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BioC 3.4: BUILD report for AtlasRDF on zin1

This page was generated on 2016-09-21 03:38:45 -0700 (Wed, 21 Sep 2016).

Package 71/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AtlasRDF 1.9.0
James Malone
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AtlasRDF
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded [ ERROR ] skipped 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  ERROR  skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: AtlasRDF
Version: 1.9.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data AtlasRDF
StartedAt: 2016-09-19 23:57:48 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 23:57:52 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 3.7 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data AtlasRDF
###
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* checking for file ‘AtlasRDF/DESCRIPTION’ ... OK
* preparing ‘AtlasRDF’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: hash
hash-2.2.6 provided by Decision Patterns

Loading required package: SPARQL
Loading required package: XML
Loading required package: RCurl
Loading required package: bitops
An error occured when trying SPARQL query for includeOnlySubclasses function Error: XML content does not seem to be XML: 'virtuoso.jdbc4.VirtuosoException: Connection failed: Connection refused'

Error in retrieving subclasses of class efo:EFO_0000408

Error: processing vignette 'AtlasRDF_vignette.Rnw' failed with diagnostics:
 chunk 13 
Error : trying to get slot "p.value" from an object of a basic class ("NULL") with no slots
Execution halted