Hi
Thanks a lot for your suggestions. I had problems compiling R with gcc
on Solaris, that's why I decided to install the pre-compiled version. I
am in the process of compiling now using the Sun Studio compiler and it
is, so far, working wonderfully. I will continue installing it and if I
have any other errors I will reply to the list.
Sorry if my questions sounded naive, but I don't have a lot of
experience with Solaris, I am more a Linux person.
Thanks again
Paulo
Prof Brian Ripley wrote:
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
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