[BioC] 64-bit R - problem with affxparser

[Martin Morgan]

Hi Michael --

On 03/22/2010 03:59 PM, Michael Imbeault wrote:
> Hi,
> 
> A toolchain to build bioC packages from source under R win 64 bit is
> available at http://download.cos.name/incoming/Rtools64.zip  (see
> https://stat.ethz.ch/pipermail/r-devel/2010-January/056280.html for the
> original post by Gong Yu).

but this

https://stat.ethz.ch/pipermail/r-devel/2010-March/056815.html

suggests that the tool chain used at CRAN is different.

> However, some packages don't build/compile correctly, notably affxparser
> (see the liverpool build / check for affxparser at
> http://bioconductor.org/checkResults/2.6/bioc-LATEST/).
> 
> This blocks the build of the aroma.affymetrix package under R win 64
> (among others) as it depends on it - could we find the source of this
> problem (I cc'd Dr. Hansen, the maintainer of the package)? This is a
> problem for many users right now
> (http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/1c01fdd3b243d3ec/5160fa633ea399a4?lnk=raot#5160fa633ea399a4).

I don't think Zaid or others on this thread communicated with the Bioc
mailing list; maybe with Kasper directly? The hard-core Windows
64-bitters can check out affxparser 1.19.0 from svn (r42686; 1.19.0 did
build successfully on Windows, and is the version that Windows
biocLite() retrieves for win32). Which is not to say that Kasper won't
address the Windows issues...

Martin

> 
> See
> http://bioconductor.org/checkResults/2.6/bioc-LATEST/affxparser/liverpool-checksrc.html
> for a detailed view of the install.out log.
> 
> Regards,
> Michael
> 
> 
> On 22/03/2010 5:11 PM, Martin Morgan wrote:
>> On 03/22/2010 12:28 PM, Jin, Jp wrote:
>>   
>>> Dear list,
>>>
>>> I would want to install R/bioconductor to my 64-bit machine with
>>> Windows 7 installed. When are the 64-bit R build and bioconductor
>>> available? will R 2.11 are Bio C 2.6  work with Windows 7?
>>>      
>> Hi --
>>
>> 32 bit R / Bioc installs on 64-bit windows 7.
>>
>> There is a 64-bit Windows R-devel; follow the 'windows64' link from a
>> CRAN 'R binaries' page, e.g., at http://cran.fhcrc.org/bin/. There may
>> be 64-bit Bioconductor packages in the next release but that is not
>> certain. You will still be able to build your own 64-bit packages,
>> although I am not exactly clear on details about the compiler required
>> and availability of an appropriate Windows build tool chain.
>>
>> Martin
>>
>>   
>>> Thanks,
>>>
>>> Jp Jin
>>>
>>> [[alternative HTML version deleted]]
>>>
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>>>      
>>
>>    


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

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