[Bioc-devel] no visible binding warning messages

[Keith Satterley]

Can you help me overcome warning messages that I am getting with R-2.6.0alpha. 
My package compiles without these warning messages under R-2.5.1.

When running the command:

R CMD check affylmGUI

I get over 400 lines of warning messages like:

* checking R code for possible problems ... NOTE
affylmGUI: no visible binding for global variable
   affylmGUIenvironment
affylmGUI: no visible binding for global variable .affylmGUIglobals
affylmGUI : <anonymous>: no visible binding for global variable
   .affylmGUIglobals
affyPlotMA: no visible binding for global variable
   affylmGUIenvironment
affyPlotMA: no visible binding for global variable .affylmGUIglobals
affyPlotMA : plotFunction: no visible binding for global variable
   .affylmGUIglobals
...

If I set the environment variable _R_CHECK_USE_CODETOOLS_ to false,
I don't get any of these messages and the package compiles fine - no errors, no 
warnings. However I need to remove all these warnings by the deadline date. I 
assume it has something to do with a NAMESPACE, but I haven't worked this out 
very well yet. I can still install this version of affylmGUI and it works OK.

I have googled for "no visible binding for global variable", but find mainly 
reports of other packages at various locations having similar problems. One 
email from Brian Ripley responding to Robert Hankin, didn't help me solve my 
problem.

I tried a NAMESPACE file consisting of
###
#  All variables exported other than those starting with "."
exportPattern("^[^\\.]")
import("limma")
import("tcltk")
###

and changed my .First.lib function to .onLoad, but I ran into problems with the 
.onLoad function and it didn't help with the error messages. I have some way to 
go yet before I understand how I should apply a NAMESPACE and a .onLoad function.

One other point, each variable name in the error message in my DOS Cmd window 
has a hex character immediately before it and just after it. The character 
before each variable name is E6 and the character after each name is C6 - this 
seems a bit odd, but not a real problem as the messages are clear!

Some advice would be appreciated.

My sessionInfo is:
 > sessionInfo()
R version 2.6.0 alpha (2007-09-05 r42787)
i386-pc-mingw32

locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252

attached base packages:
[1] tools     tcltk     stats     graphics  grDevices datasets  utils 
methods   base

other attached packages:
[1] affylmGUI_1.11.5       affy_1.15.7            preprocessCore_0.99.12 
affyio_1.5.8
[5] Biobase_1.15.33        limma_2.11.11
 >

cheers,

Keith
========================
Keith Satterley
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
Parkville, Melbourne,
Victoria, Australia