Package: GeneSpring

Version: 2.27.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings GeneSpring_2.27.0.tar.gz

StartedAt: 2011-04-19 12:12:16 -0700 (Tue, 19 Apr 2011)

EndedAt: 2011-04-19 12:12:40 -0700 (Tue, 19 Apr 2011)

EllapsedTime: 23.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GeneSpring.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/GeneSpring.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-06 r55347)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneSpring/DESCRIPTION’ ... OK
* this is package ‘GeneSpring’ version ‘2.27.0’
* 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 ... WARNING
Codoc mismatches from documentation object 'GSload.exp':
GSload.exp
  Code: function(filename = "GS_R_in.txt", EOF = "///", chunk = 1)
  Docs: function(filename = "GS_R_in.txt", EOF = "///", chunk = 1,
                 append = FALSE)
  Argument names in docs not in code:
    append
GSload.expBC
  Code: function(filename = "GS_R_in.txt", EOF = "///", chunk = 1)
  Docs: function(filename = "GS_R_in.txt", EOF = "///", chunk = 1,
                 append = TRUE)
  Argument names in docs not in code:
    append

Codoc mismatches from documentation object 'GSload.int':
GSload.int
  Code: function(filename = "GS_R_in.txt", EOF = "///", chunk = 1)
  Docs: function(filename = "GS_R_in.txt")
  Argument names in code not in docs:
    EOF chunk
GSload.intBC
  Code: function(filename = "GS_R_in.txt", EOF = "///", chunk = 1)
  Docs: function(filename = "GS_R_in.txt", what = "nor")
  Argument names in code not in docs:
    EOF chunk
  Argument names in docs not in code:
    what
  Mismatches in argument names:
    Position: 2 Code: EOF Docs: what

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  ‘/loc/home/biocbuild/bbs-2.9-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 ...
*** tangling vignette sources ...
   ‘GeneSpring.Rnw’ 
** testing if installed package can be loaded

* DONE (GeneSpring)

name	user	system	elapsed
GSint	0.012	0.000	0.011
GSint2BC	0.264	0.008	0.277
GSload.genelist	0.012	0.000	0.011
GSsave.exp	0.108	0.004	0.111