Package: MergeMaid

Version: 2.29.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MergeMaid_2.29.1.tar.gz

StartedAt: 2012-06-21 01:37:09 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 01:39:32 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 142.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MergeMaid.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/MergeMaid.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MergeMaid/DESCRIPTION' ... OK
* this is package 'MergeMaid' version '2.29.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'MergeMaid' 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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
.plot.mergeExpressionSet: warning in signif(score, digit = 3): partial
  argument match of 'digit' to 'digits'
.fdr.mergeCor: no visible global function definition for '.getnull'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'geneNames' 'geneNames<-'
Undocumented S4 methods:
  generic 'geneNames<-' and siglist 'mergeExpressionSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... 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.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/MergeMaid.Rcheck/00check.log'
for details.

* installing *source* package 'MergeMaid' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'MergeMaid'
Creating a generic function for 'hist' from package 'graphics' in package 'MergeMaid'
Creating a generic function for 'summary' from package 'base' in package 'MergeMaid'
** help
*** installing help indices
** building package indices
** installing vignettes
   'MergeMaid.Rnw' 
** testing if installed package can be loaded

* DONE (MergeMaid)

name	user	system	elapsed
class.mergeCoeff	2.975	0.061	3.124
class.mergeCor	6.611	0.091	7.007
class.mergeExpressionSet	14.737	0.101	15.232
intCor	8.765	0.157	9.075
intcorDens	34.212	0.364	35.830
intersection	0.636	0.024	0.669
mergeExprs	7.102	0.187	7.354
modelOutcome	3.686	0.041	3.839