Started by upstream project "BIOFORMATS-test-repo" build number 239
originally caused by:
Started by upstream project "Trigger" build number 264
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/jenkins16551154142120236969.sh
+ '[' scanr = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_37638_merge_ci -v /uod/idr/repos/curated/scanr:/data -v /uod/idr-scratch/merge-ci/curated/scanr:/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] 03:02:46,875 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 03:02:46,876 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 03:02:46,876 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 03:02:46,877 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 03:02:46,878 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 03:02:46,878 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 03:02:46,878 |-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] 03:02:46,878 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 03:02:46,878 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 03:02:46,879 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 03:02:46,879 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 03:02:46,879 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 03:02:47,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 03:02:47,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 03:02:47,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 03:02:47,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 03:02:47,059 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 03:02:47,059 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 03:02:47,059 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 03:02:47,060 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 03:02:47,060 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 03:02:47,060 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 03:02:47,060 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 182 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-30 03:02:47,069] [main] java.version = 17.0.2
[testng] 03:02:47,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 03:02:47,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:02:47,110 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-30_03-02-47.log]
[testng] 03:02:47,111 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-10-30 03:02:47,113] [main] testng.directory = /data
[testng] [2024-10-30 03:02:47,113] [main] testng.configDirectory = /config
[testng] [2024-10-30 03:02:47,121] [main] testng.multiplier = 1.0
[testng] [2024-10-30 03:02:47,122] [main] testng.in-memory = false
[testng] [2024-10-30 03:02:47,123] [main] testng.allow-missing = false
[testng] [2024-10-30 03:02:47,123] [main] user.language = en
[testng] [2024-10-30 03:02:47,123] [main] user.country = ${user.country}
[testng] [2024-10-30 03:02:47,123] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-10-30 03:07:24,130] [main] ----------------------------------------
[testng] [2024-10-30 03:07:24,130] [main] Total files: 2169
[testng] [2024-10-30 03:07:24,130] [main] Scan time: 277.007 s (127 ms/file)
[testng] [2024-10-30 03:07:24,130] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 17 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-30 03:28:31,526] [pool-1-thread-1] Initializing /data/christian/example/experiment_descriptor.xml:
[testng] 03:28:31,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 03:28:31,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:28:31,528 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-30_03-28-31.log]
[testng] 03:28:31,528 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75e86f38 - End of configuration.
[testng] [2024-10-30 03:28:32,444] [pool-1-thread-12] Initializing /data/gideon/experiment_descriptor.xml:
[testng] 03:28:32,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 03:28:32,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:28:32,446 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-30_03-28-32.log]
[testng] 03:28:32,446 |-INFO in ch.qos.logback.core.sift.SiftProcessor@741703f5 - End of configuration.
[testng] [2024-10-30 03:29:09,760] [pool-1-thread-11] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml:
[testng] 03:29:09,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 03:29:09,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:29:09,762 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-30_03-29-09.log]
[testng] 03:29:09,763 |-INFO in ch.qos.logback.core.sift.SiftProcessor@607f1474 - End of configuration.
[testng] [2024-10-30 03:30:19,100] [pool-1-thread-10] Initializing /data/nadine/experiment_descriptor.xml:
[testng] 03:30:19,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 03:30:19,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:30:19,101 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-30_03-30-19.log]
[testng] 03:30:19,102 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7914afa9 - End of configuration.
[testng] [2024-10-30 03:30:20,629] [pool-1-thread-9] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml:
[testng] 03:30:20,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 03:30:20,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:30:20,630 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-30_03-30-20.log]
[testng] 03:30:20,630 |-INFO in ch.qos.logback.core.sift.SiftProcessor@783b7106 - End of configuration.
[testng] [2024-10-30 03:30:34,225] [pool-1-thread-8] Initializing /data/juergen/Experiment/experiment_descriptor.xml:
[testng] 03:30:34,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 03:30:34,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:30:34,226 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-30_03-30-34.log]
[testng] 03:30:34,227 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c31bd20 - End of configuration.
[testng] [2024-10-30 03:30:36,194] [pool-1-thread-7] Initializing /data/ruben/20100827_004/experiment_descriptor.xml:
[testng] 03:30:36,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 03:30:36,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:30:36,196 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-30_03-30-36.log]
[testng] 03:30:36,196 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43ee698f - End of configuration.
[testng] [2024-10-30 03:32:02,647] [pool-1-thread-6] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml:
[testng] 03:32:02,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 03:32:02,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:32:02,649 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-30_03-32-02.log]
[testng] 03:32:02,650 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22c27c61 - End of configuration.
[testng] [2024-10-30 03:35:22,157] [pool-1-thread-5] Initializing /data/ruben/plate_002/experiment_descriptor.xml:
[testng] 03:35:22,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 03:35:22,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:35:22,158 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-30_03-35-22.log]
[testng] 03:35:22,159 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c0ac1f7 - End of configuration.
[testng] [2024-10-30 03:35:24,708] [pool-1-thread-4] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml:
[testng] 03:35:24,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 03:35:24,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:35:24,709 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-30_03-35-24.log]
[testng] 03:35:24,709 |-INFO in ch.qos.logback.core.sift.SiftProcessor@763c82e3 - End of configuration.
[testng] [2024-10-30 03:35:56,850] [pool-1-thread-3] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml:
[testng] 03:35:56,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 03:35:56,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:35:56,852 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-30_03-35-56.log]
[testng] 03:35:56,852 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b13bd2 - End of configuration.
[testng] [2024-10-30 03:38:59,251] [pool-1-thread-2] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml:
[testng] 03:38:59,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 03:38:59,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:38:59,253 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-30_03-38-59.log]
[testng] 03:38:59,253 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c6dc7be - End of configuration.
[testng] [2024-10-30 03:39:53,751] [pool-1-thread-1] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml:
[testng] [2024-10-30 03:43:32,416] [pool-1-thread-8] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml:
[testng] [2024-10-30 03:44:54,829] [pool-1-thread-10] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml:
[testng] [2024-10-30 03:48:56,475] [pool-1-thread-5] Initializing /data/embl/Maik_001/experiment_descriptor.xml:
[testng] [2024-10-30 03:53:43,885] [pool-1-thread-9] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml:
[testng] 04:54:33,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 04:54:33,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:54:33,123 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-30_04-54-33.log]
[testng] 04:54:33,124 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d994789 - End of configuration.
[testng] 04:55:23,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 04:55:23,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:55:23,174 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-30_04-55-23.log]
[testng] 04:55:23,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e423064 - End of configuration.
[testng] 04:55:55,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 04:55:55,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:55:55,782 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-30_04-55-55.log]
[testng] 04:55:55,783 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55836c3e - End of configuration.
[testng] 04:57:01,531 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 04:57:01,531 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:57:01,532 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-30_04-57-01.log]
[testng] 04:57:01,532 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e213a1c - End of configuration.
[testng] 05:03:12,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 05:03:12,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:03:12,562 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-30_05-03-12.log]
[testng] 05:03:12,563 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d449860 - 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: 120 minutes 30 seconds
Finished: SUCCESS