aroma.affymetrix and R 64bit

[zaid]

Is there support for aroma.affymetrix under R 64 bit?

[Henrik Bengtsson]

On Mon, Mar 1, 2010 at 6:38 PM, zaid <za...@genomedx.com> wrote:
> Is there support for aroma.affymetrix under R 64 bit?

Definitely on Linux. Are you asking about Windows 64-bit? Then, I
think so, cf:

http://cran.r-project.org/web/checks/check_results_aroma.affymetrix.html

but I don't have machines to test it myself - someone out there with a
Win64 system that can test? You should also be aware of the 'Update 2
on MinGW-w64 builds for 64-bit Windows' (March 1, 2010) post on
R-devel:

http://tolstoy.newcastle.edu.au/R/e9/devel/10/03/0598.html

/Henrik

>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
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[zaid]

I'm using March 1st 64bit version on Windows but for some reason
affxparser seems to be unavailable.

On Mar 1, 9:48 am, Henrik Bengtsson <henrik.bengts...@gmail.com>
wrote:

> > For more options, visit this group athttp://groups.google.com/group/aroma-affymetrix?hl=en- Hide quoted text -
>
> - Show quoted text -

[Henrik Bengtsson]

So affxparser is built by the Bioconductor framework. Please post to
the BioC mailing list and ask there - they should be able to tell what
the Win64 plans are.

/Henrik

[zaid]

Thanks will do.

So basically aroma.affymetrix package won't install until we figure
out the affparser issue?

Thanks

On Mar 1, 12:44 pm, Henrik Bengtsson <henrik.bengts...@gmail.com>
wrote:

> >> > For more options, visit this group athttp://groups.google.com/group/aroma-affymetrix?hl=en-Hide quoted text -

[Henrik Bengtsson]

On Mon, Mar 1, 2010 at 10:11 PM, zaid <za...@genomedx.com> wrote:
> Thanks will do.
>
> So basically aroma.affymetrix package won't install until we figure
> out the affparser issue?

Look at

http://cran.r-project.org/web/packages/aroma.affymetrix/

There you see that 'affxparser' is listed under "Depends:", which
means it is a required package (==you have to have required packages
installed before installing aroma.affymetrix). FYI, packages under
"Imports:" are also required. Packages under "Suggests:" are not
required.

Note that according to the information on (sent you this before and
available via the above URL):

http://cran.r-project.org/web/checks/check_results_aroma.affymetrix.html

the CRAN build/check servers, and especially
'r-devel-windows64-x86_64', can build/check the aroma.affymetrix
package (there is only a NOTE which is ok) on Win64. This implies
that they have a Win64 version of affxparser available. I don't know
where they got it from; that's why I ask you to post to BioC.

/Henrik

[zaid]

Thanks.

On Mar 1, 1:17 pm, Henrik Bengtsson <henrik.bengts...@gmail.com>
wrote:

> >> >> > For more options, visit this group athttp://groups.google.com/group/aroma-affymetrix?hl=en-Hidequoted text -