Package: SBMLR

Version: 1.31.0

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check SBMLR_1.31.0.tar.gz

RetCode: 0

Time: 114.0 seconds

Status: WARNINGS

CheckDir: SBMLR.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/SBMLR.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'SBMLR/DESCRIPTION' ... OK
* this is package 'SBMLR' version '1.31.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'SBMLR' 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 ... WARNING
==:
  function(e1, e2)
==.SBML:
  function(model1, model2, ...)

See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
makeLaw: multiple local function definitions for 'lawTempl' with
  different formal arguments
==.SBML: no visible binding for global variable 'S0'
==.SBML: no visible binding for global variable 'BC'
==.SBML: no visible binding for global variable 'sIDs'
==.SBML: no visible binding for global variable 'rLaws'
==.SBML: no visible binding for global variable 'rIDs'
==.SBML: no visible binding for global variable 'V0'
simulate: no visible binding for global variable 'nStates'
simulate : fderiv: no visible binding for global variable 'nReactions'
simulate : fderiv: no visible binding for global variable 'nStates'
simulate : fderiv: no visible binding for global variable 'S0'
simulate : fderiv: no visible binding for global variable 'BC'
simulate : fderiv: no visible binding for global variable 'nRules'
simulate : fderiv: no visible binding for global variable 'rIDs'
simulate : fderiv: no visible binding for global variable 'incid'
simulate : fderiv: no visible binding for global variable 'y0'
simulate: no visible binding for global variable 'y0'
* 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 ... NOTE
S3 methods shown with full name in documentation object '==.SBML':
  ==.SBML

S3 methods shown with full name in documentation object 'summary.SBML':
  summary.SBML

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* creating SBMLR-Ex.R ... OK
* checking examples ... OK
* creating SBMLR-manual.tex ... OK
* checking SBMLR-manual.tex ... OK

WARNING: There was 1 warning, see
  /extra/loc/biocbuild/bbs-2.1-bioc/meat/SBMLR.Rcheck/00check.log
for details

* Installing *source* package 'SBMLR' ...
** R
** inst
** preparing package for lazy loading
Loading required package: XML
Loading required package: odesolve
** help
Note: unmatched right brace in 'summary.SBML' on or after line 16
 >>> Building/Updating help pages for package 'SBMLR'
     Formats: text html latex example 
  equateModels                      text    html    latex   example
  makeLaw                           text    html    latex   example
  readSBML                          text    html    latex   example
  readSBMLR                         text    html    latex   example
  saveSBML                          text    html    latex   example
  saveSBMLR                         text    html    latex   example
  simulate                          text    html    latex   example
  summary.SBML                      text    html    latex   example
** building package indices ...
* DONE (SBMLR)