Dear Michael and Martin,

First of all apologies to everybody else for hijacking the discussion, I
guess it's not very relevant to the Bioconductor list at this point. Maybe
we can keep the next emails off the list?

The main reason for using R/Bioconductor within Cygwin is convenience. I
work almost exclusively from a Cygwin terminal and using the R console or
the Rscript command from within my Cygwin terminal is a lot more convenient
than having to fire up Windows' Rgui.
However, I'm still new to Cygwin (new job!), so I wasn't even aware that it
was possible to use Windows R from Cygwin. May I ask how?

Thank you.
Best,


On 15 July 2013 12:53, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> 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@gene.com> wrote:
>>
>>  Hi Enrico,
>>>
>>> On Mon, Jul 15, 2013 at 1:10 AM, Enrico Ferrero
>>> <enricoferrero86@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/ <http://bioconductor.org/install/>
>>>
>>> HTH,
>>>
>>> -steve
>>>
>>> --
>>> Steve Lianoglou
>>> Computational Biologist
>>> Bioinformatics and Computational Biology
>>> Genentech
>>>
>>>
>>
>>
>>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>



-- 
Enrico Ferrero
PhD Student
Steve Russell Lab - Department of Genetics
FlyChip - Cambridge Systems Biology Centre
University of Cambridge

e.ferrero@gen.cam.ac.uk
http://flypress.gen.cam.ac.uk/

	[[alternative HTML version deleted]]

