Started by upstream project "BIOFORMATS-test-repo" build number 364
originally caused by:
Started by upstream project "Trigger" build number 390
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/jenkins2793230583886106035.sh
+ '[' scanr = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_58089_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] 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] 03:26:52,157 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15
[testng] 03:26:52,159 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service.
[testng] 03:26:52,159 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 03:26:52,160 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 03:26:52,161 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 03:26:52,162 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 03:26:52,162 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 03:26:52,162 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 03:26:52,163 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 03:26:52,164 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 03:26:52,164 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 03:26:52,165 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 03:26:52,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 03:26:52,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 03:26:52,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 03:26:52,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 03:26:52,370 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 03:26:52,370 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 03:26:52,370 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 03:26:52,371 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 03:26:52,371 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration.
[testng] 03:26:52,371 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point
[testng] 03:26:52,372 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 209 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2025-03-04 03:26:52,380] [main] java.version = 11.0.16
[testng] 03:26:52,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 03:26:52,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:26:52,424 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-04_03-26-52.log]
[testng] 03:26:52,425 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration.
[testng] [2025-03-04 03:26:52,427] [main] testng.directory = /data
[testng] [2025-03-04 03:26:52,427] [main] testng.configDirectory = /config
[testng] [2025-03-04 03:26:52,437] [main] testng.multiplier = 1.0
[testng] [2025-03-04 03:26:52,438] [main] testng.in-memory = false
[testng] [2025-03-04 03:26:52,438] [main] testng.allow-missing = false
[testng] [2025-03-04 03:26:52,438] [main] user.language = en
[testng] [2025-03-04 03:26:52,438] [main] user.country = ${user.country}
[testng] [2025-03-04 03:26:52,439] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2025-03-04 03:31:08,343] [main] ----------------------------------------
[testng] [2025-03-04 03:31:08,344] [main] Total files: 2169
[testng] [2025-03-04 03:31:08,344] [main] Scan time: 255.904 s (117 ms/file)
[testng] [2025-03-04 03:31:08,344] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 17 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2025-03-04 03:47:51,553] [pool-1-thread-1] Initializing /data/juergen/Experiment/experiment_descriptor.xml:
[testng] 03:47:51,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 03:47:51,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:47:51,556 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-04_03-47-51.log]
[testng] 03:47:51,557 |-INFO in ch.qos.logback.core.sift.SiftProcessor@420484ef - End of configuration.
[testng] [2025-03-04 03:47:52,079] [pool-1-thread-12] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml:
[testng] 03:47:52,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 03:47:52,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:47:52,081 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-04_03-47-52.log]
[testng] 03:47:52,081 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9fbbe15 - End of configuration.
[testng] [2025-03-04 03:48:48,176] [pool-1-thread-11] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml:
[testng] 03:48:48,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 03:48:48,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:48:48,177 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-04_03-48-48.log]
[testng] 03:48:48,178 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10a9ebb3 - End of configuration.
[testng] [2025-03-04 03:49:29,022] [pool-1-thread-10] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml:
[testng] 03:49:29,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 03:49:29,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:49:29,023 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-04_03-49-29.log]
[testng] 03:49:29,023 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f80ba9b - End of configuration.
[testng] [2025-03-04 03:49:38,571] [pool-1-thread-9] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml:
[testng] 03:49:38,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 03:49:38,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:49:38,572 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-04_03-49-38.log]
[testng] 03:49:38,573 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d167824 - End of configuration.
[testng] [2025-03-04 03:50:16,517] [pool-1-thread-8] Initializing /data/christian/example/experiment_descriptor.xml:
[testng] 03:50:16,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 03:50:16,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:50:16,519 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-04_03-50-16.log]
[testng] 03:50:16,519 |-INFO in ch.qos.logback.core.sift.SiftProcessor@188caed5 - End of configuration.
[testng] [2025-03-04 03:50:17,253] [pool-1-thread-7] Initializing /data/ruben/plate_002/experiment_descriptor.xml:
[testng] 03:50:17,253 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 03:50:17,253 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:50:17,254 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-04_03-50-17.log]
[testng] 03:50:17,254 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dddb586 - End of configuration.
[testng] [2025-03-04 03:50:19,478] [pool-1-thread-6] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml:
[testng] 03:50:19,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 03:50:19,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:50:19,479 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-04_03-50-19.log]
[testng] 03:50:19,479 |-INFO in ch.qos.logback.core.sift.SiftProcessor@604fc004 - End of configuration.
[testng] [2025-03-04 03:50:32,913] [pool-1-thread-5] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml:
[testng] 03:50:32,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 03:50:32,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:50:32,914 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-04_03-50-32.log]
[testng] 03:50:32,914 |-INFO in ch.qos.logback.core.sift.SiftProcessor@635c5e5d - End of configuration.
[testng] [2025-03-04 03:51:13,084] [pool-1-thread-4] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml:
[testng] 03:51:13,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 03:51:13,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:51:13,085 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-04_03-51-13.log]
[testng] 03:51:13,086 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fb86c3a - End of configuration.
[testng] [2025-03-04 03:53:08,521] [pool-1-thread-3] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml:
[testng] 03:53:08,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 03:53:08,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:53:08,523 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-04_03-53-08.log]
[testng] 03:53:08,523 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78759326 - End of configuration.
[testng] [2025-03-04 03:54:44,046] [pool-1-thread-2] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml:
[testng] 03:54:44,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 03:54:44,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:54:44,047 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-04_03-54-44.log]
[testng] 03:54:44,047 |-INFO in ch.qos.logback.core.sift.SiftProcessor@516c0687 - End of configuration.
[testng] [2025-03-04 03:56:33,355] [pool-1-thread-8] Initializing /data/gideon/experiment_descriptor.xml:
[testng] [2025-03-04 03:57:01,657] [pool-1-thread-1] Initializing /data/ruben/20100827_004/experiment_descriptor.xml:
[testng] [2025-03-04 03:59:36,917] [pool-1-thread-7] Initializing /data/nadine/experiment_descriptor.xml:
[testng] [2025-03-04 04:00:11,770] [pool-1-thread-7] Initializing /data/embl/Maik_001/experiment_descriptor.xml:
[testng] [2025-03-04 04:07:15,047] [pool-1-thread-7] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml:
[testng] 05:15:34,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 05:15:34,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:15:34,283 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-04_05-15-34.log]
[testng] 05:15:34,284 |-INFO in ch.qos.logback.core.sift.SiftProcessor@538aa704 - End of configuration.
[testng] 05:15:35,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 05:15:35,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:15:35,819 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-04_05-15-35.log]
[testng] 05:15:35,820 |-INFO in ch.qos.logback.core.sift.SiftProcessor@470faac3 - End of configuration.
[testng] 05:18:59,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 05:18:59,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:18:59,851 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-04_05-18-59.log]
[testng] 05:18:59,851 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a1c257c - End of configuration.
[testng] 05:19:09,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 05:19:09,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:19:09,688 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-04_05-19-09.log]
[testng] 05:19:09,688 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f139c3d - End of configuration.
[testng] 05:25:34,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 05:25:34,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:25:34,225 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-04_05-25-34.log]
[testng] 05:25:34,225 |-INFO in ch.qos.logback.core.sift.SiftProcessor@260754f6 - 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: 118 minutes 45 seconds
Finished: SUCCESS