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

Seth Falcon sfalcon at fhcrc.org
Fri Oct 14 19:49:57 CEST 2005

On 14 Oct 2005, gordonp at ucalgary.ca wrote:
> 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?

Just some clarification:
Bioconductor is a collection of contributed R packages.  An R package
that includes C code can specify a configure script.  Many packages do
specify such a script and use autoconf to create it.  

It may be that the package(s) you are trying to use either need to be
more explicit about their requirements or need other fixes to make
them more compatible.

I'm still a bit unsure about what exactly you are seeing.

>> 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...

There are notes on memory management in the Writing R Extensions
manual.  You can call malloc, but there are many advantages to using
R's memory management.

+ seth

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