Package: pickgene

Version: 1.29.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pickgene_1.29.0.tar.gz

StartedAt: 2012-06-21 02:35:03 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 02:35:35 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 31.9 seconds

RetCode: 0

Status:  OK

CheckDir: pickgene.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/pickgene.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'pickgene/DESCRIPTION' ... OK
* this is package 'pickgene' version '1.29.0'
* 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 whether package 'pickgene' can be installed ... OK
* checking installed package size ... 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 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
do.oddsplot: warning in em.ggb(data[[conditions[1]]],
  data[[conditions[2]]], theta, theta[1:3], print = TRUE): partial
  argument match of 'print' to 'printit'
pickgene.poly: warning in pickgene.two(y[, i], intensity, geneid =
  geneID, singlelevel = singlelevel, npick = npickgene, ylab =
  ylabs[i], ...): partial argument match of 'npick' to 'npickgene'
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 ... NOTE
prepare_Rd: Simulation.pickgene.Rd:8: Dropping empty section \keyword
prepare_Rd: Simulation.pickgene.Rd:5-6: Dropping empty section \usage
prepare_Rd: Simulation.pickgene.Rd:7: 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 examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/pickgene.Rcheck/00check.log'
for details.

* installing *source* package 'pickgene' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'pickgene.Rnw' 
** testing if installed package can be loaded

* DONE (pickgene)

name	user	system	elapsed
Simulation.pickgene	1.074	0.154	1.241
em.ggb	0.000	0.000	0.001
model.pickgene	0.012	0.001	0.013
oddsplot	0	0	0
pickgene	0	0	0
robustscale	0.000	0.000	0.001