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Message-id:	<51DC2ECD.2060208@cygwin.com>
Date:	Tue, 09 Jul 2013 11:39:57 -0400
From:	"Larry Hall (Cygwin)" <reply-to-list-only-lh AT cygwin DOT com>
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To:	cygwin AT cygwin DOT com
Subject:	Re: mingw/math.h not found while compiling R packages
References:	<CAO22HXfu6pQCOOsjKSyU+mmFD8k0=SFPG1q4-XhokiFqjer3GA AT mail DOT gmail DOT com>
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On 7/9/2013 6:12 AM, Enrico Ferrero wrote:
> Hi,
>
> I have R installed through Cygwin ports, and I am trying to compile some
> external R packages (from Bioconductor).
>
> When doing so, I get the following error while building the IRanges
> Bioconductor 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
>
> As far as I understand, this is an issue related to paths/links on Cygwin,
> as math.h is indeed installed by the mingw-runtime package, but R
> apparently can't find it.
>
> If you want to reproduce the issue just install R through the Cygwin ports,
> open an R session and write:
>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite()
>
> which will perform a standard Bioconductor installation.
>
> Can anybody please help me to find a fix or workaround for this?
> Any help is really appreciated.

If you are using the R from Cygwin Ports, it must be an old package since
R is no longer offered there.  I suggest you install the R package from the
Cygwin distribution instead and retry.  Since this list supports the Cygwin
distribution only, this would put your issue firmly on-topic for this list
if you can still reproduce it.  For Cygwin Ports packages, they are
supported through the Ports site:

<http://sourceware.org/cygwinports/>

If you have a package from that site and have questions, problems, or
comments, it's best to consult the mailing list there.


-- 
Larry

_____________________________________________________________________

A: Yes.
 > Q: Are you sure?
 >> A: Because it reverses the logical flow of conversation.
 >>> Q: Why is top posting annoying in email?

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