Started by upstream project "BIOFORMATS-test-repo" build number 98
originally caused by:
Started by upstream project "Trigger" build number 109
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9
[BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins42510617744257123.sh
+ '[' mrc = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_15121_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
[javac] warning: [options] bootstrap class path not set in conjunction with -source 8
[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release
[javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
[javac] 4 warnings
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] 01:36:42,179 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:36:42,180 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service.
[testng] 01:36:42,180 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:36:42,181 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:36:42,181 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:36:42,182 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:36:42,182 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:36:42,182 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:36:42,182 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:36:42,183 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:36:42,183 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:36:42,184 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:36:42,342 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:36:42,342 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:36:42,366 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:36:42,366 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:36:42,372 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:36:42,372 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:36:42,373 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:36:42,373 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:36:42,373 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration.
[testng] 01:36:42,374 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point
[testng] 01:36:42,374 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 192 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-20 01:36:42,382] [main] java.version = 21
[testng] 01:36:42,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:36:42,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:42,425 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-20_01-36-42.log]
[testng] 01:36:42,427 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration.
[testng] [2024-06-20 01:36:42,429] [main] testng.directory = /data
[testng] [2024-06-20 01:36:42,429] [main] testng.configDirectory = /config
[testng] [2024-06-20 01:36:42,437] [main] testng.multiplier = 1.0
[testng] [2024-06-20 01:36:42,438] [main] testng.in-memory = false
[testng] [2024-06-20 01:36:42,438] [main] testng.allow-missing = false
[testng] [2024-06-20 01:36:42,438] [main] user.language = en
[testng] [2024-06-20 01:36:42,438] [main] user.country = ${user.country}
[testng] [2024-06-20 01:36:42,438] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-06-20 01:36:43,418] [main] ----------------------------------------
[testng] [2024-06-20 01:36:43,418] [main] Total files: 20
[testng] [2024-06-20 01:36:43,418] [main] Scan time: 0.98 s (49 ms/file)
[testng] [2024-06-20 01:36:43,419] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 20 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-20 01:36:43,914] [pool-1-thread-1] Initializing /data/samples/1160.mrc:
[testng] 01:36:43,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:36:43,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:43,916 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-20_01-36-43.log]
[testng] 01:36:43,917 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c729613 - End of configuration.
[testng] [2024-06-20 01:36:43,935] [pool-1-thread-12] Initializing /data/samples/golgi.mrc:
[testng] 01:36:43,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:36:43,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:43,937 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-20_01-36-43.log]
[testng] 01:36:43,937 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7736b718 - End of configuration.
[testng] [2024-06-20 01:36:43,948] [pool-1-thread-11] Initializing /data/ascb/514_9903.mrc:
[testng] 01:36:43,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:36:43,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:43,949 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-20_01-36-43.log]
[testng] 01:36:43,949 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30f2af39 - End of configuration.
[testng] [2024-06-20 01:36:44,319] [pool-1-thread-10] Initializing /data/ascb/cfa1071.mrc:
[testng] 01:36:44,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:36:44,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:44,322 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-20_01-36-44.log]
[testng] 01:36:44,322 |-INFO in ch.qos.logback.core.sift.SiftProcessor@378b64e6 - End of configuration.
[testng] [2024-06-20 01:36:44,337] [pool-1-thread-9] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc:
[testng] 01:36:44,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:36:44,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:44,338 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-20_01-36-44.log]
[testng] 01:36:44,338 |-INFO in ch.qos.logback.core.sift.SiftProcessor@170c98bf - End of configuration.
[testng] [2024-06-20 01:36:44,353] [pool-1-thread-8] Initializing /data/jcb/thylakoid5.rec:
[testng] 01:36:44,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:36:44,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:44,353 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-20_01-36-44.log]
[testng] 01:36:44,354 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25ad83a7 - End of configuration.
[testng] [2024-06-20 01:36:44,372] [pool-1-thread-7] Initializing /data/dan/two.mrc:
[testng] 01:36:44,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:36:44,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:44,373 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-20_01-36-44.log]
[testng] 01:36:44,374 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5aaf6bdb - End of configuration.
[testng] [2024-06-20 01:36:44,394] [pool-1-thread-6] Initializing /data/bioformats2raw-198/test_uint8.mrc:
[testng] 01:36:44,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:36:44,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:44,395 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-20_01-36-44.log]
[testng] 01:36:44,396 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7239624e - End of configuration.
[testng] [2024-06-20 01:36:44,408] [pool-1-thread-5] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc:
[testng] 01:36:44,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:36:44,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:44,409 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-20_01-36-44.log]
[testng] 01:36:44,409 |-INFO in ch.qos.logback.core.sift.SiftProcessor@142833ef - End of configuration.
[testng] [2024-06-20 01:36:44,424] [pool-1-thread-4] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map:
[testng] 01:36:44,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:36:44,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:44,426 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-20_01-36-44.log]
[testng] 01:36:44,426 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18d78af2 - End of configuration.
[testng] [2024-06-20 01:36:44,462] [pool-1-thread-3] Initializing /data/dan/three.mrc:
[testng] 01:36:44,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:36:44,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:44,463 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-20_01-36-44.log]
[testng] 01:36:44,464 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4593b5ee - End of configuration.
[testng] [2024-06-20 01:36:44,476] [pool-1-thread-2] Initializing /data/ascb/c191ali.mrc:
[testng] 01:36:44,477 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:36:44,477 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:44,478 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-20_01-36-44.log]
[testng] 01:36:44,478 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4401d17e - End of configuration.
[testng] [2024-06-20 01:36:45,886] [pool-1-thread-6] Initializing /data/ticket-10073/wtjoin4.rec:
[testng] [2024-06-20 01:36:45,915] [pool-1-thread-12] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc:
[testng] [2024-06-20 01:36:45,938] [pool-1-thread-4] Initializing /data/jcb/thyl-apr23-4.rec:
[testng] [2024-06-20 01:36:46,124] [pool-1-thread-2] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc:
[testng] [2024-06-20 01:36:46,225] [pool-1-thread-5] Initializing /data/dan/one.mrc:
[testng] [2024-06-20 01:36:46,404] [pool-1-thread-12] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc:
[testng] [2024-06-20 01:36:46,550] [pool-1-thread-8] Initializing /data/ascb/c191.st:
[testng] [2024-06-20 01:36:46,560] [pool-1-thread-4] Initializing /data/strand/Series1_A.mrc:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1060, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 11 seconds
Finished: SUCCESS