Package: cosmoGUI

Version: 1.12.0

Command: /home/biocbuild/bbs-2.5-bioc/R/bin/R CMD check --no-vignettes cosmoGUI_1.12.0.tar.gz

StartedAt: 2009-12-14 04:09:52 -0800 (Mon, 14 Dec 2009)

EndedAt: 2009-12-14 04:10:16 -0800 (Mon, 14 Dec 2009)

EllapsedTime: 23.6 seconds

RetCode: 0

Status: OK

CheckDir: cosmoGUI.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.5-bioc/meat/cosmoGUI.Rcheck'
* using R version 2.10.0 (2009-10-26)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'cosmoGUI/DESCRIPTION' ... OK
* this is package 'cosmoGUI' version '1.12.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'cosmoGUI' 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 whether the name space 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
advanced: no visible binding for '<<-' assignment to ‘COSMO.WIDGET’
advancedBuild: no visible binding for '<<-' assignment to
  ‘COSMO.CONSTRAINTS’
constraintBuilder: no visible binding for global variable
  ‘COSMO.CONSTRAINTS’
constraintBuilder: no visible binding for '<<-' assignment to
  ‘COSMO.CONSTRAINTS’
mysample: no visible binding for '<<-' assignment to ‘COSMO.WIDGET’
sampleA: no visible binding for '<<-' assignment to ‘COSMO.CONSTRAINTS’
sampleICBound: no visible binding for '<<-' assignment to
  ‘COSMO.CONSTRAINTS’
sampleICStep: no visible binding for '<<-' assignment to
  ‘COSMO.CONSTRAINTS’
sampleV: no visible binding for '<<-' assignment to ‘COSMO.CONSTRAINTS’
subMotif: no visible binding for '<<-' assignment to
  ‘COSMO.CONSTRAINTS’
* checking Rd files ... NOTE
prepare_Rd: constraintBuilder.Rd:35-36: Dropping empty section \seealso
* 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 examples ... OK
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package ‘cosmoGUI’ ...
** R
** preparing package for lazy loading
Loading required package: widgetTools
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: DynDoc
Loading required package: tools
Loading required package: seqLogo
Loading required package: grid

Welcome to cosmo version 1.12.0 

cosmo is free for research purposes only. For more details, type
license.cosmo(). Type citation('cosmo') for details on how to cite
cosmo in publications.
** help
*** installing help indices
** building package indices ...
* DONE (cosmoGUI)