From nuin at genedrift.org  Fri Sep  5 17:49:37 2008
From: nuin at genedrift.org (Paulo Nuin)
Date: Fri, 05 Sep 2008 11:49:37 -0400
Subject: [Rd] Problem installing Biobase on Solaris
In-Reply-To: <alpine.LFD.1.10.0809051526520.20807@gannet.stats.ox.ac.uk>
References: <48C13C3A.1040503@genedrift.org>
	<alpine.LFD.1.10.0809051526520.20807@gannet.stats.ox.ac.uk>
Message-ID: <48C15511.30103@genedrift.org>

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?

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
>>
>



[Rd] Problem installing Biobase on Solaris
Paulo Nuin