Started by upstream project "BIOFORMATS-test-repo" build number 10
originally caused by:
Started by upstream project "Trigger" build number 13
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/jenkins5915885101858382334.sh
+ '[' biorad-gel = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_1580_merge_ci -v /uod/idr/repos/curated/biorad-gel:/data -v /uod/idr-scratch/merge-ci/curated/biorad-gel:/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] 02:06:44,250 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:06:44,252 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 02:06:44,252 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:06:44,252 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:06:44,253 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:06:44,253 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:06:44,253 |-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] 02:06:44,253 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:06:44,254 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:06:44,255 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:06:44,255 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:06:44,255 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:06:44,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:06:44,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:06:44,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:06:44,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:06:44,475 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:06:44,475 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:06:44,475 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:06:44,476 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:06:44,476 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 02:06:44,476 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 02:06:44,476 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 222 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-03-24 02:06:44,486] [main] java.version = 17.0.2
[testng] 02:06:44,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:06:44,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:06:44,558 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-24_02-06-44.log]
[testng] 02:06:44,560 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-03-24 02:06:44,562] [main] testng.directory = /data
[testng] [2024-03-24 02:06:44,562] [main] testng.configDirectory = /config
[testng] [2024-03-24 02:06:44,582] [main] testng.multiplier = 1.0
[testng] [2024-03-24 02:06:44,583] [main] testng.in-memory = false
[testng] [2024-03-24 02:06:44,583] [main] testng.allow-missing = false
[testng] [2024-03-24 02:06:44,583] [main] user.language = en
[testng] [2024-03-24 02:06:44,583] [main] user.country = ${user.country}
[testng] [2024-03-24 02:06:44,583] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-03-24 02:06:46,438] [main] ----------------------------------------
[testng] [2024-03-24 02:06:46,438] [main] Total files: 32
[testng] [2024-03-24 02:06:46,438] [main] Scan time: 1.855 s (57 ms/file)
[testng] [2024-03-24 02:06:46,439] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 32 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-03-24 02:06:59,251] [pool-1-thread-1] Initializing /data/david/Opened in imageJ.tiff:
[testng] 02:06:59,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:06:59,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:06:59,253 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-24_02-06-59.log]
[testng] 02:06:59,254 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28de766a - End of configuration.
[testng] [2024-03-24 02:06:59,961] [pool-1-thread-12] Initializing /data/keith/test2.1sc:
[testng] 02:06:59,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:06:59,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:06:59,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-24_02-06-59.log]
[testng] 02:06:59,963 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c2b3118 - End of configuration.
[testng] [2024-03-24 02:07:00,198] [pool-1-thread-11] Initializing /data/keith/PF020328saur v3.1sc:
[testng] 02:07:00,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:07:00,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:07:00,199 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-24_02-07-00.log]
[testng] 02:07:00,200 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13724d1f - End of configuration.
[testng] [2024-03-24 02:07:00,433] [pool-1-thread-10] Initializing /data/geert/bad example1.jpg:
[testng] 02:07:00,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:07:00,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:07:00,434 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-24_02-07-00.log]
[testng] 02:07:00,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ecc8472 - End of configuration.
[testng] [2024-03-24 02:07:00,513] [pool-1-thread-9] Initializing /data/adrian/test_img.1sc:
[testng] 02:07:00,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:07:00,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:07:00,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-24_02-07-00.log]
[testng] 02:07:00,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@109f3fbb - End of configuration.
[testng] [2024-03-24 02:07:00,772] [pool-1-thread-8] Initializing /data/geert/bad example1.1sc:
[testng] 02:07:00,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:07:00,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:07:00,773 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-24_02-07-00.log]
[testng] 02:07:00,773 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d059742 - End of configuration.
[testng] [2024-03-24 02:07:01,020] [pool-1-thread-7] Initializing /data/geert/good example1.1sc:
[testng] 02:07:01,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:07:01,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:07:01,021 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-24_02-07-01.log]
[testng] 02:07:01,022 |-INFO in ch.qos.logback.core.sift.SiftProcessor@96d371b - End of configuration.
[testng] [2024-03-24 02:07:01,251] [pool-1-thread-6] Initializing /data/sylvain/2009-10-23 12hr 19min:
[testng] 02:07:01,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:07:01,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:07:01,252 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-24_02-07-01.log]
[testng] 02:07:01,252 |-INFO in ch.qos.logback.core.sift.SiftProcessor@394b5868 - End of configuration.
[testng] [2024-03-24 02:07:01,489] [pool-1-thread-5] Initializing /data/qa-16880/c-src v7.1sc:
[testng] 02:07:01,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:07:01,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:07:01,490 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-24_02-07-01.log]
[testng] 02:07:01,491 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3aae331d - End of configuration.
[testng] [2024-03-24 02:07:01,753] [pool-1-thread-4] Initializing /data/keith/test.1sc:
[testng] 02:07:01,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:07:01,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:07:01,754 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-24_02-07-01.log]
[testng] 02:07:01,755 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46718697 - End of configuration.
[testng] [2024-03-24 02:07:01,981] [pool-1-thread-3] Initializing /data/qa-29459/bad.1sc:
[testng] 02:07:01,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:07:01,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:07:01,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-24_02-07-01.log]
[testng] 02:07:01,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ad4f8d6 - End of configuration.
[testng] [2024-03-24 02:07:02,191] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 59min.tif:
[testng] 02:07:02,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:07:02,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:07:02,192 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-24_02-07-02.log]
[testng] 02:07:02,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27a885e3 - End of configuration.
[testng] [2024-03-24 02:07:06,139] [pool-1-thread-11] Initializing /data/sylvain/2009-10-26 14hr 56min.tif:
[testng] [2024-03-24 02:07:06,845] [pool-1-thread-8] Initializing /data/geert/bad example1.1sc.jpg:
[testng] [2024-03-24 02:07:06,964] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 56min:
[testng] [2024-03-24 02:07:07,156] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 57min.tif:
[testng] [2024-03-24 02:07:07,978] [pool-1-thread-12] Initializing /data/keith/PF020426MRSA v2.1sc:
[testng] [2024-03-24 02:07:08,140] [pool-1-thread-10] Initializing /data/david/Converted in Quantity One (Biorad).tiff:
[testng] [2024-03-24 02:07:08,971] [pool-1-thread-5] Initializing /data/david/Original Biorad Gel format file.1sc:
[testng] [2024-03-24 02:07:09,154] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 59min:
[testng] [2024-03-24 02:07:09,434] [pool-1-thread-6] Initializing /data/geert/good example1.1sc.jpg:
[testng] [2024-03-24 02:07:09,556] [pool-1-thread-7] Initializing /data/keith/pg020410saur3.1sc:
[testng] [2024-03-24 02:07:10,140] [pool-1-thread-1] Initializing /data/qa-29459/bad.jpg:
[testng] [2024-03-24 02:07:10,964] [pool-1-thread-2] Initializing /data/sylvain/2009-10-23 12hr 18min:
[testng] [2024-03-24 02:07:11,587] [pool-1-thread-12] Initializing /data/samples/imagesEight.1sc:
[testng] [2024-03-24 02:07:11,811] [pool-1-thread-5] Initializing /data/samples/Criterion.1sc:
[testng] [2024-03-24 02:07:12,070] [pool-1-thread-7] Initializing /data/sylvain/2009-10-23 12hr 18min.tif:
[testng] [2024-03-24 02:07:13,056] [pool-1-thread-6] Initializing /data/qa-29469/good.1sc:
[testng] [2024-03-24 02:07:13,267] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 57min:
[testng] [2024-03-24 02:07:13,577] [pool-1-thread-3] Initializing /data/sylvain/2009-10-23 12hr 19min.tif:
[testng] [2024-03-24 02:07:14,398] [pool-1-thread-8] Initializing /data/qa-29469/bad2.1sc:
[testng] [2024-03-24 02:07:14,731] [pool-1-thread-1] Initializing /data/qa-29469/bad3.1sc:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1696, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 39 seconds
Finished: SUCCESS