Started by upstream project "BIOFORMATS-test-repo" build number 209
originally caused by:
Started by upstream project "Trigger" build number 235
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/jenkins4440710443627878514.sh
+ '[' zip = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_33130_merge_ci -v /uod/idr/repos/curated/zip:/data -v /uod/idr-scratch/merge-ci/curated/zip:/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
test-automated:
[testng] File leak detector installed
[testng] 01:27:26,319 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:27:26,321 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service.
[testng] 01:27:26,321 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:27:26,322 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:27:26,322 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:27:26,322 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:27:26,323 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:27:26,323 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:27:26,323 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:27:26,324 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:27:26,324 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:27:26,324 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:27:26,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:27:26,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:27:26,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:27:26,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:27:26,612 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:27:26,612 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:27:26,612 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:27:26,613 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:27:26,613 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration.
[testng] 01:27:26,614 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point
[testng] 01:27:26,614 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 291 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-04 01:27:26,624] [main] java.version = 1.8.0_342
[testng] 01:27:26,628 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:27:26,628 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:26,674 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-04_01-27-26.log]
[testng] 01:27:26,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration.
[testng] [2024-10-04 01:27:26,678] [main] testng.directory = /data
[testng] [2024-10-04 01:27:26,678] [main] testng.configDirectory = /config
[testng] [2024-10-04 01:27:26,691] [main] testng.multiplier = 1.0
[testng] [2024-10-04 01:27:26,692] [main] testng.in-memory = false
[testng] [2024-10-04 01:27:26,692] [main] testng.allow-missing = false
[testng] [2024-10-04 01:27:26,692] [main] user.language = en
[testng] [2024-10-04 01:27:26,692] [main] user.country = ${user.country}
[testng] [2024-10-04 01:27:26,692] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-10-04 01:27:27,348] [main] ----------------------------------------
[testng] [2024-10-04 01:27:27,349] [main] Total files: 22
[testng] [2024-10-04 01:27:27,349] [main] Scan time: 0.655 s (29 ms/file)
[testng] [2024-10-04 01:27:27,349] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 22 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-04 01:28:59,768] [pool-1-thread-1] Initializing /data/samples/sdub.zip:
[testng] 01:28:59,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:28:59,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:59,769 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-04_01-28-59.log]
[testng] 01:28:59,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@487a57ef - End of configuration.
[testng] [2024-10-04 01:29:00,559] [pool-1-thread-12] Initializing /data/imagej/mri-stack.zip:
[testng] 01:29:00,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:29:00,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:00,560 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-04_01-29-00.log]
[testng] 01:29:00,560 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d6b8a40 - End of configuration.
[testng] [2024-10-04 01:29:02,278] [pool-1-thread-11] Initializing /data/imagej/hela-cells.zip:
[testng] 01:29:02,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:29:02,279 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:02,279 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-04_01-29-02.log]
[testng] 01:29:02,280 |-INFO in ch.qos.logback.core.sift.SiftProcessor@519ced01 - End of configuration.
[testng] [2024-10-04 01:29:04,940] [pool-1-thread-10] Initializing /data/imagej/watershed-animation.zip:
[testng] 01:29:04,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:29:04,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:04,941 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-04_01-29-04.log]
[testng] 01:29:04,942 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5970ff5c - End of configuration.
[testng] [2024-10-04 01:29:06,603] [pool-1-thread-9] Initializing /data/imagej/4D-Stack(256x256x20x10).zip:
[testng] 01:29:06,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:29:06,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:06,604 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-04_01-29-06.log]
[testng] 01:29:06,604 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b502474 - End of configuration.
[testng] [2024-10-04 01:29:15,719] [pool-1-thread-8] Initializing /data/imagej/gel-electrophoresis.zip:
[testng] 01:29:15,719 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:29:15,719 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:15,720 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-04_01-29-15.log]
[testng] 01:29:15,721 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31887aa8 - End of configuration.
[testng] [2024-10-04 01:29:18,721] [pool-1-thread-7] Initializing /data/imagej/cheetah_256_8.tif.zip:
[testng] 01:29:18,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:29:18,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:18,722 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-04_01-29-18.log]
[testng] 01:29:18,722 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c7c0fb6 - End of configuration.
[testng] [2024-10-04 01:29:20,709] [pool-1-thread-6] Initializing /data/imagej/xrays.zip:
[testng] 01:29:20,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:29:20,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:20,710 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-04_01-29-20.log]
[testng] 01:29:20,710 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a9b730 - End of configuration.
[testng] [2024-10-04 01:29:21,752] [pool-1-thread-5] Initializing /data/imagej/confocal-stack.zip:
[testng] 01:29:21,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:29:21,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:21,753 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-04_01-29-21.log]
[testng] 01:29:21,753 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77896d39 - End of configuration.
[testng] [2024-10-04 01:29:31,892] [pool-1-thread-4] Initializing /data/imagej/FluorescentCells.zip:
[testng] 01:29:31,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:29:31,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:31,894 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-04_01-29-31.log]
[testng] 01:29:31,894 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c94af3a - End of configuration.
[testng] [2024-10-04 01:29:33,700] [pool-1-thread-3] Initializing /data/imagej/fat-cells.zip:
[testng] 01:29:33,701 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:29:33,701 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:33,701 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-04_01-29-33.log]
[testng] 01:29:33,702 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bd23c4c - End of configuration.
[testng] [2024-10-04 01:29:38,387] [pool-1-thread-2] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip:
[testng] 01:29:38,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:29:38,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:38,388 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-04_01-29-38.log]
[testng] 01:29:38,388 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34ea6f3e - End of configuration.
[testng] [2024-10-04 01:29:52,708] [pool-1-thread-1] Initializing /data/imagej/se3.zip:
[testng] [2024-10-04 01:30:05,190] [pool-1-thread-6] Initializing /data/imagej/RatBrain.zip:
[testng] [2024-10-04 01:30:09,329] [pool-1-thread-10] Initializing /data/imagej/blood-brain-barrier.zip:
[testng] [2024-10-04 01:30:19,146] [pool-1-thread-12] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip:
[testng] [2024-10-04 01:30:21,790] [pool-1-thread-4] Initializing /data/imagej/scala-media.zip:
[testng] [2024-10-04 01:30:22,886] [pool-1-thread-7] Initializing /data/imagej/confocal-series.zip:
[testng] [2024-10-04 01:30:33,851] [pool-1-thread-6] Initializing /data/imagej/3D_Chromosome.zip:
[testng] [2024-10-04 01:30:39,939] [pool-1-thread-4] Initializing /data/imagej/flybrain.zip:
[testng] [2024-10-04 01:30:46,329] [pool-1-thread-11] Initializing /data/imagej/m51.zip:
[testng] [2024-10-04 01:30:50,373] [pool-1-thread-2] Initializing /data/samples/bat-cochlea-volume.zip:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1166, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 7 minutes 34 seconds
Finished: SUCCESS