Package: MSnbase

Version: 1.0.7

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSnbase_1.0.7.tar.gz

StartedAt: 2011-10-20 16:10:20 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 16:14:59 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 279.5 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/MSnbase.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '1.0.7'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 ... 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 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

* installing *source* package 'MSnbase' ...
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a new generic function for "plot" in "MSnbase"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (MSnbase)

name	user	system	elapsed
MSnExp-class	1.823	0.135	2.025
MSnProcess-class	0.002	0.000	0.001
MSnSet-class	6.973	0.191	7.973
NAnnotatedDataFrame-class	0.038	0.001	0.038
ReporterIons-class	0.022	0.000	0.023
TMT6	0.023	0.000	0.023
clean-methods	10.771	0.162	13.260
extractPrecSpectra-methods	1.528	0.116	1.816
extractSpectra-methods	1.469	0.093	1.640
formatRt	0	0	0
iTRAQ4	0.022	0.001	0.027
pSet-class	0.001	0.001	0.001
plot-methods	12.693	0.626	14.078
plot2d-methods	4.188	0.178	4.865
quantify-methods	7.007	0.188	8.001
readIspyData	0.000	0.001	0.000
readMzXMLData	1.439	0.120	1.829
removePeaks-methods	10.694	0.137	11.102
trimMz-methods	1.544	0.098	1.660