Package: MLP

Version: 1.0.0

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch MLP_1.0.0.tar.gz

StartedAt: 2011-10-20 15:31:01 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 15:34:58 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 236.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MLP.Rcheck

Warnings: 8

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/MLP.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MLP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MLP' version '1.0.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'MLP' can be installed ... WARNING
Found the following significant warnings:
  Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
  Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
See 'D:/biocbld/bbs-2.8-bioc/meat/MLP.Rcheck/00install.out' for details.
* checking installed package size ... 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
See section 'Generic functions and methods' of the 'Writing R
Extensions' manual.
* checking replacement functions ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... NOTE
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
* checking Rd \usage sections ... NOTE
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' call not declared from: mouse4302mmentrezg.db
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test.MLP.R'
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: mouse4302mmentrezg.db
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   UsingMLP.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 8 warnings, see
  'D:/biocbld/bbs-2.8-bioc/meat/MLP.Rcheck/00check.log'
for details

* installing *source* package 'MLP' ...
** R
** inst
** preparing package for lazy loading
File type 'perl' not found or no open command associated with it.
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
File type 'perl' not found or no open command associated with it.
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
Warning messages:
1: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2 
2: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2 

* DONE (MLP)

name	user	system	elapsed
MLP	34.34	0.73	35.28
getGeneSets	20.64	0.77	74.12
mlpBarplot	0.11	0.00	0.11
plot.MLP	3.04	0.05	3.33
plotGOgraph	0.64	0.01	0.65
plotGeneSetSignificance	0.89	0.02	0.91