BioC 2.13: CHECK report for MSstats on perceval

Package: MSstats

Version: 2.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSstats_2.0.1.tar.gz

StartedAt: 2014-04-05 02:57:56 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:03:33 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 337.2 seconds

RetCode: 0

Status:  OK

CheckDir: MSstats.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/MSstats.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘2.0.1’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSstats’ can be installed ... [29s/31s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... 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 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
.fit.model: no visible binding for global variable ‘LABEL’
.fit.model: no visible binding for global variable ‘i’
.fit.model.single: no visible binding for global variable ‘i’
.fit.model.single: no visible binding for global variable ‘LABEL’
.iter.wls.fit.model: no visible binding for global variable ‘weight’
dataProcess: no visible binding for global variable ‘LABEL’
dataProcessPlots: no visible binding for global variable ‘LABEL’
groupComparisonPlots: no visible binding for global variable
  ‘which.Protein’
groupComparisonPlots: no visible binding for global variable
  ‘adj.pvalue’
groupComparisonPlots: no visible binding for global variable ‘logFC’
groupComparisonPlots: no visible binding for global variable ‘ciw’
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘MSstats.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [46s/48s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
dataProcessPlots     12.861  0.181  13.305
groupComparisonPlots  4.793  0.130   5.914
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/MSstats.Rcheck/00check.log’
for details.

* installing *source* package ‘MSstats’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.11.0)
than is installed on your system (0.11.1). This might lead to errors
when loading mzR. If you encounter such issues, please send
a report, including the output of sessionInfo() to the Bioc
mailing list -- http://www.bioconductor.org/help/mailing-list.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.11.0)
than is installed on your system (0.11.1). This might lead to errors
when loading mzR. If you encounter such issues, please send
a report, including the output of sessionInfo() to the Bioc
mailing list -- http://www.bioconductor.org/help/mailing-list.
* DONE (MSstats)

name	user	system	elapsed
QuantData	0.140	0.011	0.161
RawData	0.014	0.003	0.019
dataProcess	0.307	0.013	0.332
dataProcessPlots	12.861	0.181	13.305
designSampleSize	1.568	0.048	1.665
designSampleSizePlots	1.091	0.053	1.257
groupComparison	2.751	0.085	2.919
groupComparisonPlots	4.793	0.130	5.914
modelBasedQCPlots	1.843	0.046	1.938
quantification	1.913	0.034	2.006
testResultMultiComparisons	0.771	0.025	0.857
testResultOneComparison	0.724	0.027	0.780
transformMSnSetToMSstats	0.992	0.024	1.072
transformMSstatsToMSnSet	0.158	0.005	0.166