This is the mail archive of the
mailing list for the Cygwin project.
Re: mingw/math.h not found while compiling R packages
- From: Enrico Ferrero <enricoferrero86 at gmail dot com>
- To: cygwin at cygwin dot com
- Date: Thu, 11 Jul 2013 21:51:38 +0100
- 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>
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:
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
> 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.
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 ?
Any help is very appreciated, thank you.
On 11 July 2013 18:28, marco atzeri <firstname.lastname@example.org> wrote:
> Il 7/11/2013 6:35 PM, Enrico Ferrero ha scritto:
>> Hi Larry,
>> Thank you for your reply and advice.
>>> 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
>>> Cygwin distribution instead and retry. Since this list supports the
>>> distribution only, this would put your issue firmly on-topic for this
>>> if you can still reproduce it. For Cygwin Ports packages, they are
>>> supported through the Ports site:
>>> If you have a package from that site and have questions, problems, or
>>> comments, it's best to consult the mailing list there.
>> I got confused in my first email for some reason, but I'm definitely
>> using R (version 2.15.1) from the Cygwin distribution, not the ports.
>> I just made a clean R installation just to make sure and I still get
>> the same error message:
>>> 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 ‘IRanges’
>>> * removing ‘/usr/lib/R/site-library/IRanges’
>> I've read there are some other problems with MinGW these days, maybe
>> this one is related?
>> In any case, is there anything I can do to try to solve the issue?
>> Bioconductor is vital to me and using R from within Windows is causing
>> me a lot of headaches.
> Hi Enrico,
> could you clarify your issue with the R cygwin package ?
> Are you trying to compile some addon ? How ?
> Problem reports: http://cygwin.com/problems.html
> FAQ: http://cygwin.com/faq/
> Documentation: http://cygwin.com/docs.html
> Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple
Problem reports: http://cygwin.com/problems.html
Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple