BioC 2.13: CHECK report for pickgene on moscato1

Package: pickgene

Version: 1.34.0

Command: rm -rf pickgene.buildbin-libdir && mkdir pickgene.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pickgene.buildbin-libdir pickgene_1.34.0.tar.gz >pickgene-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=pickgene.buildbin-libdir --install="check:pickgene-install.out" --force-multiarch --no-vignettes --timings pickgene_1.34.0.tar.gz && mv pickgene.buildbin-libdir/* pickgene.Rcheck/ && rmdir pickgene.buildbin-libdir

StartedAt: 2014-04-05 05:50:22 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 05:50:58 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 36.7 seconds

RetCode: 0

Status:  OK

CheckDir: pickgene.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/pickgene.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pickgene/DESCRIPTION' ... OK
* this is package 'pickgene' version '1.34.0'
* 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 whether package 'pickgene' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
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 (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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'pickgene.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [2s] OK
** running examples for arch 'x64' ... [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
  'D:/biocbld/bbs-2.13-bioc/meat/pickgene.Rcheck/00check.log'
for details.

install for i386

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

install for x64

* installing *source* package 'pickgene' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pickgene' as pickgene_1.34.0.zip
* DONE (pickgene)

name	user	system	elapsed
Simulation.pickgene	0.85	0.02	0.88
em.ggb	0	0	0
model.pickgene	0.01	0.00	0.02
oddsplot	0	0	0
pickgene	0	0	0
robustscale	0	0	0

name	user	system	elapsed
Simulation.pickgene	0.86	0.02	0.87
em.ggb	0	0	0
model.pickgene	0.02	0.00	0.01
oddsplot	0	0	0
pickgene	0	0	0
robustscale	0	0	0