From ripley at stats.ox.ac.uk  Sun Aug 31 16:40:43 2008
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Sun, 31 Aug 2008 15:40:43 +0100 (BST)
Subject: [Rd] specifying compiler path in configure
In-Reply-To: <6b93d1830808290922l12e7d611i3e37d1e3fa9489f8@mail.gmail.com>
References: <6b93d1830808271321v27af0532w56b0d278b32073c@mail.gmail.com>
	<alpine.LFD.1.10.0808272133040.27712@gannet.stats.ox.ac.uk>
	<6b93d1830808290922l12e7d611i3e37d1e3fa9489f8@mail.gmail.com>
Message-ID: <alpine.LFD.1.10.0808311536400.2427@gannet.stats.ox.ac.uk>

On Fri, 29 Aug 2008, Mark Kimpel wrote:

> After reading over the relevant sections of the manual more carefully,
> I now see where the information is presented and I was able to get R
> to compile with an alternate version of gcc. On thing, however,
> remains unclear to me. If R is compiled with a non-default version of
> a compiler, are subsequent add-on packages and updated automatically
> directed to use the alternate or is it necessary to include this

R uses the compiler used to build it unless told otherwise.  That *is* the 
default, as far a R is concerned -- it knows about no other.

> information in 'install.packages' and 'update.packages'? If the
> latter, then it is unclear to me how this is accomplished. Below is my
> best attempt at putting this instruction into install.packages and it
> failed to produce the intended result, with gcc-4.3 being used instead
> of 4.2.
>
> install.packages("affxparser", repos=repos,configure.args =
> c('CC=/usr/bin/gcc-4.2', 'CXX=/usr/bin/g++-4.2'))

You set environment variables via Sys.setenv() ....

>
> Thanks, Mark
>
> On Wed, Aug 27, 2008 at 4:38 PM, Prof Brian Ripley
> <ripley at stats.ox.ac.uk> wrote:
>> On Wed, 27 Aug 2008, Mark Kimpel wrote:
>>
>>> I'm having trouble building some packages while running Debian Lenny
>>> (testing) and suspect that the issues are related to the default use
>>> of gcc-4.3.
>>
>> You might want to compare your problems with the CRAN checks at
>>
>> http://cran.r-project.org/web/checks/check_summary.html
>>
>> as those are run with gcc 4.3.x on Debian testing.  From memory, the
>> problems are confined to C++-(mis)using packages.
>>
>>> With Lenny, build-essentials depends on 4.3, so I'd like
>>> to leave it installed but have also installed 4.2.1. How do I tell
>>> ./configure the path to 4.2.1 ? I"m sure it's an option, but I don't
>>> see it documented in the R-admin manual.
>>
>> From configure --help:
>>
>>  CC          C compiler command
>>  CFLAGS      C compiler flags
>>
>> There are many examples of setting CC in the R-admin manual, and the first
>> para of 'Essential Programs' seems to me to tell you that as well.
>>
>> --
>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>> University of Oxford,             Tel:  +44 1865 272861 (self)
>> 1 South Parks Road,                     +44 1865 272866 (PA)
>> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>>
>
>
>
> -- 
> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
>
> 15032 Hunter Court, Westfield, IN 46074
>
> (317) 490-5129 Work, & Mobile & VoiceMail
> (317) 663-0513 Home (no voice mail please)
>
> ******************************************************************
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] specifying compiler path in configure
Prof Brian Ripley