[Bioc-devel] Newbie Question - How to submit patches

Paul Gordon gordonp at ucalgary.ca
Fri Oct 14 19:10:11 CEST 2005

Robert Gentleman wrote:

> As for coding standards etc, I refer you to the document Writing R 
> Extensions, and possibly to the R Installation and Administration 
> Guide (both of which should have come with your R).

Thanks for the pointer, it has lot of good tips.  This document though 
seems to use ANSI as a baseline:

The following tools can "safely be assumed" for R extensions.

    * An ISO 9899, also known as ISO C89 or ANSI C compiler...Any
      extensions, such as POSIX or ISO C99, must be tested for,
      typically using Autoconf

Does bioconductor use autoconf, or perhaps autoconf doesn't catch the 
flag requirement as it should?

> Perhaps if you showed us the real output from your compiler more could 
> be determined and less guessed. I see from your second email that you 
> did not in fact find the "first" declaration in the file, but rather 
> the first that was not at the start of a block.
>  I've created
>> patches for the few source files affected (using malloc() to 
>> dynamically create these arrays), but how should I submit these?  Am 
>> I the first person not using gcc under Unix?
>  I suspect not.
>  And no we really don't want to malloc, Ralloc might be lived with, 
> but first let's make sure we agree on the problem and then see what 
> the fix is.

Since it is only allocated once, realloc and malloc function 
equivalently, so I chose the former (one less parameter to type :-))  
I've attached my revisions for your perusal (relevant lines are label 
with a comment with my name).  Once again, I'm new to R and 
Bioconductor, so my questions are not meant to insult anyone's code, but 
rather to help me understand how I can get my development in line with 
the R way...

>   Robert
>> Thanks in advance for your input,
>> Paul Gordon
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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