Started by upstream project "BIOFORMATS-test-repo" build number 187
originally caused by:
Started by upstream project "Trigger" build number 209
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6
[BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins14332495932765578360.sh
+ '[' gatan-dm2 = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_29567_merge_ci -v /uod/idr/repos/curated/gatan-dm2:/data -v /uod/idr-scratch/merge-ci/curated/gatan-dm2:/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] 01:58:58,585 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:58:58,587 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service.
[testng] 01:58:58,587 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:58:58,588 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:58:58,588 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:58:58,588 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:58:58,589 |-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] 01:58:58,589 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:58:58,589 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:58:58,589 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:58:58,589 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:58:58,590 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:58:58,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:58:58,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:58:58,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:58:58,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:58:58,839 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:58:58,839 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:58:58,840 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:58:58,840 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:58:58,840 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration.
[testng] 01:58:58,841 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point
[testng] 01:58:58,841 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 252 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-09-13 01:58:58,850] [main] java.version = 1.8.0_342
[testng] 01:58:58,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:58:58,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:58:58,898 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-13_01-58-58.log]
[testng] 01:58:58,899 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration.
[testng] [2024-09-13 01:58:58,901] [main] testng.directory = /data
[testng] [2024-09-13 01:58:58,901] [main] testng.configDirectory = /config
[testng] [2024-09-13 01:58:58,913] [main] testng.multiplier = 1.0
[testng] [2024-09-13 01:58:58,914] [main] testng.in-memory = false
[testng] [2024-09-13 01:58:58,914] [main] testng.allow-missing = false
[testng] [2024-09-13 01:58:58,914] [main] user.language = en
[testng] [2024-09-13 01:58:58,914] [main] user.country = ${user.country}
[testng] [2024-09-13 01:58:58,914] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-09-13 01:59:00,594] [main] ----------------------------------------
[testng] [2024-09-13 01:59:00,594] [main] Total files: 25
[testng] [2024-09-13 01:59:00,594] [main] Scan time: 1.68 s (67 ms/file)
[testng] [2024-09-13 01:59:00,595] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 18 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-09-13 01:59:02,022] [pool-1-thread-1] Initializing /data/imagic/Histiocyte in Skin Dermis.dm2:
[testng] 01:59:02,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:59:02,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:59:02,023 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-13_01-59-02.log]
[testng] 01:59:02,024 |-INFO in ch.qos.logback.core.sift.SiftProcessor@676b7592 - End of configuration.
[testng] [2024-09-13 01:59:02,052] [pool-1-thread-12] Initializing /data/pang/10500x-o4:
[testng] 01:59:02,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:59:02,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:59:02,054 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-13_01-59-02.log]
[testng] 01:59:02,054 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6beabbe8 - End of configuration.
[testng] [2024-09-13 01:59:02,083] [pool-1-thread-11] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info2.png:
[testng] 01:59:02,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:59:02,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:59:02,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-13_01-59-02.log]
[testng] 01:59:02,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f477692 - End of configuration.
[testng] [2024-09-13 01:59:02,091] [pool-1-thread-10] Initializing /data/imagic/not read correctly/Zucchini.dm2:
[testng] 01:59:02,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:59:02,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:59:02,092 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-13_01-59-02.log]
[testng] 01:59:02,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bd587da - End of configuration.
[testng] [2024-09-13 01:59:02,116] [pool-1-thread-9] Initializing /data/imagic/not read correctly/Abeta Moon_preview.png:
[testng] 01:59:02,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:59:02,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:59:02,117 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-13_01-59-02.log]
[testng] 01:59:02,117 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ab17854 - End of configuration.
[testng] [2024-09-13 01:59:02,124] [pool-1-thread-8] Initializing /data/pang/screen capture of metadata/tem_dm_keywords_info.png:
[testng] 01:59:02,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:59:02,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:59:02,124 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-13_01-59-02.log]
[testng] 01:59:02,125 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f8efc24 - End of configuration.
[testng] [2024-09-13 01:59:02,129] [pool-1-thread-7] Initializing /data/pang/unproc-auto:
[testng] 01:59:02,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:59:02,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:59:02,130 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-13_01-59-02.log]
[testng] 01:59:02,130 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6679ee4c - End of configuration.
[testng] [2024-09-13 01:59:02,147] [pool-1-thread-6] Initializing /data/pang/screen capture of metadata/tem_dm_general_info.png:
[testng] 01:59:02,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:59:02,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:59:02,148 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-13_01-59-02.log]
[testng] 01:59:02,148 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c90957d - End of configuration.
[testng] [2024-09-13 01:59:02,157] [pool-1-thread-5] Initializing /data/pang/grating025k.dm2:
[testng] 01:59:02,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:59:02,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:59:02,158 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-13_01-59-02.log]
[testng] 01:59:02,158 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7031cbfe - End of configuration.
[testng] [2024-09-13 01:59:02,189] [pool-1-thread-4] Initializing /data/pang/signed:
[testng] 01:59:02,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:59:02,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:59:02,189 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-13_01-59-02.log]
[testng] 01:59:02,190 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b98fd8e - End of configuration.
[testng] [2024-09-13 01:59:02,207] [pool-1-thread-3] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info1.png:
[testng] 01:59:02,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:59:02,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:59:02,208 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-13_01-59-02.log]
[testng] 01:59:02,208 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e07f15f - End of configuration.
[testng] [2024-09-13 01:59:02,212] [pool-1-thread-2] Initializing /data/pang/DLMeD2E1_010500x03.dm2:
[testng] 01:59:02,212 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:59:02,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:59:02,213 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-13_01-59-02.log]
[testng] 01:59:02,213 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b6668e3 - End of configuration.
[testng] [2024-09-13 01:59:03,947] [pool-1-thread-8] Initializing /data/imagic/not read correctly/Zucchini_preview.png:
[testng] [2024-09-13 01:59:03,953] [pool-1-thread-5] Initializing /data/pang/screen capture of metadata/tem_dm_microscope_info.png:
[testng] [2024-09-13 01:59:03,957] [pool-1-thread-4] Initializing /data/imagic/13008.dm2:
[testng] [2024-09-13 01:59:03,973] [pool-1-thread-1] Initializing /data/imagic/not read correctly/Abeta Moon.dm2:
[testng] [2024-09-13 01:59:04,000] [pool-1-thread-2] Initializing /data/imagic/TEM 10118.dm2:
[testng] [2024-09-13 01:59:04,052] [pool-1-thread-12] Initializing /data/imagic/1-1.dm2:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 954, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 10 seconds
Finished: SUCCESS