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

[Martin Morgan]

On 7/15/2013 8:59 AM, Enrico Ferrero wrote:
> 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?

Probably I spoke too quickly; I'm not a cygwin user, other than casually and 
mostly as an ssh client. It's straight-forward to start R from cygwin -- Rterm 
--vanilla or Rgui or Rscript, assuming R is on your (cygwin's) PATH. Rgui 
launches the R GUI which is as functional as ever; Rterm --vanilla get the 
terminal version but it's not really usable -- X11 isn't available so plots go 
to Rplots.pdf and errors break to the shell. I'm not an Rscript user so don't 
know what functionalities are missing.

You never know what expertise lurks out there so I'll leave this on the mailing 
list.

Martin

>
> Thank you.
> Best,
>
>
> On 15 July 2013 12:53, Martin Morgan <mtmorgan at fhcrc.org
> <mailto:mtmorgan at 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 at gene.com
>         <mailto:lianoglou.steve at gene.com>> wrote:
>
>             Hi Enrico,
>
>             On Mon, Jul 15, 2013 at 1:10 AM, Enrico Ferrero
>             <enricoferrero86 at gmail.com <mailto: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/ <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 at gen.cam.ac.uk <mailto:e.ferrero at gen.cam.ac.uk>
> http://flypress.gen.cam.ac.uk/
>
>


-- 
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109