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Package 239/644HostnameOS / ArchBUILDCHECKBUILD BIN
gene2pathway 2.13.0
Holger Froehlich
Snapshot Date: 2013-03-07 17:01:15 -0800 (Thu, 07 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gene2pathway
Last Changed Rev: 70052 / Revision: 74044
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  ERROR  skipped 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ ERROR ] skipped  skipped 
petty Mac OS X Leopard (10.5.8) / i386  ERROR  skipped  skipped 

Summary

Package: gene2pathway
Version: 2.13.0
Command: chmod a+r gene2pathway -R && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data gene2pathway
StartedAt: 2013-03-07 23:33:29 -0800 (Thu, 07 Mar 2013)
EndedAt: 2013-03-07 23:33:54 -0800 (Thu, 07 Mar 2013)
EllapsedTime: 24.3 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

* 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