[BioC] Making data visible in packages (no visible binding for global variable ...)

[Henrik Bengtsson]

On Tue, Oct 28, 2008 at 8:52 AM, Tarca, Adi <atarca at med.wayne.edu> wrote:
>
> Thanks Richard,
> It is indeed true that I do not get anymore "no visible binding"
> message, but the script does not work anymore :).
> I guess what happens is that, when the function tries to use X, it will
> get the one defined in the function first (which is NULL)and not look
> anymore for it the the global environment where the data() call will
> bring it up and initialize it with the real values.

Easy...

X <- NULL; rm(X);
data(myX);

/Henrik

> Regards,
> Adi
>
>
>
>
>
> -----Original Message-----
> From: Richard Pearson [mailto:richard.pearson at postgrad.manchester.ac.uk]
>
> Sent: Tuesday, October 28, 2008 5:38 AM
> To: Tarca, Adi
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Making data visible in packages (no visible binding
> for global variable ...)
>
> Adi
>
> A rather inelegant way to avoid the "no visible binding" message is:
>
> X <- NULL
> data(myX)
>
> Regards
>
> Richard
>
>
> Tarca, Adi wrote:
>> Hi all,
>> I am trying to write a package that contains one function MYF which
>> requires some data (e.g. a matrix X).
>> I put the matrix X in the \data folder as a myX.Rdata file. The
>> function MYF makes a data(myX) call to make X available within MYF
>> before doing some computations.
>> The resulting package gets installed and runs fine but when I do the R
>
>> CMD CHECK I get "no visible binding for global variable X".
>> I have two questions:
>> A) is there a better way to make X visible within MYF rather than
>> making a data() call
>> B) wht should be done to fix the "no visible binding for global
>> variable".
>>
>> Thanks,
>>
>> Adi Tarca
>>
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>
> --
> Richard D. Pearson             richard.pearson at postgrad.manchester.ac.uk
> School of Computer Science,    http://www.cs.man.ac.uk/~pearsonr
> University of Manchester,      Tel: +44 161 275 6178
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