From ripley at stats.ox.ac.uk  Sat Sep  6 09:20:33 2008
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Sat, 6 Sep 2008 08:20:33 +0100 (BST)
Subject: [Rd] Problem installing Biobase on Solaris
In-Reply-To: <48C15511.30103@genedrift.org>
References: <48C13C3A.1040503@genedrift.org>
	<alpine.LFD.1.10.0809051526520.20807@gannet.stats.ox.ac.uk>
	<48C15511.30103@genedrift.org>
Message-ID: <alpine.LFD.1.10.0809060810360.18764@gannet.stats.ox.ac.uk>

Is this a pre-compiled R?  If so, please do compile from the sources on 
your own machine.  The compiler output you show is rather unusually 
complex and quite likely you are picking up some spurious headers or 
libraries.

gcc 3.4.3 is a very old compiler: sunfreeware (which is what you appear to 
be using) has 3.4.6.

I don't currently have R built on a Solaris 10 Sparc system (I do on 
amd64), but we have in the past and will again when we have a box back in 
production use.  We did find the Sun Studio compiler (which is a free 
download) worked much more smoothly than gcc and gave better performance.

On Fri, 5 Sep 2008, Paulo Nuin wrote:

> Hi
>
> I thought of that. We have gcc 3.4.3 installed
>
> /gates/sfw10/builds/sfw10-gate/usr/src/cmd/gcc/gcc-3.4.3/configure 
> --prefix=/usr/sfw --with-as=/usr/sfw/bin/gas --with-gnu-as 
> --with-ld=/usr/ccs/bin/ld --without-gnu-ld --enable-languages=c,c++ 
> --enable-shared
>
> How to make sure which compiler R is using?

Look in R_HOME/etc/Makeconf for CC.

> Thanks in advance
>
> Paulo
>
> Prof Brian Ripley wrote:
>> What compiler is this?  This is a compiler issue, not an R one.
>> 
>> My guess is that you are mixing gcc (which has __builtin_isnan) and cc 
>> (which does not).
>> 
>> On Fri, 5 Sep 2008, Paulo Nuin wrote:
>> 
>>> Hi everyone
>>> 
>>> This is my first post to the list. I had experience installing and using 
>>> Bioconductor on Linux and Windows systems but I am encountering problems 
>>> installing Biobase on Solaris running on Sparc. The package compilation 
>>> works fine, with only a warning
>>> 
>>> warning: implicit declaration of function `__builtin_isnan'
>>> 
>>> the help files are generated but in the end it fails with an error also 
>>> related __builtin_isnan
>>> 
>>> ** building package indices ...
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>> unable to load shared library 
>>> '/usr/local/lib/R/library/Biobase/libs/Biobase.so':
>>> ld.so.1: R: fatal: relocation error: file 
>>> /usr/local/lib/R/library/Biobase/libs/Biobase.so: symbol __builtin_isnan: 
>>> referenced symbol not found
>>> Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> 
>>> <Anonymous>
>>> Execution halted
>>> ERROR: installing package indices failed
>>> 
>>> The machine I am using is a Sun SPARC Victoria Falls SunOS 5.10 
>>> Generic_127111-11 sun4v sparc SUNW,T5140
>>> 
>>> I posted this message to the BioC list and it was suggested that I tried 
>>> installing any R package that needed compilation. I installed the XML 
>>> package with no problems. Any help is appreciated. Thanks in advance
>>> 
>>> Paulo
>>> 
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>> 
>> 
>
>

-- 
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] Problem installing Biobase on Solaris
Prof Brian Ripley