BioC 2.13: CHECK report for RefPlus on perceval

Package: RefPlus

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RefPlus_1.32.0.tar.gz

StartedAt: 2014-04-05 03:48:04 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:52:20 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 255.6 seconds

RetCode: 0

Status:  OK

CheckDir: RefPlus.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/RefPlus.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 ‘RefPlus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RefPlus’ version ‘1.32.0’
* 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 ‘RefPlus’ can be installed ... [15s/16s] 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
Package in Depends field not imported from: ‘affyPLM’
  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 ... OK
* checking Rd files ... NOTE
prepare_Rd: colMedians.Rd:19: Dropping empty section \references
prepare_Rd: rmaref.predict.Rd:29-30: Dropping empty section \examples
* 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’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘RefPlus.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [100s/102s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
RefPlus-package 45.127  2.213  47.966
rmaplus         27.041  2.001  30.047
rma.para        14.723  0.915  15.811
* 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 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/RefPlus.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
RefPlus-package	45.127	2.213	47.966
colMedians	0.003	0.005	0.009
normalize.quantiles2	0.004	0.005	0.010
rma.para	14.723	0.915	15.811
rmaplus	27.041	2.001	30.047