BioC 2.13: CHECK report for GeneticsDesign on perceval

Package: GeneticsDesign

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneticsDesign_1.30.0.tar.gz

StartedAt: 2014-04-05 01:32:33 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:32:58 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 25.0 seconds

RetCode: 0

Status:  OK

CheckDir: GeneticsDesign.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/GeneticsDesign.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 ‘GeneticsDesign/DESCRIPTION’ ... OK
* this is package ‘GeneticsDesign’ version ‘1.30.0’
* 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 ‘GeneticsDesign’ can be installed ... [2s/2s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
power.casectrl.plot: warning in matrix(NA, nc = J, nr = length(p)):
  partial argument match of 'nr' to 'nrow'
power.casectrl.plot: warning in matrix(NA, nc = J, nr = length(p)):
  partial argument match of 'nc' to 'ncol'
pw: warning in matrix(c(1, pi, pi, 1), nr = 2): partial argument match
  of 'nr' to 'nrow'
pw: warning in matrix(c(sd1^2, sd1 * sd2, sd1 * sd2, sd2^2), nr = 2):
  partial argument match of 'nr' to 'nrow'
simu.genotype.conti: warning in matrix(c(1, pi, pi, 1), nr = 2):
  partial argument match of 'nr' to 'nrow'
simu.genotype.conti: warning in matrix(c(sd1^2, sd1 * sd2, sd1 * sd2,
  sd2^2), nr = 2): partial argument match of 'nr' to 'nrow'
* checking Rd files ... NOTE
prepare_Rd: power.genotype.conti.Rd:36-38: Dropping empty section \details
* 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’:
  ‘GPC.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [1s/1s] 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 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/GeneticsDesign.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
GPC	0.022	0.002	0.026
GeneticPower.Quantitative.Numeric	0.015	0.001	0.017
gregorius	0.015	0.001	0.016
power.genotype.conti	0.23	0.01	0.25