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Re: mingw/math.h not found while compiling R packages
- From: marco atzeri <marco dot atzeri at gmail dot com>
- To: cygwin at cygwin dot com
- Date: Fri, 12 Jul 2013 00:02:12 +0200
- 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>
Il 7/11/2013 10:51 PM, Enrico Ferrero ha scritto:
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  is a a collection of packages for computational
biologists that is installed by compiling its packages within the R
To install the base packages (and reproduce what I believe is a bug),
one just has to type at the R prompt:
as you are not using R-3.x the last should be
During the compilation of the IRanges package , 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
/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 .
According to this page  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 ?
wrong, cygwin have its own math.h
$ cygcheck -f /usr/include/math.h
Any help is very appreciated, thank you.
I am building biocLite, it will take some time...
Problem reports: http://cygwin.com/problems.html
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