Package: MLP

Version: 0.99.2

Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings MLP_0.99.2.tar.gz

StartedAt: 2010-11-28 19:09:53 -0800 (Sun, 28 Nov 2010)

EndedAt: 2010-11-28 19:12:18 -0800 (Sun, 28 Nov 2010)

EllapsedTime: 145.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MLP.Rcheck

Warnings: 2

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/MLP.Rcheck'
* using R version 2.13.0 Under development (unstable) (2010-11-10 r53547)
* 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 '0.99.2'
* 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 ... 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 'E:/biocbld/bbs-2.8-bioc/meat/MLP.Rcheck/00install.out' for details.
* 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 package vignettes in 'inst/doc' ... WARNING
Package vignettes without corresponding PDF:


E:/biocbld/bbs-2.8-bioc/meat/MLP.Rcheck/00_pkg_src/MLP/inst/doc/UsingMLP.Rnw
 SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings, see
  'E:/biocbld/bbs-2.8-bioc/meat/MLP.Rcheck/00check.log'
for details

* 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
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: gtools
Loading required package: gdata
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
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: 'gdata'

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

    combine

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 ...
** testing if installed package can be loaded

* DONE (MLP)

name	user	system	elapsed
MLP	7.78	0.08	8.20
getGeneSets	19.20	0.47	22.75
mlpBarplot	0.06	0.01	0.08
plot.MLP	1.89	0.11	2.28
plotGOgraph	0.47	0.00	0.47
plotGeneSetSignificance	0.66	0.06	0.71