From ripley at stats.ox.ac.uk  Fri Sep  5 16:28:40 2008
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Fri, 5 Sep 2008 15:28:40 +0100 (BST)
Subject: [Rd] Problem installing Biobase on Solaris
In-Reply-To: <48C13C3A.1040503@genedrift.org>
References: <48C13C3A.1040503@genedrift.org>
Message-ID: <alpine.LFD.1.10.0809051526520.20807@gannet.stats.ox.ac.uk>

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