[BioC] 64-bit R - problem with affxparser

Michael Imbeault michael.imbeault at sympatico.ca
Tue Mar 23 08:57:18 CET 2010


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 :)


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 is outdated).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]]
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>> --
>> Martin Morgan
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
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>> Location: Arnold Building M1 B861
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