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Date:	Fri, 12 Jul 2013 00:02:12 +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>
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Il 7/11/2013 10:51 PM, Enrico Ferrero ha scritto:
> Hi,
>
> Thanks for your help, I'll try to make things clearer.
>
> I have a full installation of Cygwin, including R version 2.15.1,
> running on my Windows XP box at work.
> Bioconductor [1] is a a collection of packages for computational
> biologists that is installed by compiling its packages within the R
> environment.
> To install the base packages (and reproduce what I believe is a bug),
> one just has to type at the R prompt:
>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite()

as you are not using R-3.x the last should be

   biocLite(NULL)

>
> During the compilation of the IRanges package [2], I get the following error:
>
>> 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
>
> So, apparently, R needs the math.h library to compile IRanges but
> can't find it for some reason.

likely the package is broken and incorrectly identify cygwin for mingw.

> As far as I understand, in Cygwin, math.h is provided by the
> mingw-runtime package, part of the MinGW suite [3].
> According to this page [4] on the Cygwin website, math.h is indeed
> installed by the mingw-runtime package, so I'm trying to figure out
> why R can't access it. Maybe it's a path or symbolic links-related
> problem? Maybe it has to do with the recently mentioned issues
> affecting MinGW packages in Cygwin [5]?

wrong, cygwin have its own math.h

$ cygcheck -f /usr/include/math.h
cygwin-1.7.20-1


>
> Any help is very appreciated, thank you.

I am building biocLite, it will take some time...

>
> [1] http://www.bioconductor.org
> [2] http://www.bioconductor.org/packages/2.12/bioc/html/IRanges.html
> [3] http://www.mingw.org/
> [4] http://cygwin.com/cgi-bin2/package-cat.cgi?file=mingw-runtime%2Fmingw-runtime-3.18-3&grep=math.h
> [5] http://cygwin.com/ml/cygwin/2013-07/msg00196.html
>

Marco


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