Package: MSnbase

Version: 1.4.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSnbase_1.4.1.tar.gz

StartedAt: 2012-09-24 01:01:11 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 01:05:45 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 273.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MSnbase.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/MSnbase.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.4.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* 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 ... WARNING
Found the following significant warnings:

  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_blank' is deprecated.
  Warning: 'theme_rect' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.10-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
Creating a generic function for 'plot' from package 'graphics' in package 'MSnbase'
** 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	0.573	0.021	0.623
MSnProcess-class	0.001	0.000	0.001
MSnSet-class	0.931	0.042	1.078
NAnnotatedDataFrame-class	0.038	0.000	0.039
ReporterIons-class	0.021	0.000	0.022
TMT6	0.017	0.000	0.017
clean-methods	0.583	0.019	0.604
combineFeatures	1.059	0.025	1.084
extractPrecSpectra-methods	0.307	0.014	0.321
extractSpectra-methods	0.284	0.015	0.300
fillUp	0.008	0.000	0.008
formatRt	0.000	0.000	0.001
iTRAQ4	0.018	0.001	0.018
itraqdata	0.225	0.024	0.249
normalise-methods	6.188	0.072	6.430
pSet-class	0.001	0.000	0.002
plot-methods	2.174	0.188	2.368
plot2d-methods	1.251	0.110	1.364
plotDensity-methods	1.408	0.102	1.514
plotMzDelta-methods	14.765	3.656	18.578
plotNA-methods	5.804	0.079	5.887
precSelection	0.097	0.021	0.118
purityCorrect-methods	0.882	0.033	0.916
quantify-methods	0.806	0.021	0.829
readIspyData	0	0	0
readMSData	0.318	0.010	0.330
readMSnSet	0.000	0.000	0.001
readMgfData	0.000	0.000	0.001
removePeaks-methods	0.598	0.015	0.613
removeReporters-methods	1.035	0.056	1.095
trimMz-methods	0.287	0.011	0.298
writeMgfData-methods	0	0	0