BioC 2.13: CHECK report for affycomp on perceval

Package: affycomp

Version: 1.38.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affycomp_1.38.0.tar.gz

StartedAt: 2014-04-04 23:10:55 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:11:56 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 60.1 seconds

RetCode: 0

Status:  OK

CheckDir: affycomp.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/affycomp.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 ‘affycomp/DESCRIPTION’ ... OK
* this is package ‘affycomp’ version ‘1.38.0’
* 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 ‘affycomp’ can be installed ... [4s/4s] OK
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
* 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
Packages in Depends field not imported from:
  ‘Biobase’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 ... NOTE
affycomp.figure2b: warning in affycomp.compfig2b(list(l), method.name =
  l$method.name, add.legend = FALSE, main = main): partial argument
  match of 'method.name' to 'method.names'
affycompPlot: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
tableAll: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
tableOverallSNR: warning in vector(mode = "character", len = N):
  partial argument match of 'len' to 'length'
tableRanks: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
* 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’:
  ‘affycomp.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [9s/10s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/affycomp.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
SD	1.415	0.109	1.761
affycomp.compfigs.auxiliary	1.038	0.085	1.141
affycomp.figures.auxiliary	0.583	0.076	0.675
affycomp.table	1.526	0.109	1.702
affycompPlot	1.700	0.319	2.109