[BioC] 64-bit R - problem with affxparser

Kasper Daniel Hansen khansen at jhsph.edu
Tue Mar 23 04:20:00 CET 2010

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
is outdated).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".


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
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