BioC 2.12: CHECK report for affycoretools on george2

Package: affycoretools

Version: 1.32.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings affycoretools_1.32.1.tar.gz

StartedAt: 2013-10-08 23:54:42 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-09 00:05:48 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 665.7 seconds

RetCode: 0

Status:  OK

CheckDir: affycoretools.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/affycoretools.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affycoretools/DESCRIPTION’ ... OK
* this is package ‘affycoretools’ version ‘1.32.1’
* 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 ‘affycoretools’ can be installed ... [63s/65s] OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
* 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 ... OK
* checking R code for possible problems ... NOTE
getMainProbes: no visible binding for global variable ‘eset’
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [62s/62s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
plotDeg 27.842  0.216  28.568
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/affycoretools.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
annBM	0.004	0.004	0.005
makeVenn	0.024	0.004	0.029
plotDeg	27.842	0.216	28.568
plotPCA	1.388	0.020	1.406
vennCounts2	0.084	0.008	0.093
vennPage	0.032	0.004	0.035