[BioC] Trouble building Bioconductor

Atro Tossavainen atossava at cc.helsinki.fi
Sun Feb 19 07:25:44 CET 2006

Dear Mr Pages

> These problems seem to occur with C compilers that don't support
> declarations that appear after an executable statement in a block.
> The ability to declare a variable in the middle of a block was introduced
> in the C99 specifications. Since the C code in the postmean.c file makes
> use of this feature, you'll need a C99-compliant in order to compile it.

Thank you for the explanation.

> For a list of compilers that support C99, see:
>     http://clc-wiki.net/wiki/C_Compilers
> A recent version of gcc (>= 3.3) should work...

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platforms (except for one compiler that runs on an outdated OS on Mac).

So you're suggesting that I should recompile R, which can be quite a
heavy application, with gcc, whose code generation on platforms other
than x86 often leaves a lot to be desired, and where native compilers
that are often significantly better than gcc in other respects are
available to get any use of Bioconductor at all?  It doesn't really
sound all that appealing.

Somewhat fortunately, Sun appears to have C99 support since Studio 9,
and SGI since MIPSpro 7.4.  Perhaps all that I need to do is to upgrade
the operating systems and compiler libraries on all of the Suns and SGIs
in my herd (which means several dozen machines) to these newer versions
and I will be able to avoid gcc when compiling R.

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.
< URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS

More information about the Bioconductor mailing list