Started by upstream project "BIOFORMATS-test-repo" build number 215
originally caused by:
Started by upstream project "Trigger" build number 242
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder
[BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins12665124336797047444.sh
+ '[' mrc = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_34099_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] 1 warning
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] 02:09:22,881 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:09:22,883 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 02:09:22,883 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:09:22,883 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:09:22,884 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:09:22,884 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:09:22,885 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 02:09:22,885 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:09:22,885 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:09:22,886 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:09:22,886 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:09:22,886 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:09:23,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:09:23,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:09:23,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:09:23,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:09:23,090 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:09:23,090 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:09:23,090 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:09:23,090 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:09:23,090 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 02:09:23,091 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 02:09:23,091 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 206 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-09 02:09:23,100] [main] java.version = 17.0.2
[testng] 02:09:23,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:09:23,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:09:23,145 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-09_02-09-23.log]
[testng] 02:09:23,146 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-10-09 02:09:23,148] [main] testng.directory = /data
[testng] [2024-10-09 02:09:23,149] [main] testng.configDirectory = /config
[testng] [2024-10-09 02:09:23,158] [main] testng.multiplier = 1.0
[testng] [2024-10-09 02:09:23,158] [main] testng.in-memory = false
[testng] [2024-10-09 02:09:23,159] [main] testng.allow-missing = false
[testng] [2024-10-09 02:09:23,159] [main] user.language = en
[testng] [2024-10-09 02:09:23,159] [main] user.country = ${user.country}
[testng] [2024-10-09 02:09:23,159] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-10-09 02:09:30,476] [main] ----------------------------------------
[testng] [2024-10-09 02:09:30,477] [main] Total files: 20
[testng] [2024-10-09 02:09:30,477] [main] Scan time: 7.317 s (365 ms/file)
[testng] [2024-10-09 02:09:30,477] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 20 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-09 02:09:37,061] [pool-1-thread-1] Initializing /data/dan/one.mrc:
[testng] 02:09:37,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:09:37,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:09:37,063 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-09_02-09-37.log]
[testng] 02:09:37,064 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69a11c80 - End of configuration.
[testng] [2024-10-09 02:09:37,361] [pool-1-thread-12] Initializing /data/samples/1160.mrc:
[testng] 02:09:37,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:09:37,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:09:37,362 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-09_02-09-37.log]
[testng] 02:09:37,363 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71559fa0 - End of configuration.
[testng] [2024-10-09 02:09:37,656] [pool-1-thread-11] Initializing /data/ascb/c191ali.mrc:
[testng] 02:09:37,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:09:37,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:09:37,658 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-09_02-09-37.log]
[testng] 02:09:37,658 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73fe09b - End of configuration.
[testng] [2024-10-09 02:09:38,455] [pool-1-thread-10] Initializing /data/bioformats2raw-198/test_uint8.mrc:
[testng] 02:09:38,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:09:38,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:09:38,456 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-09_02-09-38.log]
[testng] 02:09:38,456 |-INFO in ch.qos.logback.core.sift.SiftProcessor@528b6fee - End of configuration.
[testng] [2024-10-09 02:09:38,826] [pool-1-thread-9] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc:
[testng] 02:09:38,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:09:38,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:09:38,827 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-09_02-09-38.log]
[testng] 02:09:38,828 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e3710da - End of configuration.
[testng] [2024-10-09 02:09:39,216] [pool-1-thread-8] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc:
[testng] 02:09:39,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:09:39,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:09:39,217 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-09_02-09-39.log]
[testng] 02:09:39,217 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e206dd - End of configuration.
[testng] [2024-10-09 02:09:39,722] [pool-1-thread-7] Initializing /data/jcb/thylakoid5.rec:
[testng] 02:09:39,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:09:39,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:09:39,723 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-09_02-09-39.log]
[testng] 02:09:39,723 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c0165b7 - End of configuration.
[testng] [2024-10-09 02:09:40,027] [pool-1-thread-6] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc:
[testng] 02:09:40,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:09:40,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:09:40,028 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-09_02-09-40.log]
[testng] 02:09:40,028 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a49712d - End of configuration.
[testng] [2024-10-09 02:09:40,339] [pool-1-thread-5] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc:
[testng] 02:09:40,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:09:40,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:09:40,340 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-09_02-09-40.log]
[testng] 02:09:40,340 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34aaa8c2 - End of configuration.
[testng] [2024-10-09 02:09:40,685] [pool-1-thread-4] Initializing /data/dan/three.mrc:
[testng] 02:09:40,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:09:40,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:09:40,686 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-09_02-09-40.log]
[testng] 02:09:40,687 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c1e8179 - End of configuration.
[testng] [2024-10-09 02:09:40,974] [pool-1-thread-3] Initializing /data/ascb/cfa1071.mrc:
[testng] 02:09:40,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:09:40,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:09:40,975 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-09_02-09-40.log]
[testng] 02:09:40,976 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bc12d6 - End of configuration.
[testng] [2024-10-09 02:09:41,295] [pool-1-thread-2] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map:
[testng] 02:09:41,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:09:41,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:09:41,296 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-09_02-09-41.log]
[testng] 02:09:41,297 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5726210a - End of configuration.
[testng] [2024-10-09 02:09:46,324] [pool-1-thread-10] Initializing /data/ticket-10073/wtjoin4.rec:
[testng] [2024-10-09 02:09:46,639] [pool-1-thread-5] Initializing /data/samples/golgi.mrc:
[testng] [2024-10-09 02:09:46,980] [pool-1-thread-2] Initializing /data/ascb/c191.st:
[testng] [2024-10-09 02:09:47,266] [pool-1-thread-9] Initializing /data/dan/two.mrc:
[testng] [2024-10-09 02:09:47,666] [pool-1-thread-11] Initializing /data/ascb/514_9903.mrc:
[testng] [2024-10-09 02:09:48,041] [pool-1-thread-7] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc:
[testng] [2024-10-09 02:09:48,398] [pool-1-thread-6] Initializing /data/jcb/thyl-apr23-4.rec:
[testng] [2024-10-09 02:09:48,814] [pool-1-thread-1] 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: 38 seconds
Finished: SUCCESS