BioC 2.13: CHECK report for MSnbase on perceval

Package: MSnbase

Version: 1.10.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSnbase_1.10.4.tar.gz

StartedAt: 2014-04-05 02:57:40 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:03:31 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 351.5 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/MSnbase.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 ‘MSnbase/DESCRIPTION’ ... OK
* this is package ‘MSnbase’ version ‘1.10.4’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSnbase’ can be installed ... [21s/23s] 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 ... NOTE
Unexported object imported by a ‘:::’ call: ‘Biobase:::.showAnnotatedDataFrame’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘MSnbase-demo.Rnw’, ‘MSnbase-development.Rnw’, ‘MSnbase-io.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [85s/95s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
writeMzTabData        9.455  0.138  18.168
readMgfData           8.846  0.115   9.080
plotMzDelta-methods   5.571  0.131   5.783
nQuants               5.408  0.032   5.496
plotNA-methods        5.100  0.061   5.295
exprsToRatios-methods 5.007  0.049   5.119
normalise-methods     5.024  0.031   5.142
impute-methods        4.840  0.032   5.078
purityCorrect-methods 4.780  0.065   5.019
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [44s/45s]
 [45s/46s] OK
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ call not declared from: ‘multicore’
* 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 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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
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.
Creating a generic function for ‘scale’ from package ‘base’ in package ‘MSnbase’
** 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 (MSnbase)

name	user	system	elapsed
MSnExp-class	0.516	0.027	0.584
MSnProcess-class	0.008	0.001	0.009
MSnSet-class	1.704	0.046	1.782
NAnnotatedDataFrame-class	0.039	0.003	0.046
ReporterIons-class	0.032	0.004	0.036
TMT6	0.044	0.003	0.048
chromatogram-methods	0.095	0.023	0.208
clean-methods	2.295	0.023	2.365
combineFeatures	0.870	0.013	0.892
exprsToRatios-methods	5.007	0.049	5.119
extractPrecSpectra-methods	0.496	0.006	0.503
featureCV	0.598	0.014	0.657
fillUp	0.022	0.005	0.031
formatRt	0.006	0.002	0.012
getVariableName	0.013	0.004	0.017
iTRAQ4	0.034	0.005	0.046
impute-methods	4.840	0.032	5.078
itraqdata	0.090	0.009	0.100
nQuants	5.408	0.032	5.496
normalise-methods	5.024	0.031	5.142
pSet-class	0.022	0.007	0.029
plot-methods	1.856	0.087	2.012
plot2d-methods	1.470	0.041	1.554
plotDensity-methods	1.271	0.023	1.319
plotMzDelta-methods	5.571	0.131	5.783
plotNA-methods	5.100	0.061	5.295
precSelection	0.080	0.004	0.084
purityCorrect-methods	4.780	0.065	5.019
quantify-methods	4.565	0.062	4.696
readIspyData	0.003	0.002	0.005
readMSData	0.513	0.015	0.532
readMSnSet	0.003	0.007	0.011
readMgfData	8.846	0.115	9.080
readMzTabData	0.387	0.007	0.713
removePeaks-methods	2.765	0.083	2.887
removeReporters-methods	0.959	0.026	1.001
trimMz-methods	0.185	0.017	0.205
writeMgfData-methods	0.035	0.012	0.048
writeMzTabData	9.455	0.138	18.168
xic-methods	0.009	0.006	0.015