Started by upstream project "BIOFORMATS-test-repo" build number 83
originally caused by:
Started by upstream project "Trigger" build number 93
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5
[BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins7920306721634123885.sh
+ '[' bruker = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_12736_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] 02:23:33,866 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:23:33,867 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 02:23:33,867 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:23:33,868 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:23:33,869 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:23:33,869 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:23:33,869 |-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] 02:23:33,869 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:23:33,870 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:23:33,870 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:23:33,870 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:23:33,871 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:23:34,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:23:34,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:23:34,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:23:34,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:23:34,210 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:23:34,211 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:23:34,211 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:23:34,212 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:23:34,212 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 02:23:34,215 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 02:23:34,216 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 345 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-05 02:23:34,237] [main] java.version = 17.0.2
[testng] 02:23:34,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:23:34,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:23:34,303 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-05_02-23-34.log]
[testng] 02:23:34,307 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-06-05 02:23:34,311] [main] testng.directory = /data
[testng] [2024-06-05 02:23:34,312] [main] testng.configDirectory = /config
[testng] [2024-06-05 02:23:34,330] [main] testng.multiplier = 1.0
[testng] [2024-06-05 02:23:34,332] [main] testng.in-memory = false
[testng] [2024-06-05 02:23:34,333] [main] testng.allow-missing = false
[testng] [2024-06-05 02:23:34,333] [main] user.language = en
[testng] [2024-06-05 02:23:34,333] [main] user.country = ${user.country}
[testng] [2024-06-05 02:23:34,333] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-06-05 02:24:25,586] [main] ----------------------------------------
[testng] [2024-06-05 02:24:25,586] [main] Total files: 826
[testng] [2024-06-05 02:24:25,587] [main] Scan time: 51.253 s (62 ms/file)
[testng] [2024-06-05 02:24:25,587] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 17 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-05 02:24:28,847] [pool-1-thread-1] Initializing /data/wis/RA_240912_m1.g71/1/acqp:
[testng] 02:24:28,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:24:28,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:24:28,857 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-05_02-24-28.log]
[testng] 02:24:28,858 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2eae290c - End of configuration.
[testng] [2024-06-05 02:24:29,115] [pool-1-thread-12] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif:
[testng] 02:24:29,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:24:29,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:24:29,116 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-05_02-24-29.log]
[testng] 02:24:29,117 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56af8fea - End of configuration.
[testng] [2024-06-05 02:24:29,170] [pool-1-thread-11] Initializing /data/wis/RA_060110.051/1/acqp:
[testng] 02:24:29,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:24:29,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:24:29,171 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-05_02-24-29.log]
[testng] 02:24:29,172 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b531779 - End of configuration.
[testng] [2024-06-05 02:24:29,288] [pool-1-thread-10] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif:
[testng] 02:24:29,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:24:29,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:24:29,290 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-05_02-24-29.log]
[testng] 02:24:29,290 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2bce9cdc - End of configuration.
[testng] [2024-06-05 02:24:29,345] [pool-1-thread-9] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif:
[testng] 02:24:29,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:24:29,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:24:29,346 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-05_02-24-29.log]
[testng] 02:24:29,347 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47e3378c - End of configuration.
[testng] [2024-06-05 02:24:29,393] [pool-1-thread-8] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif:
[testng] 02:24:29,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:24:29,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:24:29,394 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-05_02-24-29.log]
[testng] 02:24:29,394 |-INFO in ch.qos.logback.core.sift.SiftProcessor@160f7ff4 - End of configuration.
[testng] [2024-06-05 02:24:29,430] [pool-1-thread-7] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif:
[testng] 02:24:29,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:24:29,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:24:29,431 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-05_02-24-29.log]
[testng] 02:24:29,431 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32bfee9e - End of configuration.
[testng] [2024-06-05 02:24:29,485] [pool-1-thread-6] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif:
[testng] 02:24:29,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:24:29,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:24:29,487 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-05_02-24-29.log]
[testng] 02:24:29,487 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2551f980 - End of configuration.
[testng] [2024-06-05 02:24:29,532] [pool-1-thread-5] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif:
[testng] 02:24:29,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:24:29,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:24:29,533 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-05_02-24-29.log]
[testng] 02:24:29,534 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c39d611 - End of configuration.
[testng] [2024-06-05 02:24:29,580] [pool-1-thread-4] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif:
[testng] 02:24:29,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:24:29,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:24:29,581 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-05_02-24-29.log]
[testng] 02:24:29,582 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59dea1af - End of configuration.
[testng] [2024-06-05 02:24:29,651] [pool-1-thread-3] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif:
[testng] 02:24:29,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:24:29,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:24:29,653 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-05_02-24-29.log]
[testng] 02:24:29,653 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73486367 - End of configuration.
[testng] [2024-06-05 02:24:29,702] [pool-1-thread-2] Initializing /data/samples/dimension-mismatch/1/acqp:
[testng] 02:24:29,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:24:29,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:24:29,704 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-05_02-24-29.log]
[testng] 02:24:29,704 |-INFO in ch.qos.logback.core.sift.SiftProcessor@771d1763 - End of configuration.
[testng] [2024-06-05 02:24:31,393] [pool-1-thread-2] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif:
[testng] [2024-06-05 02:24:32,117] [pool-1-thread-10] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif:
[testng] [2024-06-05 02:24:32,184] [pool-1-thread-6] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif:
[testng] [2024-06-05 02:24:32,249] [pool-1-thread-3] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif:
[testng] [2024-06-05 02:24:32,303] [pool-1-thread-9] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.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 21 seconds
Finished: SUCCESS