Package: GeneSpring

Version: 2.25.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneSpring_2.25.0.tar.gz

StartedAt: 2011-03-17 16:23:50 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 16:24:18 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 27.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GeneSpring.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/GeneSpring.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GeneSpring/DESCRIPTION' ... OK
* this is package 'GeneSpring' version '2.25.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GeneSpring' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: GSload.exp.Rd:90-91: Dropping empty section \examples
prepare_Rd: GSload.genelist.Rd:70-71: Dropping empty section \seealso
prepare_Rd: GSload.int.Rd:78-79: Dropping empty section \examples
* 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 ... WARNING
Assignments in \usage in documentation object 'GSint2BC':
  expr.set <- GSint2BC(interpretation, what = "nor")
  gs.int <- BC2GSint(exprSet)

Assignments in \usage in documentation object 'GSload.exp':
  gs.int <- GSload.exp(filename = "GS_R_in.txt", EOF = "///", chunk = 1, 
      append = FALSE)
  expr.set <- GSload.expBC(filename = "GS_R_in.txt", EOF = "///", 
      chunk = 1, append = TRUE)

Assignments in \usage in documentation object 'GSload.genelist':
  glist <- GSload.genelist(filename = "GS_R_in.txt", EOF = "///", 
      chunk = 1)

Assignments in \usage in documentation object 'GSload.int':
  gs.int <- GSload.int(filename = "GS_R_in.txt")
  expr.set <- GSload.intBC(filename = "GS_R_in.txt", what = "nor")

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  '/Users/biocbuild/bbs-2.8-bioc/meat/GeneSpring.Rcheck/00check.log'
for details

* installing *source* package 'GeneSpring' ...
** R
** inst
** preparing package for lazy loading

Welcome to Bioconductor

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

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GeneSpring)

name	user	system	elapsed
GSint	0.008	0.000	0.008
GSint2BC	0.260	0.003	0.271
GSload.genelist	0.013	0.001	0.014
GSsave.exp	0.106	0.003	0.109