[Bioc-devel] Installing pkg with configure with support to multiple architectures

Steve Lianoglou mailinglist.honeypot at gmail.com
Fri Jan 27 15:36:57 CET 2012


Speaking for R-on-mac -- Isn't a multi-arch build the default as long
as your R was compiled as multi-arch?

For instance, if I try to source compile any packge (w/ c code) using
a "release" version of R (d/l'd from CRAN), it will by default compile
the package for x86_64 and i386, unless I specify `R CMD INSTALL

Now, if I'm compiling the same package using a my own source-compiled
version of R (which is only compiled as 64 bit), then it won't build
the i386 version of the package.

So, I guess my question is if this behavior you are seeing is when
using an R you built yourself, or is it an official CRAN build?

If it's the official build, I'd also be confused as to how some
package were built w/o being multiarch (unless you specifically asked
them to be built that way).


On Fri, Jan 27, 2012 at 8:29 AM, Benilton Carvalho
<beniltoncarvalho at gmail.com> wrote:
> Thanks Dan and Martin,
> Dan, yes, your assumption is correct (I'm trying to do this on a Mac).
> The major problem (actually, annoyance) for me is when something like
> the following happens (running R under x86_64 and installing via
> install.packages/biocLite):
> - Install pkg1, which has a configure script... Then, pkg1 is
> installed under x86_64;
> - (try to) install pkg2, which does not have a configure script, but
> depends on pkg1.... it installs the x86_64 part just fine, but the
> i386 fails (because pkg1 isnt available under i386)... then the whole
> installation of pkg2 fails.
> Maybe it's just something basic I'm missing from my end?
> b
> On 26 January 2012 21:49, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>> On Thu, Jan 26, 2012 at 12:45 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>>> On 01/26/2012 06:01 AM, Benilton Carvalho wrote:
>>>> A package with a configure file is installed only on the architecture
>>>> that called the install script.
>>>> So I need to, manually, do:
>>>> R --arch x86_64 CMD INSTALL oligo_version.tar.gz
>>>> R --arch i386 CMD INSTALL --libs-only oligo_version.tar.gz
>>>> Is there anything I can add to the package in order to automate this?
>>> Hi Benilton -- on a not-quite-current R-devel, I have
>>>> R CMD INSTALL --help
>>> ...
>>> and on Windows only
>>>      --force-biarch    attempt to build both architectures
>>>                        even if there is a non-empty configure.win
>>>      --merge-multiarch bi-arch by merging from a tarball
>>> (from R-exts section 1.3.1 of a current R-devel it looks like this argument
>>> might be --force-multiarch)
>> --force-multiarch is an argument to R CMD check, unfortunately not R
>> As far as I know, for Mac (which I am guessing you are asking about)
>> there is no R-centric way to do this; you could automate it with a
>> script.
>> Dan
>>> Martin
>>>> Thanks,
>>>> b
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Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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