Package: MSnbase

Version: 1.2.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch MSnbase_1.2.0.tar.gz

StartedAt: 2012-01-09 04:25:49 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 04:29:48 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 238.8 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 2.14.1 (2011-12-22)
* 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 '1.2.0'
* 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 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
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	0.34	0.00	0.41
MSnProcess-class	0	0	0
MSnSet-class	0.48	0.00	0.48
NAnnotatedDataFrame-class	0.02	0.00	0.02
ReporterIons-class	0.01	0.00	0.01
TMT6	0.02	0.00	0.02
clean-methods	0.27	0.00	0.26
combineFeatures	0.45	0.00	0.46
extractPrecSpectra-methods	0.11	0.00	0.11
extractSpectra-methods	0.14	0.00	0.14
fillUp	0	0	0
formatRt	0	0	0
iTRAQ4	0.01	0.00	0.01
itraqdata	0.08	0.00	0.08
normalise-methods	3.35	0.03	3.56
pSet-class	0	0	0
plot-methods	3.86	0.00	3.86
plot2d-methods	2.95	0.00	2.96
plotDensity-methods	2.89	0.00	2.89
plotMzDelta-methods	33.78	1.47	35.26
precSelection	0.06	0.00	0.06
purityCorrect-methods	0.58	0.00	0.58
quantify-methods	0.6	0.0	0.6
readIspyData	0	0	0
readMSData	0.14	0.00	0.14
readMSnSet	0	0	0
readMgfData	0	0	0
readMzXMLData	0.65	0.03	0.73
removePeaks-methods	0.24	0.02	0.25
removeReporters-methods	2.53	0.00	2.53
trimMz-methods	0.12	0.00	0.13
writeMgfData-methods	0	0	0