Started by upstream project "BIOFORMATS-test-repo" build number 5
originally caused by:
Started by upstream project "Trigger" build number 6
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7
[BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins11514633306571008599.sh
+ '[' mrc = slidebook ']'
++ date +%u
+ '[' 1 -le 1 ']'
+ DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR'
+ sudo docker run --rm --name BIOFORMATS-test-folder_686_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 -Duser.language=fr -Duser.country=FR
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] 00:46:53,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:46:53,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:46:53,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:46:53,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:46:53,858 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:46:53,858 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:46:53,858 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:46:53,859 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:46:53,859 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5c30a9b0 - End of configuration.
[testng] 00:46:53,860 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@7a69b07 - Registering current configuration as safe fallback point
[testng] 00:46:53,860 |-INFO in ch.qos.logback.classic.util.ContextInitializer@5e82df6a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 394 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-03-18 00:46:53,870] [main] java.version = 1.8.0_342
[testng] 00:46:53,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:46:53,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:46:53,923 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-18_00-46-53.log]
[testng] 00:46:53,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration.
[testng] [2024-03-18 00:46:53,927] [main] testng.directory = /data
[testng] [2024-03-18 00:46:53,927] [main] testng.configDirectory = /config
[testng] [2024-03-18 00:46:54,445] [main] testng.multiplier = 1.0
[testng] [2024-03-18 00:46:54,445] [main] testng.in-memory = false
[testng] [2024-03-18 00:46:54,445] [main] testng.allow-missing = false
[testng] [2024-03-18 00:46:54,445] [main] user.language = fr
[testng] [2024-03-18 00:46:54,445] [main] user.country = FR
[testng] [2024-03-18 00:46:54,445] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-03-18 00:46:58,488] [main] ----------------------------------------
[testng] [2024-03-18 00:46:58,489] [main] Total files: 20
[testng] [2024-03-18 00:46:58,489] [main] Scan time: 4.042 s (202 ms/file)
[testng] [2024-03-18 00:46:58,489] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 20 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-03-18 00:47:02,313] [pool-1-thread-1] Initializing /data/ascb/c191.st:
[testng] 00:47:02,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:47:02,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:02,314 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-18_00-47-02.log]
[testng] 00:47:02,315 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ca68aa6 - End of configuration.
[testng] [2024-03-18 00:47:02,483] [pool-1-thread-12] Initializing /data/dan/one.mrc:
[testng] 00:47:02,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:47:02,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:02,484 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-18_00-47-02.log]
[testng] 00:47:02,485 |-INFO in ch.qos.logback.core.sift.SiftProcessor@553c8196 - End of configuration.
[testng] [2024-03-18 00:47:02,669] [pool-1-thread-11] Initializing /data/bioformats2raw-198/test_uint8.mrc:
[testng] 00:47:02,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:47:02,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:02,681 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-18_00-47-02.log]
[testng] 00:47:02,682 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d218b63 - End of configuration.
[testng] [2024-03-18 00:47:02,807] [pool-1-thread-10] Initializing /data/ascb/c191ali.mrc:
[testng] 00:47:02,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:47:02,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:02,808 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-18_00-47-02.log]
[testng] 00:47:02,809 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18f73a37 - End of configuration.
[testng] [2024-03-18 00:47:02,981] [pool-1-thread-9] Initializing /data/strand/Series1_A.mrc:
[testng] 00:47:02,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:47:02,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:02,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-18_00-47-02.log]
[testng] 00:47:02,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5efb7803 - End of configuration.
[testng] [2024-03-18 00:47:03,146] [pool-1-thread-8] Initializing /data/dan/two.mrc:
[testng] 00:47:03,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:47:03,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:03,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-18_00-47-03.log]
[testng] 00:47:03,147 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56f78f24 - End of configuration.
[testng] [2024-03-18 00:47:03,280] [pool-1-thread-7] Initializing /data/samples/golgi.mrc:
[testng] 00:47:03,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:47:03,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:03,281 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-18_00-47-03.log]
[testng] 00:47:03,282 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4322e9ef - End of configuration.
[testng] [2024-03-18 00:47:03,408] [pool-1-thread-6] Initializing /data/ticket-10073/wtjoin4.rec:
[testng] 00:47:03,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:47:03,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:03,409 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-18_00-47-03.log]
[testng] 00:47:03,410 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64c15fbe - End of configuration.
[testng] [2024-03-18 00:47:03,548] [pool-1-thread-5] Initializing /data/jcb/thyl-apr23-4.rec:
[testng] 00:47:03,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:47:03,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:03,550 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-18_00-47-03.log]
[testng] 00:47:03,550 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c64a71a - End of configuration.
[testng] [2024-03-18 00:47:03,667] [pool-1-thread-4] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc:
[testng] 00:47:03,667 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:47:03,667 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:03,668 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-18_00-47-03.log]
[testng] 00:47:03,669 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47a6a28f - End of configuration.
[testng] [2024-03-18 00:47:03,801] [pool-1-thread-3] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map:
[testng] 00:47:03,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:47:03,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:03,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-18_00-47-03.log]
[testng] 00:47:03,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c9625fc - End of configuration.
[testng] [2024-03-18 00:47:03,975] [pool-1-thread-2] Initializing /data/ascb/514_9903.mrc:
[testng] 00:47:03,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:47:03,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:47:03,976 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-18_00-47-03.log]
[testng] 00:47:03,976 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5718b32 - End of configuration.
[testng] [2024-03-18 00:47:07,049] [pool-1-thread-3] Initializing /data/dan/three.mrc:
[testng] [2024-03-18 00:47:07,199] [pool-1-thread-11] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc:
[testng] [2024-03-18 00:47:07,444] [pool-1-thread-7] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc:
[testng] [2024-03-18 00:47:07,561] [pool-1-thread-5] Initializing /data/jcb/thylakoid5.rec:
[testng] [2024-03-18 00:47:07,665] [pool-1-thread-10] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc:
[testng] [2024-03-18 00:47:07,814] [pool-1-thread-1] Initializing /data/ascb/cfa1071.mrc:
[testng] [2024-03-18 00:47:08,636] [pool-1-thread-12] Initializing /data/samples/1160.mrc:
[testng] [2024-03-18 00:47:08,815] [pool-1-thread-6] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1060, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 24 seconds
Finished: SUCCESS