Package: MSnbase

Version: 1.2.3

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.2.3.tar.gz

StartedAt: 2012-03-24 01:37:39 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:41:27 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 227.9 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/MSnbase.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 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	0.444	0.016	0.459
MSnProcess-class	0.000	0.004	0.002
MSnSet-class	0.728	0.016	0.745
NAnnotatedDataFrame-class	0.028	0.000	0.027
ReporterIons-class	0.016	0.000	0.017
TMT6	0.012	0.000	0.012
clean-methods	0.484	0.012	0.496
combineFeatures	0.716	0.012	0.727
extractPrecSpectra-methods	0.368	0.004	0.371
extractSpectra-methods	0.376	0.000	0.376
fillUp	0.004	0.000	0.007
formatRt	0	0	0
iTRAQ4	0.012	0.000	0.012
itraqdata	0.060	0.000	0.062
normalise-methods	3.596	0.012	3.613
pSet-class	0.000	0.000	0.001
plot-methods	2.156	0.008	2.269
plot2d-methods	1.521	0.008	1.617
plotDensity-methods	1.520	0.004	1.555
plotMzDelta-methods	20.937	0.604	23.793
precSelection	0.056	0.000	0.057
purityCorrect-methods	0.784	0.000	0.784
quantify-methods	1.120	0.000	1.122
readIspyData	0	0	0
readMSData	0.388	0.000	0.386
readMSnSet	0	0	0
readMgfData	0	0	0
readMzXMLData	0.712	0.000	0.714
removePeaks-methods	0.536	0.000	0.540
removeReporters-methods	0.880	0.000	0.878
trimMz-methods	0.464	0.000	0.462
writeMgfData-methods	0	0	0