[BioC] 64-bit R - problem with affxparser

Michael Imbeault michael.imbeault at sympatico.ca
Thu Mar 25 07:36:52 CET 2010 

Just to report that I've been able to compile affxparser on R win 64 
using 1.19.6 from the devel contrib on bioconductor, using mingw64 
(specifically, 
http://sourceforge.net/projects/mingw-w64/files/Toolchains%20targetting%20Win64/Personal%20Builds/sezero_20100322/mingw-w64-bin_x86_64-mingw_20100322_sezero.zip/download).

No idea why the 1.18 version wouldnt compile, but problem solved anyway :)

Thanks,
Michael

On 23/03/2010 11:32 AM, Kasper Daniel Hansen wrote:
> The authoritative place to look for information is the r-devel list,
> particular the posts from R-core.  The most recent post about this
> issue is the one Martin provided a link to, which contains the
> following
>
> "We do not anticipate any major changes to the build before 2.11.0 is
> released (most likely in April), and it can now be regarded as at
> 'beta' status -- users with a 64-bit Windows OS and who do not need
> Bioconductor packages are encouraged to try it out."
>
> For specifics you should read the R-admin manual.  I am not sure if
> the R-devel version of that manual is available anywhere on the net,
> but if you have access to a R-devel build somewhere you will see it
> has a section on building for 64 bit windows.  There is also a link to
> a webpage with further comments.
>
> But you will still need to install the latest version of the mingw64
> toolchain.  I assume that eventually a snapshot will be included in
> Rtools, but that does not seem to be the case yet.
>
> Kasper
>
> On Tue, Mar 23, 2010 at 3:57 AM, Michael Imbeault
> <michael.imbeault at sympatico.ca>  wrote:
>    
>> Hello,
>>
>> Sorry for the confusion about the two issues, I was under the impression
>> that the build servers I linked to were the 64 bit version, my bad :)
>>
>> I only became aware of the affxparser on 64 bit problem yesterday, and
>> stumbled upon the aroma.affymetrix group. Having not seen a post about it on
>> the bioC list, I took the opportunity to post (and cc you). I'll try
>> tomorrow to build 1.19.6 (I don't remember which build I tried to compile
>> with mingw64).
>>
>> Regarding the instability of the keychain, do you happen to have a link
>> where I could download the latest (semi) official version? There's a lot of
>> uncertainty about this following various conversations on the web.
>>
>> Last, thanks for taking time to tackle this problem, and don't worry, I know
>> that R 64 bit under Windows is kind of bleeding edge (and bioC running on it
>> even more so) so I don't expect an overnight solution :)
>>
>> Cheers,
>> Michael
>>
>> On 22/03/2010 11:20 PM, Kasper Daniel Hansen wrote:
>>      
>>> I was not aware of the discussion on the aroma.affymetrix group.  And
>>> I was furthermore not aware of the fact that affxparser fails to build
>>> at the moment (I thought we had automatic notification of this -
>>> perhaps there is some issue with my spam filter?)  For another time,
>>> it is usually productive to contact the maintainer :)
>>>
>>> As far as I can see the Bioconductor build the OP is referring to is
>>> still using mingw32, which means that the build issue should be
>>> completely unrelated to 64 bit windows (or the information at
>>>
>>> http://bioconductor.org/checkResults/2.6/bioc-LATEST/liverpool-NodeInfo.html
>>> is outdated).
>>>
>>> I would expect affxparser to build with mingw64.  Or at least we
>>> managed to build it (version 1.19.6 to be specific) under some version
>>> of the toolchain (at that point the toolchain changed often I think)
>>> with help from Prof. Ripley.  The toolchain has now stabilized and I
>>> am in the process of getting a 64bit Windows 7 up and running so I can
>>> make sure affxparser (and Rgraphviz - although initial results
>>> indicate that Rgraphviz will be a pain) will work on this platform.
>>>
>>> That leaves the issue of why affxparser does not build on the
>>> Bioconductor build servers.  I will look into this over the coming
>>> days, but it will be much easier when I actually have a windows box to
>>> test on.
>>>
>>> Finally, in general I suggest that people who want to use 64 bit
>>> Windows arm themselves with some patience.  This is a new platform and
>>> it is only very recently that the R windows team settled on which
>>> compiler they (probably) will use and mingw64 is still somewhat
>>> experimental (as I understand).  To top it off, not everyone has a 64
>>> bit windows box lying around for testing, so it will still take a
>>> while for things to be "normal".
>>>
>>> Kasper
>>>
>>> On Mon, Mar 22, 2010 at 7:45 PM, Martin Morgan<mtmorgan at fhcrc.org>    wrote:
>>>
>>>        
>>>> 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]]
>>>>>>>
>>>>>>> _______________________________________________ Bioconductor mailing
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>>>>>>>
>>>>>>>
>>>>>>>                
>>>>>>
>>>>>>              
>>>> --
>>>> Martin Morgan
>>>> 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
>>>>
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>>>>
>>>>          
>>>
>>>        
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>>      
>
>

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