Started by upstream project "BIOFORMATS-test-repo" build number 384
originally caused by:
Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3
[BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins8448631778678260233.sh
+ '[' nifti = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_60831_merge_ci -v /uod/idr/repos/curated/nifti:/data -v /uod/idr-scratch/merge-ci/curated/nifti:/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] 20:39:21,503 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15
[testng] 20:39:21,504 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service.
[testng] 20:39:21,504 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 20:39:21,505 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 20:39:21,505 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 20:39:21,506 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 20:39:21,506 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 20:39:21,506 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 20:39:21,506 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 20:39:21,507 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 20:39:21,507 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 20:39:21,507 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 20:39:21,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 20:39:21,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 20:39:21,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 20:39:21,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 20:39:21,690 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 20:39:21,690 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 20:39:21,690 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 20:39:21,691 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 20:39:21,691 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration.
[testng] 20:39:21,691 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point
[testng] 20:39:21,692 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 186 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2025-03-19 20:39:21,700] [main] java.version = 17.0.2
[testng] 20:39:21,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 20:39:21,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 20:39:21,741 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-19_20-39-21.log]
[testng] 20:39:21,743 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration.
[testng] [2025-03-19 20:39:21,744] [main] testng.directory = /data
[testng] [2025-03-19 20:39:21,745] [main] testng.configDirectory = /config
[testng] [2025-03-19 20:39:21,753] [main] testng.multiplier = 1.0
[testng] [2025-03-19 20:39:21,755] [main] testng.in-memory = false
[testng] [2025-03-19 20:39:21,755] [main] testng.allow-missing = false
[testng] [2025-03-19 20:39:21,755] [main] user.language = en
[testng] [2025-03-19 20:39:21,755] [main] user.country = ${user.country}
[testng] [2025-03-19 20:39:21,755] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2025-03-19 20:40:22,412] [main] ----------------------------------------
[testng] [2025-03-19 20:40:22,413] [main] Total files: 23
[testng] [2025-03-19 20:40:22,413] [main] Scan time: 60.657 s (2637 ms/file)
[testng] [2025-03-19 20:40:22,413] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 20 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2025-03-19 20:42:30,989] [pool-1-thread-1] Initializing /data/public/NIH/avg152T1_LR_nifti.nii:
[testng] 20:42:30,990 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 20:42:30,990 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 20:42:30,991 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-19_20-42-30.log]
[testng] 20:42:30,991 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b5dca13 - End of configuration.
[testng] [2025-03-19 20:42:33,567] [pool-1-thread-12] Initializing /data/public/NIH/avg152T1_RL_nifti.nii:
[testng] 20:42:33,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 20:42:33,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 20:42:33,568 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-19_20-42-33.log]
[testng] 20:42:33,568 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50088c86 - End of configuration.
[testng] [2025-03-19 20:42:36,165] [pool-1-thread-11] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr:
[testng] 20:42:36,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 20:42:36,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 20:42:36,167 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-19_20-42-36.log]
[testng] 20:42:36,167 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ceece9 - End of configuration.
[testng] [2025-03-19 20:42:38,716] [pool-1-thread-10] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr:
[testng] 20:42:38,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 20:42:38,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 20:42:38,717 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-19_20-42-38.log]
[testng] 20:42:38,717 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1149438 - End of configuration.
[testng] [2025-03-19 20:42:40,940] [pool-1-thread-9] Initializing /data/public/NIH/zstat1.nii.gz:
[testng] 20:42:40,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 20:42:40,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 20:42:40,941 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-19_20-42-40.log]
[testng] 20:42:40,941 |-INFO in ch.qos.logback.core.sift.SiftProcessor@638e7f7b - End of configuration.
[testng] [2025-03-19 20:42:50,659] [pool-1-thread-8] Initializing /data/public/NIH/minimal.nii:
[testng] 20:42:50,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 20:42:50,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 20:42:50,660 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-19_20-42-50.log]
[testng] 20:42:50,660 |-INFO in ch.qos.logback.core.sift.SiftProcessor@338317da - End of configuration.
[testng] [2025-03-19 20:42:53,195] [pool-1-thread-7] Initializing /data/public/NIH/filtered_func_data.nii.gz:
[testng] 20:42:53,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 20:42:53,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 20:42:53,196 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-19_20-42-53.log]
[testng] 20:42:53,196 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5397e18a - End of configuration.
[testng] [2025-03-19 20:43:08,921] [pool-1-thread-6] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr:
[testng] 20:43:08,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 20:43:08,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 20:43:08,923 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-19_20-43-08.log]
[testng] 20:43:08,923 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7461d7e5 - End of configuration.
[testng] [2025-03-19 20:43:12,228] [pool-1-thread-5] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr:
[testng] 20:43:12,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 20:43:12,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 20:43:12,229 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-19_20-43-12.log]
[testng] 20:43:12,229 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56a5a589 - End of configuration.
[testng] [2025-03-19 20:43:15,490] [pool-1-thread-4] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr:
[testng] 20:43:15,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 20:43:15,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 20:43:15,491 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-19_20-43-15.log]
[testng] 20:43:15,491 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20cb239 - End of configuration.
[testng] [2025-03-19 20:43:19,083] [pool-1-thread-3] Initializing /data/qa-17334/volume4d.nii:
[testng] 20:43:19,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 20:43:19,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 20:43:19,085 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-19_20-43-19.log]
[testng] 20:43:19,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b4efa30 - End of configuration.
[testng] [2025-03-19 20:43:22,871] [pool-1-thread-2] Initializing /data/public/NIH/minimal.hdr:
[testng] 20:43:22,871 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 20:43:22,871 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 20:43:22,872 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-19_20-43-22.log]
[testng] 20:43:22,872 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a67480f - End of configuration.
[testng] [2025-03-19 20:43:56,587] [pool-1-thread-8] Initializing /data/public/NIH/zstat1.nii:
[testng] [2025-03-19 20:44:01,062] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr:
[testng] [2025-03-19 20:44:05,430] [pool-1-thread-1] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz:
[testng] [2025-03-19 20:44:21,547] [pool-1-thread-3] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr:
[testng] [2025-03-19 20:44:30,312] [pool-1-thread-2] Initializing /data/public/NIH/newsirp_final_XML.nii:
[testng] [2025-03-19 20:44:34,647] [pool-1-thread-6] Initializing /data/public/NIH/filtered_func_data.nii:
[testng] [2025-03-19 20:44:38,966] [pool-1-thread-10] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz:
[testng] [2025-03-19 20:44:51,090] [pool-1-thread-5] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1060, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 6 minutes 43 seconds
Finished: SUCCESS