Package: MLP

Version: 1.1.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings MLP_1.1.0.tar.gz

StartedAt: 2011-05-09 14:38:00 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:41:09 -0700 (Mon, 09 May 2011)

EllapsedTime: 188.4 seconds

RetCode: 0

Status:  OK

CheckDir: MLP.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/MLP.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-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 '1.1.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'MLP' can be installed ... OK
* 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 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 ... 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 ... 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' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'MLP' ...
** R
** inst
** preparing package for lazy loading
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: gtools
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: 'gdata'

The following object(s) are masked from 'package:Biobase':

    combine

The following object(s) are masked from 'package:stats':

    nobs

The following object(s) are masked from 'package:utils':

    object.size

Loading required package: caTools
Loading required package: bitops
Loading required package: grid

Attaching package: 'gplots'

The following object(s) are masked from 'package:plotrix':

    plotCI

The following object(s) are masked from 'package:stats':

    lowess

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'UsingMLP.Rnw' 
** testing if installed package can be loaded

* DONE (MLP)

name	user	system	elapsed
MLP	33.19	0.81	34.11
getGeneSets	21.56	0.79	25.81
mlpBarplot	0.11	0.00	0.11
plot.MLP	2.91	0.04	3.83
plotGOgraph	0.56	0.02	0.58
plotGeneSetSignificance	0.98	0.01	1.00