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()
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.
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]?
Any help is very appreciated, thank you.
[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
On 11 July 2013 18:28, marco atzeri <marco.atz...@gmail.com> 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
>>> 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
>>
>>
>> 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.
>>
>> Thanks!
>> Best,
>>
>> Enrico
>>
>
>
> Hi Enrico,
> could you clarify your issue with the R cygwin package ?
> Are you trying to compile some addon ? How ?
>
>
>
> Regards
> Marco
>
>
>
> --
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--
Enrico
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