[Bioc-devel] no visible binding for global variable message

Laurent Gautier lgautier at gmail.com
Fri Apr 4 15:23:44 CEST 2008

2008/4/3, Seth Falcon <seth at userprimary.net>:
> * On 2008-04-04 at 00:04 +1100 Keith Satterley wrote:

>  > Dealing with the one problem at a time, I thought I would address the
>  > no visible binding for global variable
>  >    'affylmGUIenvironment'
>  > message which occurred in many functions, one for example was the
>  > "ViewRNATargets" function.
>  > "affylmGUIenvironment" is set in the affylmGUI function with the line:
>  >
>  > assign("affylmGUIenvironment",new.env(),.GlobalEnv)
> There's probably a cleaner way to code this now.  I would consider
>  creating the environment within your package instead of the global
>  envirnt.  And mostly for readability, I would not use assignsign() and
>  get() when working with environments, but instead [[ and <-.  So you
>  could have:
>  affylmGUIenvironment <- new.env(hash=TRUE, parent=emptyenv())
>  Read the help page for details, but generally if you are using an
>  environment as a hashtable you don't what it to inherit bindings and
>  parent=emptyenv() is what you want.

I missed that one "new" feature with environments:
methods "[[" and "[[<-".

Looking quickly at the current development bioconductor code,
it seems that "assign" is still very much used.


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