Package: MSnbase

Version: 1.2.3

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSnbase_1.2.3.tar.gz

StartedAt: 2012-03-24 02:42:07 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:47:10 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 302.9 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 2.14.2 (2012-02-29)
* 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 '1.2.3'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 ... NOTE
plot.Spectrum2: no visible binding for global variable 'alpha'
readMSnSet: no visible binding for global variable 'stringAsFactors'
* 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 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
** inst
** preparing package for lazy loading
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' 
   'MSnbase-io.Rnw' 
** testing if installed package can be loaded

* DONE (MSnbase)

name	user	system	elapsed
MSnExp-class	0.633	0.026	0.710
MSnProcess-class	0.002	0.000	0.003
MSnSet-class	0.940	0.040	1.099
NAnnotatedDataFrame-class	0.036	0.001	0.037
ReporterIons-class	0.020	0.001	0.025
TMT6	0.024	0.001	0.025
clean-methods	0.545	0.021	0.588
combineFeatures	0.851	0.023	0.896
extractPrecSpectra-methods	0.350	0.019	0.407
extractSpectra-methods	0.354	0.018	0.435
fillUp	0.013	0.000	0.015
formatRt	0.000	0.000	0.001
iTRAQ4	0.021	0.001	0.023
itraqdata	0.261	0.027	0.310
normalise-methods	5.217	0.083	5.398
pSet-class	0.001	0.000	0.002
plot-methods	2.504	0.232	2.818
plot2d-methods	1.718	0.121	2.081
plotDensity-methods	1.600	0.107	1.739
plotMzDelta-methods	20.264	4.943	26.233
precSelection	0.085	0.027	0.113
purityCorrect-methods	1.077	0.055	1.254
quantify-methods	0.937	0.023	1.030
readIspyData	0	0	0
readMSData	0.344	0.013	0.360
readMSnSet	0.001	0.000	0.000
readMgfData	0.001	0.001	0.000
readMzXMLData	0.544	0.019	0.603
removePeaks-methods	0.562	0.015	0.577
removeReporters-methods	1.246	0.078	1.341
trimMz-methods	0.388	0.016	0.409
writeMgfData-methods	0.000	0.001	0.001