Package: MSnbase

Version: 1.4.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.4.0.tar.gz

StartedAt: 2012-04-01 02:17:37 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 02:20:27 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 170.4 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/MSnbase.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSnbase/DESCRIPTION' ... OK
* this is package 'MSnbase' version '1.4.0'
* 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 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'
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 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
  '/loc/home/hpages/test-puck5/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	0.428	0.000	0.433
MSnProcess-class	0.000	0.000	0.001
MSnSet-class	0.636	0.072	0.800
NAnnotatedDataFrame-class	0.024	0.000	0.024
ReporterIons-class	0.016	0.004	0.019
TMT6	0.016	0.000	0.014
clean-methods	0.412	0.020	0.438
combineFeatures	0.808	0.164	0.660
extractPrecSpectra-methods	0.240	0.016	0.262
extractSpectra-methods	0.244	0.004	0.255
fillUp	0.008	0.000	0.007
formatRt	0.000	0.000	0.001
iTRAQ4	0.016	0.000	0.014
itraqdata	0.036	0.004	0.041
normalise-methods	3.844	0.472	1.496
pSet-class	0.000	0.000	0.001
plot-methods	1.620	0.008	1.633
plot2d-methods	1.092	0.000	1.089
plotDensity-methods	0.872	0.004	0.875
plotMzDelta-methods	12.949	0.308	13.267
plotNA-methods	4.076	0.436	1.486
precSelection	0.044	0.000	0.043
purityCorrect-methods	1.272	0.312	0.720
quantify-methods	0.636	0.180	0.744
readIspyData	0	0	0
readMSData	0.232	0.028	0.265
readMSnSet	0	0	0
readMgfData	0	0	0
removePeaks-methods	0.372	0.000	0.377
removeReporters-methods	0.772	0.004	0.777
trimMz-methods	0.268	0.000	0.275
writeMgfData-methods	0	0	0