Package: MSnbase

Version: 1.6.2

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.6.2.tar.gz

StartedAt: 2013-03-25 03:14:04 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:19:02 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 297.4 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/MSnbase.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.6.2’
* 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 for left-over 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 ... OK
* 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
Examples with CPU or elapsed time > 5s
                      user system elapsed
plotMzDelta-methods 20.401   0.36  20.877
* 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/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	0.804	0.024	0.854
MSnProcess-class	0.000	0.000	0.001
MSnSet-class	1.324	0.024	1.374
NAnnotatedDataFrame-class	0.024	0.000	0.025
ReporterIons-class	0.016	0.000	0.015
TMT6	0.012	0.000	0.016
clean-methods	1.460	0.012	1.493
combineFeatures	1.076	0.008	1.110
extractPrecSpectra-methods	0.380	0.008	0.388
fillUp	0.004	0.000	0.008
formatRt	0	0	0
getVariableName	0.004	0.000	0.002
iTRAQ4	0.016	0.000	0.015
itraqdata	0.068	0.000	0.067
nQuants	4.224	0.016	4.463
normalise-methods	4.337	0.004	4.391
pSet-class	0.000	0.000	0.001
plot-methods	1.772	0.000	1.821
plot2d-methods	1.436	0.016	2.042
plotDensity-methods	1.120	0.012	1.133
plotMzDelta-methods	20.401	0.360	20.877
plotNA-methods	4.493	0.008	4.566
precSelection	0.068	0.000	0.064
purityCorrect-methods	4.060	0.016	4.225
quantify-methods	4.312	0.012	4.369
readIspyData	0	0	0
readMSData	0.400	0.012	0.422
readMSnSet	0	0	0
readMgfData	0	0	0
readMzTabData	0.004	0.000	0.000
removePeaks-methods	1.624	0.000	1.642
removeReporters-methods	1.168	0.024	1.194
trimMz-methods	0.168	0.004	0.220
writeMgfData-methods	0.000	0.000	0.001
writeMzTabData	0.000	0.000	0.001