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@2
[BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins5289258202134965946.sh
+ '[' mrc = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_33168_merge_ci -v /uod/idr/repos/curated/mrc:/data -v /uod/idr-scratch/merge-ci/curated/mrc:/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] 01:49:38,756 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:49:38,757 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service.
[testng] 01:49:38,757 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:49:38,758 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:49:38,758 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:49:38,759 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:49:38,759 |-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] 01:49:38,759 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:49:38,759 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:49:38,760 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:49:38,760 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:49:38,760 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:49:38,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:49:38,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:49:39,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:49:39,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:49:39,013 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:49:39,013 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:49:39,013 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:49:39,014 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:49:39,014 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration.
[testng] 01:49:39,014 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point
[testng] 01:49:39,015 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 255 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-04 01:49:39,024] [main] java.version = 1.8.0_342
[testng] 01:49:39,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:49:39,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:49:39,070 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-04_01-49-39.log]
[testng] 01:49:39,072 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration.
[testng] [2024-10-04 01:49:39,074] [main] testng.directory = /data
[testng] [2024-10-04 01:49:39,074] [main] testng.configDirectory = /config
[testng] [2024-10-04 01:49:39,086] [main] testng.multiplier = 1.0
[testng] [2024-10-04 01:49:39,086] [main] testng.in-memory = false
[testng] [2024-10-04 01:49:39,086] [main] testng.allow-missing = false
[testng] [2024-10-04 01:49:39,086] [main] user.language = en
[testng] [2024-10-04 01:49:39,086] [main] user.country = ${user.country}
[testng] [2024-10-04 01:49:39,086] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-10-04 01:49:44,804] [main] ----------------------------------------
[testng] [2024-10-04 01:49:44,804] [main] Total files: 20
[testng] [2024-10-04 01:49:44,804] [main] Scan time: 5.718 s (285 ms/file)
[testng] [2024-10-04 01:49:44,804] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 20 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-04 01:49:50,129] [pool-1-thread-1] Initializing /data/ascb/c191ali.mrc:
[testng] 01:49:50,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:49:50,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:49:50,131 |-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_01-49-50.log]
[testng] 01:49:50,132 |-INFO in ch.qos.logback.core.sift.SiftProcessor@490bc666 - End of configuration.
[testng] [2024-10-04 01:49:50,388] [pool-1-thread-12] Initializing /data/ticket-10073/wtjoin4.rec:
[testng] 01:49:50,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:49:50,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:49:50,389 |-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_01-49-50.log]
[testng] 01:49:50,390 |-INFO in ch.qos.logback.core.sift.SiftProcessor@105b377b - End of configuration.
[testng] [2024-10-04 01:49:50,572] [pool-1-thread-11] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc:
[testng] 01:49:50,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:49:50,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:49:50,573 |-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_01-49-50.log]
[testng] 01:49:50,573 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26b3a9bb - End of configuration.
[testng] [2024-10-04 01:49:50,853] [pool-1-thread-10] Initializing /data/strand/Series1_A.mrc:
[testng] 01:49:50,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:49:50,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:49:50,854 |-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_01-49-50.log]
[testng] 01:49:50,855 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5235277 - End of configuration.
[testng] [2024-10-04 01:49:51,061] [pool-1-thread-9] Initializing /data/samples/golgi.mrc:
[testng] 01:49:51,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:49:51,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:49:51,062 |-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_01-49-51.log]
[testng] 01:49:51,063 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23e78f8 - End of configuration.
[testng] [2024-10-04 01:49:51,314] [pool-1-thread-8] Initializing /data/dan/three.mrc:
[testng] 01:49:51,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:49:51,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:49:51,315 |-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_01-49-51.log]
[testng] 01:49:51,315 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3813a89 - End of configuration.
[testng] [2024-10-04 01:49:51,562] [pool-1-thread-7] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc:
[testng] 01:49:51,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:49:51,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:49:51,563 |-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_01-49-51.log]
[testng] 01:49:51,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@166ed973 - End of configuration.
[testng] [2024-10-04 01:49:52,110] [pool-1-thread-6] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map:
[testng] 01:49:52,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:49:52,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:49:52,111 |-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_01-49-52.log]
[testng] 01:49:52,111 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34f43095 - End of configuration.
[testng] [2024-10-04 01:49:52,294] [pool-1-thread-5] Initializing /data/dan/one.mrc:
[testng] 01:49:52,294 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:49:52,294 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:49:52,295 |-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_01-49-52.log]
[testng] 01:49:52,296 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e5194a6 - End of configuration.
[testng] [2024-10-04 01:49:52,470] [pool-1-thread-4] Initializing /data/dan/two.mrc:
[testng] 01:49:52,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:49:52,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:49:52,471 |-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_01-49-52.log]
[testng] 01:49:52,472 |-INFO in ch.qos.logback.core.sift.SiftProcessor@eb3ba8 - End of configuration.
[testng] [2024-10-04 01:49:52,752] [pool-1-thread-3] Initializing /data/ascb/514_9903.mrc:
[testng] 01:49:52,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:49:52,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:49:52,753 |-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_01-49-52.log]
[testng] 01:49:52,754 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c5111a9 - End of configuration.
[testng] [2024-10-04 01:49:52,985] [pool-1-thread-2] Initializing /data/jcb/thyl-apr23-4.rec:
[testng] 01:49:52,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:49:52,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:49:52,986 |-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_01-49-52.log]
[testng] 01:49:52,987 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b25bc0f - End of configuration.
[testng] [2024-10-04 01:49:56,899] [pool-1-thread-6] Initializing /data/ascb/c191.st:
[testng] [2024-10-04 01:49:57,070] [pool-1-thread-11] Initializing /data/samples/1160.mrc:
[testng] [2024-10-04 01:49:57,262] [pool-1-thread-2] Initializing /data/bioformats2raw-198/test_uint8.mrc:
[testng] [2024-10-04 01:49:57,445] [pool-1-thread-9] Initializing /data/ascb/cfa1071.mrc:
[testng] [2024-10-04 01:49:58,035] [pool-1-thread-1] Initializing /data/jcb/thylakoid5.rec:
[testng] [2024-10-04 01:49:58,261] [pool-1-thread-7] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc:
[testng] [2024-10-04 01:49:58,487] [pool-1-thread-5] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc:
[testng] [2024-10-04 01:49:58,859] [pool-1-thread-8] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1060, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 29 seconds
Finished: SUCCESS