Package: gene2pathway

Version: 2.13.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data gene2pathway

StartedAt: 2013-03-07 23:19:17 -0800 (Thu, 07 Mar 2013)

EndedAt: 2013-03-07 23:19:52 -0800 (Thu, 07 Mar 2013)

EllapsedTime: 34.6 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

* checking for file 'gene2pathway/DESCRIPTION' ... OK
* preparing 'gene2pathway':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Loading required package: kernlab
Loading required package: biomaRt
Loading required package: KEGGSOAP
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

*** Deprecation warning ***: Package 'KEGGSOAP' is deprecated.  Use
    KEGGREST instead.
Loading required package: RBGL
Loading required package: graph
Loading required package: AnnotationDbi
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: org.Dm.eg.db
Loading required package: DBI

Loading required package: keggorthology
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db



Error: processing vignette 'gene2pathway.Rnw' failed with diagnostics:
 chunk 4 
Error in .SOAP(KEGGserver, "list_organisms", "", action = KEGGaction,  : 
  object 'KEGGxmlns' not found
Execution halted