Started by upstream project "BIOFORMATS-test-repo" build number 266
originally caused by:
Started by upstream project "Trigger" build number 289
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder
[BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins5860434690411869223.sh
+ '[' cellomics = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_42044_merge_ci -v /uod/idr/repos/curated/cellomics:/data -v /uod/idr-scratch/merge-ci/curated/cellomics:/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] 03:37:43,968 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 03:37:43,970 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 03:37:43,970 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 03:37:43,971 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 03:37:43,971 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 03:37:43,971 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 03:37:43,971 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 03:37:43,971 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 03:37:43,972 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 03:37:43,972 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 03:37:43,973 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 03:37:43,973 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 03:37:44,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 03:37:44,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 03:37:44,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 03:37:44,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 03:37:44,150 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 03:37:44,151 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 03:37:44,151 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 03:37:44,151 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 03:37:44,151 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 03:37:44,152 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 03:37:44,152 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 180 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-24 03:37:44,160] [main] java.version = 17.0.2
[testng] 03:37:44,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 03:37:44,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:37:44,201 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-24_03-37-44.log]
[testng] 03:37:44,202 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-11-24 03:37:44,204] [main] testng.directory = /data
[testng] [2024-11-24 03:37:44,204] [main] testng.configDirectory = /config
[testng] [2024-11-24 03:37:44,212] [main] testng.multiplier = 1.0
[testng] [2024-11-24 03:37:44,213] [main] testng.in-memory = false
[testng] [2024-11-24 03:37:44,213] [main] testng.allow-missing = false
[testng] [2024-11-24 03:37:44,213] [main] user.language = en
[testng] [2024-11-24 03:37:44,214] [main] user.country = ${user.country}
[testng] [2024-11-24 03:37:44,214] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-11-24 03:38:08,573] [main] ----------------------------------------
[testng] [2024-11-24 03:38:08,573] [main] Total files: 2539
[testng] [2024-11-24 03:38:08,574] [main] Scan time: 24.359 s (9 ms/file)
[testng] [2024-11-24 03:38:08,574] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 17 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-24 03:38:29,874] [pool-1-thread-1] Initializing /data/samples/sparse-plate/plate_E03f00d0.C01:
[testng] 03:38:29,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 03:38:29,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:38:29,877 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-24_03-38-29.log]
[testng] 03:38:29,877 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e6aeca7 - End of configuration.
[testng] [2024-11-24 03:38:30,179] [pool-1-thread-12] Initializing /data/samples/plate-size/plate_B03f00d0.C01:
[testng] 03:38:30,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 03:38:30,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:38:30,180 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-24_03-38-30.log]
[testng] 03:38:30,180 |-INFO in ch.qos.logback.core.sift.SiftProcessor@308ac299 - End of configuration.
[testng] [2024-11-24 03:38:30,479] [pool-1-thread-11] Initializing /data/omar/FB03f03o2.DIB:
[testng] 03:38:30,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 03:38:30,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:38:30,480 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-24_03-38-30.log]
[testng] 03:38:30,480 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68a111ae - End of configuration.
[testng] [2024-11-24 03:38:30,768] [pool-1-thread-10] Initializing /data/omar/FB03f00o2.C01:
[testng] 03:38:30,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 03:38:30,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:38:30,769 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-24_03-38-30.log]
[testng] 03:38:30,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d726947 - End of configuration.
[testng] [2024-11-24 03:38:31,081] [pool-1-thread-9] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00o1.C01:
[testng] 03:38:31,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 03:38:31,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:38:31,082 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-24_03-38-31.log]
[testng] 03:38:31,082 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13781e7 - End of configuration.
[testng] [2024-11-24 03:38:31,437] [pool-1-thread-8] Initializing /data/harri/MFGTMP-PC_111018140003/MFGTMP-PC_111018140003_E04f00d0.C01:
[testng] 03:38:31,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 03:38:31,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:38:31,438 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-24_03-38-31.log]
[testng] 03:38:31,438 |-INFO in ch.qos.logback.core.sift.SiftProcessor@629fa43d - End of configuration.
[testng] [2024-11-24 03:38:31,792] [pool-1-thread-7] Initializing /data/lee/AS_09125_050116030001_D03f00d0.DIB:
[testng] 03:38:31,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 03:38:31,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:38:31,793 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-24_03-38-31.log]
[testng] 03:38:31,793 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a10c7ca - End of configuration.
[testng] [2024-11-24 03:38:32,080] [pool-1-thread-6] Initializing /data/qa-21720/AS_09125_050117190001_A14f00d0.DIB:
[testng] 03:38:32,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 03:38:32,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:38:32,081 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-24_03-38-32.log]
[testng] 03:38:32,081 |-INFO in ch.qos.logback.core.sift.SiftProcessor@148c9c87 - End of configuration.
[testng] [2024-11-24 03:38:32,382] [pool-1-thread-5] Initializing /data/public/BBBC001/AS_09125_050118150001_A03f00d0.DIB:
[testng] 03:38:32,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 03:38:32,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:38:32,383 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-24_03-38-32.log]
[testng] 03:38:32,383 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27c23bfe - End of configuration.
[testng] [2024-11-24 03:38:32,690] [pool-1-thread-4] Initializing /data/johannes/MFGTMP_081222130005_E07f00d0.C01:
[testng] 03:38:32,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 03:38:32,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:38:32,691 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-24_03-38-32.log]
[testng] 03:38:32,692 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3424afd6 - End of configuration.
[testng] [2024-11-24 03:38:33,002] [pool-1-thread-3] Initializing /data/lee/icd002235_090127090001_a01f00d1.c01:
[testng] 03:38:33,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 03:38:33,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:38:33,003 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-24_03-38-33.log]
[testng] 03:38:33,004 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32f18ab0 - End of configuration.
[testng] [2024-11-24 03:38:33,310] [pool-1-thread-2] Initializing /data/omar/FB03f00d0.C01:
[testng] 03:38:33,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 03:38:33,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:38:33,311 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-24_03-38-33.log]
[testng] 03:38:33,312 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7932e1ab - End of configuration.
[testng] [2024-11-24 03:38:37,468] [pool-1-thread-7] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00d0.C01:
[testng] [2024-11-24 03:38:37,979] [pool-1-thread-11] Initializing /data/samples/different-field-count/plate_B03f00d0.C01:
[testng] [2024-11-24 03:38:40,593] [pool-1-thread-4] Initializing /data/johannes/MFGTMP_081128200001_A02f239d1.C01:
[testng] [2024-11-24 03:38:40,984] [pool-1-thread-3] Initializing /data/omar/FB03f00d1.C01:
[testng] [2024-11-24 03:38:41,389] [pool-1-thread-10] Initializing /data/omar/FB03f00o1.C01:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 901, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 34 minutes 59 seconds
Finished: SUCCESS