BioC 2.13: CHECK report for affyPara on perceval

Package: affyPara

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affyPara_1.22.0.tar.gz

StartedAt: 2014-04-04 23:14:31 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:16:23 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 112.9 seconds

RetCode: 0

Status:  OK

CheckDir: affyPara.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/affyPara.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 ‘affyPara/DESCRIPTION’ ... OK
* this is package ‘affyPara’ version ‘1.22.0’
* 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 ‘affyPara’ can be installed ... [8s/9s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘affy’
A package should be listed in only one of these fields.
* 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
‘library’ or ‘require’ calls to packages already attached by Depends:
  ‘affy’ ‘aplpack’ ‘snow’ ‘vsn’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘affyio’ ‘aplpack’ ‘methods’ ‘snow’ ‘vsn’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ‘:::’ calls:
  ‘vsn:::isSmall’ ‘vsn:::optimparNames’ ‘vsn:::pstartHeuristic’
  ‘vsn:::vsnLTS’
  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 ... NOTE
Foreign function call to a different package:
  .Call("ReadHeader", ..., PACKAGE = "affyio")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘vsnAddonBoxplots_20-40-60.pdf’ from 515Kb to 45Kb
     compacted ‘vsnStudy.pdf’ from 2095Kb to 318Kb
     compacted ‘vsnSubsamplesBoxplot_25.pdf’ from 213Kb to 20Kb
     compacted ‘vsnSubsamplesBoxplot_50.pdf’ from 529Kb to 44Kb
  consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... NOTE
The following directories should probably not be installed:
  ‘fig’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘affyPara.Rnw’, ‘vsnStudy.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [16s/16s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mergeSplitObjects 7.666  0.401   8.162
* 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 6 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/affyPara.Rcheck/00check.log’
for details.

* installing *source* package ‘affyPara’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (affyPara)

name	user	system	elapsed
MAplotPara	0.010	0.001	0.011
bgcPara	0.134	0.002	0.139
boxplotPara	0.012	0.002	0.015
computeExprSetPara	0.011	0.002	0.013
distributeFiles	0.007	0.001	0.009
mergeSplitObjects	7.666	0.401	8.162
normalizeAffyBatchConstantPara	0.004	0.006	0.010
normalizeAffyBatchInvariantsetPara	0.003	0.013	0.017
normalizeAffyBatchLoessPara	0.004	0.008	0.013
normalizeAffyBatchLoessParaIter	0.026	0.013	0.039
normalizeAffyBatchQuantilesPara	0.004	0.007	0.011
preproPara	0.028	0.010	0.046
qa	0.004	0.008	0.015
readAffybatchPara	0.003	0.007	0.011
removeDistributedFiles	0.003	0.008	0.012
rmaPara	0.003	0.007	0.011
snowReplace	0.003	0.006	0.010
split	2.996	0.283	3.331
vsnPara	0.003	0.008	0.011