Package: affyPara

Version: 1.19.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affyPara_1.19.2.tar.gz

StartedAt: 2013-03-25 01:02:29 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:04:10 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 101.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: affyPara.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/affyPara.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'affyPara/DESCRIPTION' ... OK
* this is package 'affyPara' version '1.19.2'
* 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 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 ... [7s/7s] WARNING
Found the following significant warnings:
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
See '/Users/biocbuild/bbs-2.12-bioc/meat/affyPara.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call with 'PACKAGE' argument in 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 examples ... [10s/10s] WARNING
Found the following significant warnings:

  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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

WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/affyPara.Rcheck/00check.log'
for details.

* installing *source* package 'affyPara' ...
** R
** inst
** preparing package for lazy loading
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
** help
*** installing help indices
** building package indices
** installing vignettes
   'affyPara.Rnw' 
   'vsnStudy.Rnw' 
** testing if installed package can be loaded
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
* DONE (affyPara)

name	user	system	elapsed
MAplotPara	0.013	0.009	0.021
bgcPara	0.009	0.007	0.016
boxplotPara	0.010	0.008	0.018
computeExprSetPara	0.011	0.008	0.019
distributeFiles	0.008	0.007	0.015
mergeSplitObjects	3.551	0.502	4.067
normalizeAffyBatchConstantPara	0.005	0.009	0.013
normalizeAffyBatchInvariantsetPara	0.004	0.009	0.014
normalizeAffyBatchLoessPara	0.024	0.016	0.040
normalizeAffyBatchLoessParaIter	0.005	0.008	0.013
normalizeAffyBatchQuantilesPara	0.024	0.016	0.039
preproPara	0.005	0.010	0.015
qa	0.005	0.009	0.014
readAffybatchPara	0.005	0.008	0.013
removeDistributedFiles	0.004	0.007	0.012
rmaPara	0.024	0.014	0.039
snowReplace	0.002	0.004	0.007
split	1.519	0.377	1.904
vsnPara	0.004	0.007	0.011