R help - Feb 2008 - OT: installing the XML package - xmlOutputBufferCreateBuffer problem

Hi,

first of, my apologies for the possibly off-topic message regarding a  
problem when installing the XML package (I meant to post at omegahat- 
help, but  I get 404 at http://www.omegahat.org/mailman/listinfo)

When installing the XML package using:

install.packages("XML")

everything seems to go fine... but then I try to load the package and  
I get:

 > library(XML)
Error in dyn.load(file, ...) :
   unable to load shared library '/microarray/bin/R-devel/library/XML/ 
libs/XML.so':
   /microarray/bin/R-devel/library/XML/libs/XML.so: undefined symbol:  
xmlOutputBufferCreateBuffer
Error : .onLoad failed in 'loadNamespace' for 'XML'
Error: package/namespace load failed for 'XML'

Suggestions?

thanks a lot,

b

 > sessionInfo()
R version 2.7.0 Under development (unstable) (2007-10-10 r43139)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.iso885915;LC_NUMERIC=C;LC_TIME=en_US.iso885915;LC_COLLATE=en_US.iso885915;LC_MONETARY=en_US.iso885915;LC_MESSAGES=en_US.iso885915;LC_PAPER=en_US.iso885915;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.iso885915;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tcltk_2.7.0 tools_2.7.0

$ xml2-config --version
2.6.23

$ uname -a
Linux compute-0-35.local 2.6.9-42.ELsmp #1 SMP Wed Jul 12 23:32:02 EDT  
2006 x86_64 x86_64 x86_64 GNU/Linux

You need a later version of libxml2 (or at least, a different one as 
possibly an older one would also work).  I met this on Windows -- 2.6.23 
is old (more than 2 years), and I believe 2.6.28, 2.6.30 and 2.6.31 work.

The Omegahat lists have been defunct for a while, AFAIK.  I'd have used 
R-devel for this one ('discussion unintelligible to non-programmers').
Although not relevant here, there is a general principle that questions 
about the R-devel version of R should go to R-devel.

On Fri, 15 Feb 2008, Benilton Carvalho wrote:
> Hi,
>
> first of, my apologies for the possibly off-topic message regarding a
problem
> when installing the XML package (I meant to post at omegahat-help, but  I
get
> 404 at http://www.omegahat.org/mailman/listinfo)
>
> When installing the XML package using:
>
> install.packages("XML")
>
> everything seems to go fine... but then I try to load the package and I
get:
>
>> library(XML)
> Error in dyn.load(file, ...) :
> unable to load shared library 
> '/microarray/bin/R-devel/library/XML/libs/XML.so':
> /microarray/bin/R-devel/library/XML/libs/XML.so: undefined symbol: 
> xmlOutputBufferCreateBuffer
> Error : .onLoad failed in 'loadNamespace' for 'XML'
> Error: package/namespace load failed for 'XML'
>
> Suggestions?
>
> thanks a lot,
>
> b
>
>> sessionInfo()
> R version 2.7.0 Under development (unstable) (2007-10-10 r43139)
> x86_64-unknown-linux-gnu
If you are going to use R-devel, we suggest you at least use a recent 
version.  That one is lacking all the bug fixes in 2.6.1 and 2.6.2, as 
well as lots of nice features.
> locale:
>
LC_CTYPE=en_US.iso885915;LC_NUMERIC=C;LC_TIME=en_US.iso885915;LC_COLLATE=en_US.iso885915;LC_MONETARY=en_US.iso885915;LC_MESSAGES=en_US.iso885915;LC_PAPER=en_US.iso885915;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.iso885915;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tcltk_2.7.0 tools_2.7.0
>
> $ xml2-config --version
> 2.6.23

-- 
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