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installing XML in linux

6 messages · Mahbub Latif, Douglas Bates, Robert Burrows +2 more

Mahbub Latif
# 
Hi,

I was trying to install XML package in a linux
(dabian) machine and got the following error message.
I am not sure whether there is any error in my linux
installion. I appreciate suggestions to install XML
properly in this machine. 

Thanks in advance.

Mahbub.

######Errors#### 
$ R CMD INSTALL -l /usr/local/lib/R/library/
XML_0.93-4.tar.gz 
* Installing *source* package 'XML' ...
creating cache ./config.cache
checking for gcc... gcc
checking whether the C compiler (gcc  ) works... yes
checking whether the C compiler (gcc  ) is a
cross-compiler... no
checking whether we are using GNU C... yes
checking whether gcc accepts -g... yes
checking how to run the C preprocessor... gcc -E
checking for xml-config... no
checking for libxml/parser.h... no
checking for gnome-xml/parser.h... no
checking for libxml/parser.h... (cached) no
checking for gnome-xml/parser.h... (cached) no
checking for libxml/parser.h... (cached) no
Cannot find parser.h. Set the value of the environment
variable
    LIBXML_INCDIR
to point to where it can be found.
ERROR: configuration failed for package 'XML'
_                
platform i686-pc-linux-gnu
arch     i686             
os       linux-gnu        
system   i686, linux-gnu  
status                    
major    1                
minor    7.0              
year     2003             
month    04               
day      16               
language R
Douglas Bates
# 
You will need to install the Debian package libxml-dev before you can
install the R XML package.

Mahbub Latif <ahmlatif at yahoo.com> writes:
Mahbub Latif
# 
Thanks a lot Prof Bates. One more thing... What Debian
packages should I install to install R packages
Rgraphviz and rhdf5?

Mahbub.
--- Douglas Bates <bates at stat.wisc.edu> wrote:
Robert Burrows
#
On 9 Jun 2003, Douglas Bates wrote:

            

      
      
      
    

        
and note that the package is really looking for 'libxml/parser.h'. On my
machine, for example, parser.h is in /usr/include/libxml2/libxml/, so I
have LIBXML_INCDIR=/usr/include/libxml2.

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
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On Mon, Jun 09, 2003 at 06:03:55AM -0700, Mahbub Latif wrote:

            

      
      
      
    

        
For any given 'foo' I usually start by 

$ apt-cache search foo		# may return lots
$ apt-cache search libfoo	# more focussed for libraries

In this case, assumimg you want standard hdf5 (and not the mpich and lam
variants that are also available) and 

$ apt-get install libhdf5-serial-dev graphviz  

but I do not know if the graphviz package has all you need.

One day we may have suitable .deb packages for this to make installation of
complex CRAN / bioC packages a litte easier.

Dirk

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Duncan Temple Lang
    

    

      
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Robert Burrows wrote:

            

      
      
      
    

        
Thanks for pointing out the fact that one can set LIBXML_INCDIR and it
is definitely a good thing. In this particular case, however, I hope
that the configuration should work automatically without any additional
manual settings. The configure script should be using

 xml2-config --cflags

and that should return -I/usr/include/libxml2 and libxml/parser.h is
then duly found within that directory.

If this isn't the case, I'd be happy to find out and change things.
Unfortunately, conflicts between libxml and libxml2, use of libxml/
and gnome-xml/, etc... make this a complex configuration.