Back to the "Multiple platform build/check report"[A] B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.5: BUILD report for AtlasRDF on malbec2

This page was generated on 2017-08-16 13:15:28 -0400 (Wed, 16 Aug 2017).

Package 75/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AtlasRDF 1.12.0
Simon Jupp
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/AtlasRDF
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded [ ERROR ] skipped 
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  ERROR  skipped  skipped 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: AtlasRDF
Version: 1.12.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data AtlasRDF
StartedAt: 2017-08-15 19:30:13 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 19:31:09 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 56.7 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data AtlasRDF
###
##############################################################################
##############################################################################


* 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: Virtuoso Communications Link Failure (timeout) : Connection reset'

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