[BioC] IRanges is broken in Cygwin (mingw/math.h)

[Enrico Ferrero]

Hi,

Installation of Bioconductor fails on Cygwin because of a compilation
error in the IRanges package:

> In file included from IntervalTree.c:3:0:
> common.h:59:24: fatal error: mingw/math.h: No such file or directory
> compilation terminated.
> /usr/lib/R/etc/Makeconf:121: recipe for target `IntervalTree.o' failed
> make: *** [IntervalTree.o] Error 1
> ERROR: compilation failed for package =91IRanges=92

I got some help to fix this from Marco Atzeri in the Cygwin mailing
list and the problem seems to be a perhaps unnecessary '#include
<mingw/math.h>' directive.

This patch by Marco fixes the problem, allowing compilation of IRanges
on Cygwin:

-------------------------------------------------------
--- orig/IRanges/src/common.h   2013-02-22 04:36:50.000000000 +0100
+++ IRanges/src/common.h        2013-07-12 00:19:05.922405200 +0200
@@ -55,10 +55,6 @@
 #endif
 #endif

-#ifdef __CYGWIN32__
-#include <mingw/math.h>
-#endif
-
 #ifndef NAN
 #define NAN (0.0 / 0.0)
 #endif
---------------------------------------------------------

The patch (and a handy patched package) can also be found at:
http://matzeri.altervista.org/works/R/

Can this be fixed upstream?
Thank you.

Best,

--
Enrico Ferrero