Started by upstream project "BIOFORMATS-test-repo" build number 294
originally caused by:
Started by upstream project "Trigger" build number 313
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/jenkins7088440434091105545.sh
+ '[' bruker = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_46542_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] 12:40:27,564 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 12:40:27,565 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 12:40:27,565 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 12:40:27,566 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 12:40:27,566 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 12:40:27,566 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 12:40:27,567 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 12:40:27,567 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 12:40:27,567 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 12:40:27,568 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 12:40:27,568 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 12:40:27,568 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 12:40:27,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 12:40:27,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 12:40:27,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 12:40:27,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 12:40:27,750 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 12:40:27,750 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 12:40:27,750 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 12:40:27,751 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 12:40:27,751 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 12:40:27,751 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 12:40:27,751 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 184 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-12-18 12:40:27,760] [main] java.version = 17.0.2
[testng] 12:40:27,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 12:40:27,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:40:27,801 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-18_12-40-27.log]
[testng] 12:40:27,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-12-18 12:40:27,804] [main] testng.directory = /data
[testng] [2024-12-18 12:40:27,805] [main] testng.configDirectory = /config
[testng] [2024-12-18 12:40:27,813] [main] testng.multiplier = 1.0
[testng] [2024-12-18 12:40:27,813] [main] testng.in-memory = false
[testng] [2024-12-18 12:40:27,813] [main] testng.allow-missing = false
[testng] [2024-12-18 12:40:27,814] [main] user.language = en
[testng] [2024-12-18 12:40:27,814] [main] user.country = ${user.country}
[testng] [2024-12-18 12:40:27,814] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-12-18 14:12:46,724] [main] ----------------------------------------
[testng] [2024-12-18 14:12:46,724] [main] Total files: 826
[testng] [2024-12-18 14:12:46,724] [main] Scan time: 5538.91 s (6705 ms/file)
[testng] [2024-12-18 14:12:46,724] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 17 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-12-18 14:17:43,476] [pool-1-thread-1] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif:
[testng] 14:17:43,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 14:17:43,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 14:17:43,478 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-18_14-17-43.log]
[testng] 14:17:43,479 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9263f39 - End of configuration.
[testng] [2024-12-18 14:17:49,855] [pool-1-thread-12] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif:
[testng] 14:17:49,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 14:17:49,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 14:17:49,856 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-18_14-17-49.log]
[testng] 14:17:49,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ad238b1 - End of configuration.
[testng] [2024-12-18 14:17:55,963] [pool-1-thread-11] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif:
[testng] 14:17:55,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 14:17:55,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 14:17:55,964 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-18_14-17-55.log]
[testng] 14:17:55,964 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48ba7317 - End of configuration.
[testng] [2024-12-18 14:18:02,217] [pool-1-thread-10] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif:
[testng] 14:18:02,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 14:18:02,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 14:18:02,218 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-18_14-18-02.log]
[testng] 14:18:02,219 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15e80250 - End of configuration.
[testng] [2024-12-18 14:18:08,440] [pool-1-thread-9] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif:
[testng] 14:18:08,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 14:18:08,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 14:18:08,441 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-18_14-18-08.log]
[testng] 14:18:08,441 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51a15d4a - End of configuration.
[testng] [2024-12-18 14:18:14,691] [pool-1-thread-8] Initializing /data/wis/RA_060110.051/1/acqp:
[testng] 14:18:14,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 14:18:14,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 14:18:14,692 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-18_14-18-14.log]
[testng] 14:18:14,692 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c91519d - End of configuration.
[testng] [2024-12-18 14:18:36,421] [pool-1-thread-7] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif:
[testng] 14:18:36,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 14:18:36,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 14:18:36,423 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-18_14-18-36.log]
[testng] 14:18:36,423 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d2a3847 - End of configuration.
[testng] [2024-12-18 14:18:45,796] [pool-1-thread-6] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif:
[testng] 14:18:45,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 14:18:45,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 14:18:45,797 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-18_14-18-45.log]
[testng] 14:18:45,797 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68b54c21 - End of configuration.
[testng] [2024-12-18 14:18:53,937] [pool-1-thread-5] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif:
[testng] 14:18:53,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 14:18:53,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 14:18:53,938 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-18_14-18-53.log]
[testng] 14:18:53,938 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ed01331 - End of configuration.
[testng] [2024-12-18 14:19:01,928] [pool-1-thread-4] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif:
[testng] 14:19:01,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 14:19:01,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 14:19:01,929 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-18_14-19-01.log]
[testng] 14:19:01,929 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69ed8a3f - End of configuration.
[testng] [2024-12-18 14:19:11,419] [pool-1-thread-3] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif:
[testng] 14:19:11,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 14:19:11,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 14:19:11,420 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-18_14-19-11.log]
[testng] 14:19:11,420 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38a39334 - End of configuration.
[testng] [2024-12-18 14:19:22,190] [pool-1-thread-2] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif:
[testng] 14:19:22,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 14:19:22,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 14:19:22,191 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-18_14-19-22.log]
[testng] 14:19:22,191 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37c15a9f - End of configuration.
[testng] [2024-12-18 14:20:16,636] [pool-1-thread-6] Initializing /data/wis/RA_240912_m1.g71/1/acqp:
[testng] [2024-12-18 14:20:31,425] [pool-1-thread-11] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif:
[testng] [2024-12-18 14:20:35,608] [pool-1-thread-1] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif:
[testng] [2024-12-18 14:20:39,497] [pool-1-thread-2] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif:
[testng] [2024-12-18 14:20:44,991] [pool-1-thread-12] Initializing /data/samples/dimension-mismatch/1/acqp:
[testng] 15:25:30,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 15:25:30,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 15:25:30,222 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-18_15-25-30.log]
[testng] 15:25:30,223 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71522fb7 - End of configuration.
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 901, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 165 minutes 16 seconds
Finished: SUCCESS