Started by upstream project "BIOFORMATS-test-repo" build number 81
originally caused by:
Started by upstream project "Trigger" build number 89
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8
[BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins1871346196122458917.sh
+ '[' bruker = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_12408_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] WARNING: An illegal reflective access operation has occurred
[testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket
[testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener
[testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
[testng] WARNING: All illegal access operations will be denied in a future release
[testng] File leak detector installed
[testng] 02:32:46,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:32:46,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:32:46,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:32:46,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:32:46,623 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:32:46,623 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:32:46,623 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:32:46,624 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:32:46,624 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@41a0aa7d - End of configuration.
[testng] 02:32:46,639 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6574a52c - Registering current configuration as safe fallback point
[testng] 02:32:46,639 |-INFO in ch.qos.logback.classic.util.ContextInitializer@6c1a5b54 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 704 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-01 02:32:46,659] [main] java.version = 11.0.16
[testng] 02:32:46,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:32:46,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:32:46,821 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-01_02-32-46.log]
[testng] 02:32:46,823 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-06-01 02:32:46,836] [main] testng.directory = /data
[testng] [2024-06-01 02:32:46,836] [main] testng.configDirectory = /config
[testng] [2024-06-01 02:32:46,971] [main] testng.multiplier = 1.0
[testng] [2024-06-01 02:32:46,974] [main] testng.in-memory = false
[testng] [2024-06-01 02:32:46,974] [main] testng.allow-missing = false
[testng] [2024-06-01 02:32:46,975] [main] user.language = en
[testng] [2024-06-01 02:32:46,975] [main] user.country = ${user.country}
[testng] [2024-06-01 02:32:46,975] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-06-01 02:33:35,372] [main] ----------------------------------------
[testng] [2024-06-01 02:33:35,372] [main] Total files: 826
[testng] [2024-06-01 02:33:35,373] [main] Scan time: 48.397 s (58 ms/file)
[testng] [2024-06-01 02:33:35,373] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 17 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-01 02:33:39,023] [pool-1-thread-1] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif:
[testng] 02:33:39,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:33:39,024 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:39,025 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-01_02-33-39.log]
[testng] 02:33:39,026 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a7f343a - End of configuration.
[testng] [2024-06-01 02:33:39,144] [pool-1-thread-12] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif:
[testng] 02:33:39,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:33:39,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:39,146 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-01_02-33-39.log]
[testng] 02:33:39,146 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e4576c0 - End of configuration.
[testng] [2024-06-01 02:33:39,250] [pool-1-thread-11] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif:
[testng] 02:33:39,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:33:39,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:39,261 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-01_02-33-39.log]
[testng] 02:33:39,262 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ccb31f1 - End of configuration.
[testng] [2024-06-01 02:33:39,391] [pool-1-thread-10] Initializing /data/wis/RA_240912_m1.g71/1/acqp:
[testng] 02:33:39,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:33:39,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:39,393 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-01_02-33-39.log]
[testng] 02:33:39,394 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2aee526f - End of configuration.
[testng] [2024-06-01 02:33:39,685] [pool-1-thread-9] Initializing /data/samples/dimension-mismatch/1/acqp:
[testng] 02:33:39,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:33:39,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:39,687 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-01_02-33-39.log]
[testng] 02:33:39,688 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d98bd7e - End of configuration.
[testng] [2024-06-01 02:33:39,730] [pool-1-thread-8] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif:
[testng] 02:33:39,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:33:39,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:39,731 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-01_02-33-39.log]
[testng] 02:33:39,732 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10ec712d - End of configuration.
[testng] [2024-06-01 02:33:39,814] [pool-1-thread-7] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif:
[testng] 02:33:39,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:33:39,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:39,815 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-01_02-33-39.log]
[testng] 02:33:39,816 |-INFO in ch.qos.logback.core.sift.SiftProcessor@764513e5 - End of configuration.
[testng] [2024-06-01 02:33:39,878] [pool-1-thread-6] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif:
[testng] 02:33:39,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:33:39,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:39,880 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-01_02-33-39.log]
[testng] 02:33:39,880 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f648f92 - End of configuration.
[testng] [2024-06-01 02:33:40,017] [pool-1-thread-5] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif:
[testng] 02:33:40,017 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:33:40,017 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:40,018 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-01_02-33-40.log]
[testng] 02:33:40,019 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2473ee6e - End of configuration.
[testng] [2024-06-01 02:33:40,068] [pool-1-thread-4] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif:
[testng] 02:33:40,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:33:40,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:40,069 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-01_02-33-40.log]
[testng] 02:33:40,070 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4eb25d8b - End of configuration.
[testng] [2024-06-01 02:33:40,128] [pool-1-thread-3] Initializing /data/wis/RA_060110.051/1/acqp:
[testng] 02:33:40,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:33:40,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:40,129 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-01_02-33-40.log]
[testng] 02:33:40,130 |-INFO in ch.qos.logback.core.sift.SiftProcessor@459a1ca - End of configuration.
[testng] [2024-06-01 02:33:40,231] [pool-1-thread-2] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif:
[testng] 02:33:40,231 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:33:40,231 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:40,232 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-01_02-33-40.log]
[testng] 02:33:40,233 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bf2783e - End of configuration.
[testng] [2024-06-01 02:33:44,744] [pool-1-thread-11] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif:
[testng] [2024-06-01 02:33:44,815] [pool-1-thread-7] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif:
[testng] [2024-06-01 02:33:44,887] [pool-1-thread-1] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif:
[testng] [2024-06-01 02:33:44,969] [pool-1-thread-6] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif:
[testng] [2024-06-01 02:33:45,043] [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: 1 minute 29 seconds
Finished: SUCCESS