Package: MSnbase

Version: 1.5.10

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSnbase_1.5.10.tar.gz

StartedAt: 2012-06-21 01:55:22 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 02:01:35 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 372.7 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/MSnbase.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.5.10'
* 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
quantify.MSnExp: no visible global function definition for
  'registerDoMC'
* 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 installed files from '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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/MSnbase.Rcheck/00check.log'
for details.

* installing *source* package 'MSnbase' ...
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'MSnbase-demo.Rnw' 
   'MSnbase-development.Rnw' 
   'MSnbase-io.Rnw' 
** testing if installed package can be loaded

* DONE (MSnbase)

name	user	system	elapsed
MSnExp-class	0.656	0.032	0.762
MSnProcess-class	0.002	0.001	0.002
MSnSet-class	1.092	0.322	1.754
NAnnotatedDataFrame-class	0.036	0.000	0.037
ReporterIons-class	0.028	0.000	0.029
TMT6	0.021	0.001	0.021
clean-methods	0.608	0.048	0.660
combineFeatures	1.402	0.410	1.812
extractPrecSpectra-methods	0.427	0.062	0.515
fillUp	0.012	0.001	0.013
formatRt	0.000	0.000	0.001
getVariableName	0.002	0.000	0.003
iTRAQ4	0.023	0.001	0.024
itraqdata	0.440	0.030	0.498
nQuants	4.635	0.533	5.505
normalise-methods	6.538	0.587	4.903
pSet-class	0.001	0.000	0.001
plot-methods	2.246	0.230	2.520
plot2d-methods	1.783	0.140	2.024
plotDensity-methods	1.522	0.131	1.676
plotMzDelta-methods	19.231	5.134	24.678
plotNA-methods	6.791	0.630	5.577
precSelection	0.083	0.022	0.111
purityCorrect-methods	4.034	0.608	2.015
quantify-methods	3.747	0.575	4.926
readIspyData	0	0	0
readMSData	0.400	0.053	0.538
readMSnSet	0.001	0.001	0.000
readMgfData	0	0	0
readMzTabData	0.371	0.006	0.823
removePeaks-methods	0.619	0.023	0.699
removeReporters-methods	1.235	0.070	1.422
trimMz-methods	0.414	0.017	0.462
writeMgfData-methods	0.001	0.001	0.001
writeMzTabData	10.920	0.855	20.360