Started by upstream project "BIOFORMATS-test-repo" build number 297
originally caused by:
Started by upstream project "Trigger" build number 319
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3
[BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins7977345446644909420.sh
+ '[' leica-tcs = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_47046_merge_ci -v /uod/idr/repos/curated/leica-tcs:/data -v /uod/idr-scratch/merge-ci/curated/leica-tcs:/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] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml
[resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.3.8-SNAPSHOT/maven-metadata.xml
[resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml
[resolver:resolve] Resolving artifacts
[resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml
[resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.3.8-SNAPSHOT/maven-metadata.xml
[resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml
compile-tests:
[resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml
[resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.3.8-SNAPSHOT/maven-metadata.xml
[resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml
[resolver:resolve] Resolving artifacts
[resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml
[resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.3.8-SNAPSHOT/maven-metadata.xml
[resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml
[javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test
test-automated:
[testng] File leak detector installed
[testng] 04:47:02,745 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 04:47:02,747 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service.
[testng] 04:47:02,747 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 04:47:02,748 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 04:47:02,748 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 04:47:02,748 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 04:47:02,749 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 04:47:02,749 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 04:47:02,749 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 04:47:02,749 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 04:47:02,749 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 04:47:02,750 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 04:47:02,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 04:47:02,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 04:47:02,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 04:47:02,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 04:47:03,003 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 04:47:03,003 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 04:47:03,003 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 04:47:03,004 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 04:47:03,004 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration.
[testng] 04:47:03,004 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point
[testng] 04:47:03,005 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 256 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-12-24 04:47:03,014] [main] java.version = 1.8.0_342
[testng] 04:47:03,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 04:47:03,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:47:03,062 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-24_04-47-03.log]
[testng] 04:47:03,063 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration.
[testng] [2024-12-24 04:47:03,065] [main] testng.directory = /data
[testng] [2024-12-24 04:47:03,065] [main] testng.configDirectory = /config
[testng] [2024-12-24 04:47:03,077] [main] testng.multiplier = 1.0
[testng] [2024-12-24 04:47:03,077] [main] testng.in-memory = false
[testng] [2024-12-24 04:47:03,077] [main] testng.allow-missing = false
[testng] [2024-12-24 04:47:03,077] [main] user.language = en
[testng] [2024-12-24 04:47:03,077] [main] user.country = ${user.country}
[testng] [2024-12-24 04:47:03,077] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-12-24 04:47:18,490] [main] ----------------------------------------
[testng] [2024-12-24 04:47:18,491] [main] Total files: 944
[testng] [2024-12-24 04:47:18,491] [main] Scan time: 15.413 s (16 ms/file)
[testng] [2024-12-24 04:47:18,491] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 15 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-12-24 04:49:48,419] [pool-1-thread-1] Initializing /data/stjude/Antoday1dblmysglGRP.tif:
[testng] 04:49:48,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 04:49:48,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:49:48,420 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-24_04-49-48.log]
[testng] 04:49:48,421 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e430a34 - End of configuration.
[testng] [2024-12-24 04:49:50,580] [pool-1-thread-12] Initializing /data/brian/Series002_z01.tif:
[testng] 04:49:50,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 04:49:50,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:49:50,581 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-24_04-49-50.log]
[testng] 04:49:50,582 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dbbab47 - End of configuration.
[testng] [2024-12-24 04:49:53,703] [pool-1-thread-11] Initializing /data/brian/Series002_z00_ch00.tif:
[testng] 04:49:53,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 04:49:53,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:49:53,704 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-24_04-49-53.log]
[testng] 04:49:53,704 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ee135bf - End of configuration.
[testng] [2024-12-24 04:49:56,021] [pool-1-thread-10] Initializing /data/primate/Leica_Image.tif:
[testng] 04:49:56,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 04:49:56,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:49:56,022 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-24_04-49-56.log]
[testng] 04:49:56,022 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44bef7c5 - End of configuration.
[testng] [2024-12-24 04:49:58,368] [pool-1-thread-9] Initializing /data/dave/series 35/042911_Series035_t00_z000_ch00.tif:
[testng] 04:49:58,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 04:49:58,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:49:58,369 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-24_04-49-58.log]
[testng] 04:49:58,370 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57e52b6c - End of configuration.
[testng] [2024-12-24 04:51:26,618] [pool-1-thread-8] Initializing /data/stjude/AntoDayzerocy3OVP.tif:
[testng] 04:51:26,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 04:51:26,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:51:26,620 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-24_04-51-26.log]
[testng] 04:51:26,620 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c2eeb8e - End of configuration.
[testng] [2024-12-24 04:51:29,324] [pool-1-thread-7] Initializing /data/stjude/AntoDay4dblmyGRP.tif:
[testng] 04:51:29,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 04:51:29,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:51:29,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-24_04-51-29.log]
[testng] 04:51:29,325 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bc7c04a - End of configuration.
[testng] [2024-12-24 04:51:31,715] [pool-1-thread-6] Initializing /data/stjude/AntoDayzerocy3GRP.tif:
[testng] 04:51:31,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 04:51:31,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:51:31,716 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-24_04-51-31.log]
[testng] 04:51:31,717 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33c5c1b3 - End of configuration.
[testng] [2024-12-24 04:51:34,382] [pool-1-thread-5] Initializing /data/stjude/Antoday1dblcatsglGRP.tif:
[testng] 04:51:34,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 04:51:34,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:51:34,383 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-24_04-51-34.log]
[testng] 04:51:34,383 |-INFO in ch.qos.logback.core.sift.SiftProcessor@424f215f - End of configuration.
[testng] [2024-12-24 04:51:36,801] [pool-1-thread-4] Initializing /data/stjude/AntoDay1dblGRP.tif:
[testng] 04:51:36,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 04:51:36,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:51:36,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-24_04-51-36.log]
[testng] 04:51:36,802 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57f68ed9 - End of configuration.
[testng] [2024-12-24 04:51:39,437] [pool-1-thread-3] Initializing /data/stjude/AntoDay4dblcatdataGRP.tif:
[testng] 04:51:39,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 04:51:39,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:51:39,438 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-24_04-51-39.log]
[testng] 04:51:39,438 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63884e5d - End of configuration.
[testng] [2024-12-24 04:51:42,176] [pool-1-thread-2] Initializing /data/martin/Series028_z00_ch00.tif:
[testng] 04:51:42,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 04:51:42,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:51:42,176 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-24_04-51-42.log]
[testng] 04:51:42,177 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b7b99e9 - End of configuration.
[testng] [2024-12-24 04:52:01,384] [pool-1-thread-10] Initializing /data/stjude/Antoday1dblcat2dataGRP.tif:
[testng] [2024-12-24 04:52:08,957] [pool-1-thread-12] Initializing /data/stjude/AntoDay4dblmy2GRP.tif:
[testng] [2024-12-24 04:52:12,197] [pool-1-thread-7] Initializing /data/stjude/AntoDay1cy3/c01f0001.TIF:
[testng] 06:57:07,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 06:57:07,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:57:07,653 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-24_06-57-07.log]
[testng] 06:57:07,654 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26586b74 - End of configuration.
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 795, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 130 minutes 12 seconds
Finished: SUCCESS