104 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-14_03-48-42.log]
[testng] 03:48:42,105 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fbfd071 - End of configuration.
[testng] [2024-11-14 03:48:43,920] [pool-1-thread-2] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif:
[testng] 03:48:43,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 03:48:43,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:48:43,920 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-14_03-48-43.log]
[testng] 03:48:43,921 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c2a1d3c - End of configuration.
[testng] [2024-11-14 03:48:58,534] [pool-1-thread-11] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif:
[testng] [2024-11-14 03:49:00,505] [pool-1-thread-1] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif:
[testng] [2024-11-14 03:49:02,436] [pool-1-thread-10] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif:
[testng] [2024-11-14 03:49:04,437] [pool-1-thread-8] Initializing /data/samples/dimension-mismatch/1/acqp:
[testng] [2024-11-14 03:49:06,610] [pool-1-thread-3] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 901, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 42 minutes 36 seconds
Finished: SUCCESS