Package: gene2pathway

Version: 1.9.1

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings gene2pathway_1.9.1.tar.gz

StartedAt: 2011-02-24 19:44:36 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 19:47:21 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 165.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: gene2pathway.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/gene2pathway.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gene2pathway/DESCRIPTION' ... OK
* this is package 'gene2pathway' version '1.9.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'gene2pathway' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getKEGGHierarchy: no visible binding for global variable 'keggOrthDF'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignettes without corresponding PDF:


D:/biocbld/bbs-2.8-bioc/meat/gene2pathway.Rcheck/00_pkg_src/gene2pathway/inst/doc/gene2pathway.Rnw
 SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/gene2pathway.Rcheck/00check.log'
for details

* installing *source* package 'gene2pathway' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: graph
Loading required package: Biobase

Welcome to Bioconductor

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

Loading required package: DBI
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (gene2pathway)

name	user	system	elapsed
ORF2Entrez	0.96	0.07	35.22
gene2pathway	0	0	0
gene2pathway.signaltrans	0	0	0
getComponents	0	0	0
retrain	0	0	0
retrain.signaltrans	0	0	0