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Message-ID:	<51DF7C74.2040807@gmail.com>
Date:	Fri, 12 Jul 2013 05:48:04 +0200
From:	marco atzeri <marco DOT atzeri AT gmail DOT com>
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To:	cygwin AT cygwin DOT com
Subject:	Re: mingw/math.h not found while compiling R packages
References:	<CAO22HXc6RUeTcUwMbz85x3OBb+wuLUGhnOcQvLydXJaqPi_6mw AT mail DOT gmail DOT com> <51DEEB49 DOT 5080104 AT gmail DOT com> <CAO22HXeDd4cQCcZiWfYG_7xrmKmmoZ6A_vstqKh9SBeCW9t+2w AT mail DOT gmail DOT com> <51DF2B64 DOT 5010508 AT gmail DOT com>
In-Reply-To:	<51DF2B64.5010508@gmail.com>

Il 7/12/2013 12:02 AM, marco atzeri ha scritto:
> Il 7/11/2013 10:51 PM, Enrico Ferrero ha scritto:
>> Hi,
>>
>
> I am building biocLite, it will take some time...
>

Enrico,
As I was thinking the package is broken.
I don't know why they put a wrong and useless #include directive

If you download the package and patch the source as

-------------------------------------------------------
--- 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
---------------------------------------------------------

after repacking
you can then install the local file with something like
  install.packages("/tmp/IRanges_1.16.6.tar.gz")

I put the already patched file here if you are interested:
http://matzeri.altervista.org/works/R/

Regards
Marco


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