[Bioc-devel] no visible binding for global variable message
seth at userprimary.net
Thu Apr 3 17:39:18 CEST 2008
* 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
> Dealing with the one problem at a time, I thought I would address the
> no visible binding for global variable
> message which occurred in many functions, one for example was the
> "ViewRNATargets" function.
> "affylmGUIenvironment" is set in the affylmGUI function with the line:
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
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'
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?
It would be highly advisable to add a NAMESPACE file to the package as
Seth Falcon | http://userprimary.net/user/
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