Package: MSnbase

Version: 1.1.7

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings MSnbase_1.1.7.tar.gz

StartedAt: 2011-05-09 14:41:06 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:44:35 -0700 (Mon, 09 May 2011)

EllapsedTime: 208.8 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/MSnbase.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 'MSnbase/DESCRIPTION' ... OK
* this is package 'MSnbase' version '1.1.7'
* 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
** inst
** preparing package for lazy loading

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: 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 new generic function for "plot" in "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	1.68	0.03	1.75
MSnProcess-class	0	0	0
MSnSet-class	5.01	0.01	5.11
NAnnotatedDataFrame-class	0.03	0.00	0.03
ReporterIons-class	0.02	0.00	0.01
TMT6	0.01	0.00	0.02
clean-methods	6.90	0.02	6.95
combineFeatures	4.62	0.03	4.72
extractPrecSpectra-methods	1.28	0.00	1.28
extractSpectra-methods	1.14	0.00	1.14
formatRt	0	0	0
iTRAQ4	0.02	0.00	0.02
pSet-class	0	0	0
plot-methods	9.23	0.03	9.33
plot2d-methods	2.92	0.02	2.97
purityCorrect-methods	4.89	0.01	4.90
quantify-methods	4.69	0.00	4.69
readIspyData	0	0	0
readMzXMLData	1.17	0.00	1.21
removePeaks-methods	7.05	0.02	7.11
trimMz-methods	1.32	0.00	1.36