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

Robert Gentleman rgentlem at fhcrc.org
Fri Oct 14 04:07:58 CEST 2005


Paul Gordon wrote:
> Hi all,
> I just subscribed to this list today, so sorry if my question is naive.  
> I have dowloaded and compiled R with Sun's Workshop Pro compiler to 
> optimize my performance (I find it's about 30-40% faster than gcc with 
> optimization flags), and hence it tries to compile new packages (such as 
> those in Bioconductor) with the Sun's cc too.  I have found that some 
> packages (including established ones like genefilter and gcrma) have C 
> files that compile under gcc, but don't strictly adhere to the C spec, 
> and hence don't compile for me.  More specifically, gcc lets you declare 
> variable in the middle of a function, but the C spec doesn't (in C++ you 
> can, but these source files are not flagged as C++). 

Could you point me to the particular part of the ANSI C specification 
you are talking about? I suspect that you are trying to say that ANSI C 
does not like declarations in the middle of a block?

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).

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.


> Thanks in advance for your input,
> Paul Gordon
> _______________________________________________
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Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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