Package: MSnbase

Version: 1.1.17

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSnbase_1.1.17.tar.gz

StartedAt: 2011-07-07 04:34:12 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 04:40:04 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 352.2 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/MSnbase.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 for sufficient/correct file permissions ... 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
                  old_size new_size compress
  itraqdata.RData    1.2Mb    356Kb       xz
* checking sizes of PDF files under 'inst/doc' ... 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
Creating a generic function for "plot" from package "graphics" in package "MSnbase"
** 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 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	0.723	0.029	0.764
MSnProcess-class	0.002	0.001	0.001
MSnSet-class	1.162	0.033	1.243
NAnnotatedDataFrame-class	0.040	0.001	0.041
ReporterIons-class	0.026	0.001	0.027
TMT6	0.023	0.001	0.024
clean-methods	0.686	0.018	0.736
combineFeatures	1.139	0.023	1.311
extractPrecSpectra-methods	0.473	0.015	0.497
extractSpectra-methods	0.484	0.014	0.504
formatRt	0.001	0.000	0.001
iTRAQ4	0.023	0.000	0.024
itraqdata	0.653	0.037	0.701
normalise-methods	6.410	0.099	6.589
pSet-class	0.002	0.001	0.002
plot-methods	5.914	0.242	6.236
plot2d-methods	4.508	0.130	4.725
plotDensity-methods	4.321	0.111	4.480
plotMzDelta-methods	32.151	6.509	41.576
precSelection	0.076	0.022	0.099
purityCorrect-methods	1.281	0.045	1.347
quantify-methods	1.328	0.022	1.372
readIspyData	0.000	0.000	0.001
readMzXMLData	0.573	0.015	0.593
removePeaks-methods	0.756	0.015	0.791
removeReporters-methods	4.668	0.095	4.807
trimMz-methods	0.572	0.014	0.591