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

[Benilton Carvalho]

Hi Steve,

It's the CRAN build... and it behaves as expected, as long as the
package does not have a configure script (I should make it clear that
I always install packages from the source, ie, install.packages(...,
type='source') ).

For example, Biobase does not have a configure script. Then:

biocLite('Biobase')

gives me:

* installing *source* package ‘Biobase’ ...
** libs
*** arch - i386
<bunch of stuff>
*** arch - x86_64
<another bunch>
* DONE (Biobase)

Now, affyio and affy have a configure script:

biocLite(c('affyio', 'affy'))

gives me:

* installing *source* package ‘affyio’ ...
<./configure output>
** libs
*** arch - x86_64
<bunch of stuff>
* DONE (affyio)
* installing *source* package ‘affy’ ...
<./configure output>
** libs
*** arch - x86_64
<bunch of stuff>
* DONE (affy)

Note that affyio and affy were not installed under i386.

Now, try to install gcrma (has C code, but doesn't have a configure:

biocLite('gcrma')

gives:

* installing *source* package ‘gcrma’ ...
** libs
*** arch - i386
<bunch of stuff>
*** arch - x86_64
<bunch of stuff>
*** arch - i386
Error : package ‘affy’ is not installed for 'arch=i386'
Error: loading failed
Execution halted
*** arch - x86_64
ERROR: loading failed for ‘i386’
* removing ‘/Users/carval03/Rlibs/2.14/gcrma’

So, to get this to work, I need to download the tar.gz files and do

R --arch x86_64 CMD INSTALL pkg_version.tar.gz
R --arch i386 CMD INSTALL --libs-only pkg_version.tar.gz

for pkg = affyio, affy

and I was wondering if there was an automagic way of doing this
(which, I'd hopefully bring to oligo as well).

b

On 27 January 2012 14:36, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> Hi,
>
> 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
> --no-multiarch`
>
> 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).
>
> HTH,
> -steve
>
> 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
>>> CMD INSTALL.
>>>
>>> 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
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>>
>>>>
>>>> --
>>>> Computational Biology
>>>> Fred Hutchinson Cancer Research Center
>>>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>>>>
>>>> Location: M1-B861
>>>> Telephone: 206 667-2793
>>>>
>>>>
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>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> --
> 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