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

Paul Gordon gordonp at ucalgary.ca
Thu Oct 13 21:11:57 CEST 2005

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++).  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?

Thanks in advance for your input,

Paul Gordon

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