[Bioc-devel] no visible binding for global variable message
keith at wehi.EDU.AU
Thu Apr 3 15:04:19 CEST 2008
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:
* checking R code for possible problems ... NOTE
affylmGUI: no visible binding for global variable
affylmGUI: no visible binding for global variable '.affylmGUIglobals'
affylmGUI : <anonymous>: no visible binding for global variable
There were some messages I found useful, such as " unused argument(s)"
After some investigation, I released I could load the codetools package and get
a function by function report using the checkUsage() function.
This gave me some more useful reports such as "no visible global function
definition for ‘tkrplot’".
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
"affylmGUIenvironment" is set in the affylmGUI function with the line:
Many variables are assigned to this environment with statements like:
I (or the original programmer) then used it in the ViewRNATargets function with
some code like:
Targets <- get("Targets",envir=affylmGUIenvironment)
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'
Question 1. Should I try an eliminate these "no visible binding for global
variable" warning messages from codetools?
Question 2. If I should, how can I do it and still have working code!
Thanks for any suggestions, I'm still learning a lot of the finer points of R,
R version 2.7.0 Under development (unstable) (2008-03-23 r44847)
attached base packages:
 tools tcltk stats graphics grDevices datasets utils
other attached packages:
 affylmGUI_1.13.1 affy_1.17.8 preprocessCore_1.1.5 affyio_1.7.14
The Walter and Eliza Hall Institute of Medical Research
More information about the Bioc-devel