Package: pickgene

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/2.7/Resources/bin/R CMD check pickgene_1.12.0.tar.gz

StartedAt: 2008-10-16 05:53:24 -0700 (Thu, 16 Oct 2008)

EndedAt: 2008-10-16 05:53:59 -0700 (Thu, 16 Oct 2008)

EllapsedTime: 35.0 seconds

RetCode: 0

Status: OK

CheckDir: pickgene.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.2-bioc/meat/pickgene.Rcheck'
* using R version 2.7.2 (2008-08-25)
* using session charset: ASCII
* checking for file 'pickgene/DESCRIPTION' ... OK
* this is package 'pickgene' version '1.12.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'pickgene' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 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
lod.plot: possible error in oddsplot(exp(data[[x]]), exp(data[[y]]),
  theta, col = col, xlab = xlab, ylab = ylab, chip = ""): unused
  argument(s) (chip = "")
nloglik: no visible binding for global variable '.fit.xx'
nloglik: no visible binding for global variable '.fit.yy'
nploglik: no visible binding for global variable '.fit.xx'
nploglik: no visible binding for global variable '.fit.yy'
nploglik: no visible binding for global variable '.fit.zz'
s.check1: no visible global function definition for 'lod'
s.marg: no visible binding for global variable 'x'
shrinkplot: no visible global function definition for 's.fits'
shrinkplot: no visible binding for global variable 'lims'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating pickgene-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating pickgene-manual.tex ... OK
* checking pickgene-manual.tex using pdflatex ... OK

* Installing *source* package 'pickgene' ...
** R
** inst
** preparing package for lazy loading
Loading required package: MASS
** help
Note: ignoring empty \keyword entries
Note: removing empty section \usage
Note: removing empty section \details
 >>> Building/Updating help pages for package 'pickgene'
     Formats: text html latex example 
  Simulation.pickgene               text    html    latex   example
  em.ggb                            text    html    latex   example
  model.pickgene                    text    html    latex   example
  oddsplot                          text    html    latex   example
  pickgene-internal                 text    html    latex
  pickgene                          text    html    latex   example
  robustscale                       text    html    latex   example
** building package indices ...
* DONE (pickgene)