[BioC] IRanges is broken in Cygwin (mingw/math.h)

[Martin Morgan]

On 07/15/2013 01:23 AM, Enrico Ferrero wrote:
> Hi Steve,
>
> Thanks for the clarification. I guess it's a matter of waiting for the
> Cygwin devs to update to R 3.0.1 then.
>
> In the meanwhile, may I ask (Michael?) to also patch the latest version of
> IRanges (I am guessing 1.16.6, according to my logs) for R 2.15.1?

Michael won't be able to do that. Or rather, he'll be able to patch it but the 
Bioconductor build machines will not build it -- only current and devel versions 
of Bioconductor packages are built.

I guess I'll ask the obvious, and I guess you've got a good answer, but is there 
a reason that you're using R on cygwin? I would have thought that you could 
install and manage R under Windows, and used the Windows executable from cygwin? 
If not in general, then at least for your use cases that involve IRanges?

Martin

>
> Thanks!
> Best,
>
>
> On 15 July 2013 09:17, Steve Lianoglou <lianoglou.steve at gene.com> wrote:
>
>> Hi Enrico,
>>
>> On Mon, Jul 15, 2013 at 1:10 AM, Enrico Ferrero
>> <enricoferrero86 at gmail.com> wrote:
>>> Hi Michael,
>>>
>>> I can't seem to install the latest version of IRanges.
>>> For some reason, bioLite() still tries to pull an old version of IRanges,
>>> (that still contains the bug):
>> [snip]
>>> I'm currently on R version 2.15.1 and Bioconductor version 2.11, trying
>> to
>>> upgrade to 2.12.
>>> Am I doing something wrong?
>>
>> Yes you are.
>>
>> You need to be running R-3.0.x in order to use bioc 2.12, as is
>> pointed out in the intro of the Bioconductor installation page:
>>
>> http://bioconductor.org/install/
>>
>> HTH,
>>
>> -steve
>>
>> --
>> Steve Lianoglou
>> Computational Biologist
>> Bioinformatics and Computational Biology
>> Genentech
>>
>
>
>


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