[BioC] Trouble building Bioconductor

[Atro Tossavainen]

Dear Mr Pages

>> The page contains nothing on anything related to anything else but x86
>> platforms (except for one compiler that runs on an outdated OS on Mac).
>
> Are you kidding? Nowhere it is said that the compilers listed on this
> page are for x86 only.

Aside from gcc, they are.  And indeed it says: "This page lists compiler
availability with a focus on free compilers that run on Windows and Linux."

> For example, it says that the gcc compiler (the first
> in the list) supports "Windows, Linux and many others".

Yes, I am familiar with gcc and have had 3.4.2 available on all my
platforms for quite some time.

> If your native compiler supports C99 then use it. If it does not, then
> you have alternatives, like gcc.

My issue is the fact that I am able to build R with a particular compiler
but unable to build Bioconductor with the same compiler.  It would make
sense for the requirements for R and its contributed packages to be
identical, don't you think.

> We are currently using gcc to build and check the binary packages that
> we distribute and we have no problem with it. It's free, it's open
> source, it successfully builds R on 32-bit Linux,
> 64-bit Linux, Mac OS X, Solaris, IRIX, and many more...

And makes coffee and plays gomoku.  I do not need a lecture on the merits
of gcc.  I am perfectly aware of all that you say.  However, compiling
resource-hungry software such as R with a sub-optimal compiler such as
gcc makes no sense.  It only makes sense if you don't have access to the
native compilers for the platform in question, and I dare say that most
of the academic community who have any sort of access to commercial UNIX
platforms already have access to the native compilers on those platforms
via campus licensing agreements and would always expect to compile any
software with the native compilers instead of gcc in order to reach the
maximum potential of the hardware.

-- 
Atro Tossavainen (Mr.)               / The Institute of Biotechnology at
Systems Analyst, Techno-Amish &     / the University of Helsinki, Finland,
+358-9-19158939  UNIX Dinosaur     / employs me, but my opinions are my own.
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