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

[Seth Falcon]

* On 2008-04-04 at 00:04 +1100 Keith Satterley wrote:
> Help please,
> 
> I'm checking over my affylmGUI package under R-2.7.0dev.
> 
> If I do an R CMD check affylmGUI
> 
> with the environment variable _R_CHECK_USE_CODETOOLS_ set to true
> There are no error messages and the package runs ok. However I get over 400 
> lines of messages, the first few of which are:

Do you mean that you get no errors when that var is set to false by
any chance?

> 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.

> Many variables are assigned to this environment with statements like:
> 
> assign("Targets",      data.frame(),affylmGUIenvironment)
> assign("adjustMethod","BH",         affylmGUIenvironment)
> assign("weightsPLM",   data.frame(),affylmGUIenvironment)

These could all be written like:

   affylmGUIenvironment[["Targets"]] <- data.frame()

> I (or the original programmer) then used it in the ViewRNATargets function with 
> some code like:
> 
> Targets <- get("Targets",envir=affylmGUIenvironment)

And this can be written as:

   Targets <- affylmGUIenvironment[["Targets"]]

> The affylmGUIenvironment variable was not passed to the ViewRNATargets function 
> - there were no arguments to this function.
> 
> By putting affylmGUIenvironment in as an argument to the ViewRNATargets 
> function, checkUsage(ViewRNATargets) was happy and no longer reported a non 
> visible binding for the global variable, However the function fails now with a 
> message "Error in get("Targets", envir = affylmGUIenvironment):invalid 'envir' 
> argument.

I think if the affylmGUIenvironment is defined at package scope, as
suggested above, you can define functions that refer to it without
incurring a warning from codetools (untested).

> Question 1. Should I try an eliminate these "no visible binding for global 
> variable" warning messages from codetools?

IMO, yes.

It would be highly advisable to add a NAMESPACE file to the package as
well.


+ seth

-- 
Seth Falcon | http://userprimary.net/user/