Package: MSnbase

Version: 1.6.2

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSnbase_1.6.2.tar.gz

StartedAt: 2013-03-25 00:32:57 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:37:51 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 294.0 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 2.15.3 (2013-03-01)
* 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 '1.6.2'
* 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
plotMzDelta-methods 19.387  5.267  25.249
* 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
** 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	0.637	0.037	0.678
MSnProcess-class	0.001	0.001	0.001
MSnSet-class	1.230	0.096	1.347
NAnnotatedDataFrame-class	0.026	0.001	0.027
ReporterIons-class	0.016	0.001	0.017
TMT6	0.015	0.000	0.015
clean-methods	1.868	0.039	1.933
combineFeatures	0.831	0.044	0.880
extractPrecSpectra-methods	0.338	0.022	0.366
fillUp	0.008	0.000	0.009
formatRt	0.001	0.000	0.001
getVariableName	0.002	0.000	0.002
iTRAQ4	0.017	0.001	0.018
itraqdata	0.068	0.027	0.095
nQuants	4.724	0.089	4.860
normalise-methods	4.477	0.085	4.584
pSet-class	0.000	0.000	0.001
plot-methods	1.667	0.196	2.004
plot2d-methods	1.265	0.134	1.412
plotDensity-methods	1.095	0.127	1.237
plotMzDelta-methods	19.387	5.267	25.249
plotNA-methods	4.861	0.084	4.995
precSelection	0.068	0.024	0.093
purityCorrect-methods	4.358	0.085	4.465
quantify-methods	4.546	0.089	4.701
readIspyData	0	0	0
readMSData	0.319	0.017	0.353
readMSnSet	0.000	0.000	0.001
readMgfData	0.000	0.000	0.001
readMzTabData	0	0	0
removePeaks-methods	1.757	0.102	1.876
removeReporters-methods	0.899	0.082	0.983
trimMz-methods	0.156	0.015	0.172
writeMgfData-methods	0.001	0.000	0.001
writeMzTabData	0.000	0.000	0.001