Package: categoryCompare

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data categoryCompare

StartedAt: 2013-05-01 00:36:36 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 00:41:57 -0700 (Wed, 01 May 2013)

EllapsedTime: 321.2 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

* checking for file 'categoryCompare/DESCRIPTION' ... OK
* preparing 'categoryCompare':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall,
    clusterEvalQ, clusterExport, clusterMap,
    parApply, parCapply, parLapply, parLapplyLB,
    parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce,
    anyDuplicated, as.data.frame, cbind, colnames,
    duplicated, eval, get, intersect, lapply, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rep.int, rownames, sapply,
    setdiff, sort, table, tapply, union, unique,
    unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view
    with 'browseVignettes()'. To cite Bioconductor,
    see 'citation("Biobase")', and for packages
    'citation("pkgname")'.

Loading required package: AnnotationDbi
Loading required package: org.Hs.eg.db
Loading required package: DBI



Loading required package: Category

Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics' and is not turning on duplicate class definitions for this class

KEGG.db contains mappings based on older data because
  the original resource was removed from the the
  public domain before the most recent update was
  produced. This package should now be considered
  deprecated and future versions of Bioconductor may
  not have it available.  Users who want more current
  data are encouraged to look at the KEGGREST or
  reactome.db packages

Warning in makeValidccLists(.Object) : NAs introduced by coercion

Error: processing vignette 'categoryCompare_vignette.Rnw' failed with diagnostics:
 chunk 14 (label = ExamineResultsBP) 
Error in function (type, msg, asError = TRUE)  : couldn't connect to host
Execution halted