Package: MSnbase

Version: 1.1.17

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch MSnbase_1.1.17.tar.gz

StartedAt: 2011-07-07 05:20:28 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 05:24:33 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 244.6 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/MSnbase.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSnbase/DESCRIPTION' ... OK
* this is package 'MSnbase' version '1.1.17'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'MSnbase' 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 ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R'
 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

* installing *source* package 'MSnbase' ...
** R
** data
**  moving datasets to lazyload DB
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")'.

Creating a generic function for "plot" from package "graphics" in package "MSnbase"
** inst
** preparing package for lazy loading
Warning in FUN(X[[1L]], ...) :
  Created a package name, "2011-07-07 05:20:38", when none found
Warning in FUN(X[[1L]], ...) :
  Created a package name, "2011-07-07 05:20:38", when none found
Warning in FUN(X[[1L]], ...) :
  Created a package name, "2011-07-07 05:20:38", when none found
Warning in FUN(X[[1L]], ...) :
  Created a package name, "2011-07-07 05:20:38", when none found
Warning in FUN(X[[1L]], ...) :
  Created a package name, "2011-07-07 05:20:38", when none found
Warning in FUN(X[[1L]], ...) :
  Created a package name, "2011-07-07 05:20:38", when none found
Warning in FUN(X[[1L]], ...) :
  Created a package name, "2011-07-07 05:20:38", when none found
Warning in FUN(X[[1L]], ...) :
  Created a package name, "2011-07-07 05:20:38", when none found
Warning in FUN(X[[1L]], ...) :
  Created a package name, "2011-07-07 05:20:38", when none found
Warning in FUN(X[[1L]], ...) :
  Created a package name, "2011-07-07 05:20:38", when none found
Warning in FUN(X[[1L]], ...) :
  Created a package name, "2011-07-07 05:20:38", when none found
Warning in FUN(X[[1L]], ...) :
  Created a package name, "2011-07-07 05:20:38", when none found
Warning in FUN(X[[1L]], ...) :
  Created a package name, "2011-07-07 05:20:38", when none found
Warning in FUN(X[[1L]], ...) :
  Created a package name, "2011-07-07 05:20:38", when none found
Loading required package: reshape
Loading required package: plyr

Attaching package: 'reshape'

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

    rename, round_any

Loading required package: grid
Loading required package: proto
Creating a generic function for "plot" from package "graphics" in package "MSnbase"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'MSnbase-demo.Rnw' 
   'MSnbase-development.Rnw' 
** testing if installed package can be loaded

* DONE (MSnbase)

name	user	system	elapsed
MSnExp-class	0.72	0.02	0.78
MSnProcess-class	0	0	0
MSnSet-class	0.92	0.00	0.92
NAnnotatedDataFrame-class	0.03	0.00	0.03
ReporterIons-class	0.02	0.00	0.02
TMT6	0.02	0.00	0.01
clean-methods	0.61	0.00	0.61
combineFeatures	1.09	0.00	1.10
extractPrecSpectra-methods	0.45	0.00	0.45
extractSpectra-methods	0.49	0.00	0.48
formatRt	0	0	0
iTRAQ4	0.01	0.00	0.02
itraqdata	0.75	0.00	0.75
normalise-methods	4.63	0.02	4.64
pSet-class	0	0	0
plot-methods	4.92	0.00	4.92
plot2d-methods	3.29	0.01	3.29
plotDensity-methods	3.5	0.0	3.5
plotMzDelta-methods	32.67	1.16	33.85
precSelection	0.06	0.00	0.06
purityCorrect-methods	0.97	0.00	0.97
quantify-methods	0.97	0.00	0.97
readIspyData	0	0	0
readMzXMLData	0.5	0.0	0.5
removePeaks-methods	0.59	0.00	0.59
removeReporters-methods	3.28	0.00	3.28
trimMz-methods	0.58	0.00	0.58