Skip to content

Installation of rgdal from CRAN on MACOSX does not work

5 messages · Agustin Lobo, Roger Bivand, Susumu Tanimura

Original
Agustin Lobo
# 
While the installation from
http://www.kyngchaos.com/files/software/frameworks/rgdal-0.6.29-1.zip
works fine
the installation of rgdal from CRAN on MACOSX does not work, despite
my previous message that this issue was solved as well
(my confusion was a consequence of mixing both installations in the
same session):
--- Please select a CRAN mirror for use in this session ---
probando la URL
'http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/leopard/contrib/2.12/rgdal_0.6-31.tgz'
Content type 'application/x-gzip' length 10203689 bytes (9.7 Mb)
URL abierta
==================================================
downloaded 9.7 Mb


The downloaded packages are in
	/var/folders/iR/iRxOvaG9F10viNoa7WceNU+++TI/-Tmp-//RtmpqIhqn9/downloaded_packages
Loading required package: rgdal
Loading required package: sp
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object
'/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/i386/rgdal.so':
  dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/i386/rgdal.so,
6): Library not loaded: libR.dylib
  Referenced from:
/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/i386/rgdal.so
  Reason: image not found
R version 2.12.1 (2010-12-16)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] es_ES.UTF-8/es_ES.UTF-8/C/C/es_ES.UTF-8/es_ES.UTF-8

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

other attached packages:
[1] sp_0.9-76

loaded via a namespace (and not attached):
[1] grid_2.12.1     lattice_0.19-13 tools_2.12.1

Note that rgdal.so is where it should be:

imac-de-agustin-lobo:~ agustinlobo$ ls -l
/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/i386/
total 15088
-rwxr-xr-x  1 agustinlobo  admin  7722168  4 dic 15:57 rgdal.so

This error is not solved by setting the GDAL path.

Agus
Roger Bivand
#
On Wed, 29 Dec 2010, Agustin Lobo wrote:

            

      
      
      
    

        
Please do read the error message:

            

      
      
      
    

        
'/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/i$

            

      
      
      
    

        
dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal$

            

      
      
      
    

        
/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/i3$

            

      
      
      
    

        
The image that is not found is libR.dylib, the main R dylib against which 
rgdal.so is linked. So this is still an issue of your R installation, 
possibly a multi-architecture issue (is libR.dylib the i386 version, 
guessing - is libR64.dylib the 64-bit Intel version?).

Could any OSX users who are using CRAN extra rgdal please help Agus to 
resolve this - it could be that local path modifications are hiding 
libR.dylib, or that R was installed 64-bit only, and the INSTALL_opts= 
argument to install.packages() was not set correctly? I assume that the 
CRAN extras OSX rgdal binary is built against a standard R OSX Intel 
install, which is multi-architecture.

For a fully updated rgdal, the best combination remains installing the 
full GDAL framework from Kyngchaos, the full tools collection:

http://r.research.att.com/tools/
http://cran.r-project.org/bin/macosx/tools

and install from CRAN source. For a lab, the instructor would rather build 
a local OSX rgdal binary package using the tools collection on one 
development machine with all the correct path variables set (R CMD check 
rgdal; R CMD INSTALL --build rgdal), paying attention to 
multi-architectures, and distribute to lab machines from there. This means 
that the lab instructor can keep rgdal updated if need be, as both 
Kyngchaos and CRAN extras rgdal OSX binary packages typically lag CRAN 
source.

Please also note that there are very many very old GDAL binaries out there 
that users pick up and apply, missing all the subsequent bug-fixes and 
improvements - GDAL 1.8.0 release candidate 1 is now out, so we are 
looking at an upgrade to 1.8.0 during January, which Kyngchaos will most 
likely pick up quickly, probably with a current rgdal binary.

Roger

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Agustin Lobo
    

    

      
      #
    

  


  

      
Roger,

But
http://www.kyngchaos.com/files/software/frameworks/rgdal-0.6.29-1.zip
installs with no problems on the same machine and on the same R, would that not
discard the possibility of an

            

      
      
      
    

        
as you suggest?

Please note I'm not personally in a hurry any more as we can work with
the rgdal from kyngchaos. I just want to report the error to help
having an rgdal installation for MACOSX as
simple as for Windows.
I understand installing from source will always be a bit more
difficult on MACOSX than on linux as there are some basic tools and
libraries that are missing on regular MAC systems that must be
previously installed, but this is not my concern now as I'm focusing
on installations from binaries.

Thanks!

Agus



2010/12/29 Roger Bivand <Roger.Bivand at nhh.no>:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Roger Bivand
    

    

      
      #
    

  


  

      
On Wed, 29 Dec 2010, Agustin Lobo wrote:

        

            

      
      
      
    

        
I will have access to an OSX laptop in a little over a week, and will try 
out the CRAN rgdal binaries. Just one report of installation failure isn't 
enough. I think that maybe someone on R-sig-mac might know why rgdal.so is 
looking for libR.dylib; I don't use OSX, and don't have easy access to 
such a machine, which is why I asked for others to comment.

Roger

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Susumu Tanimura
    

    

      
      #
    

  


  

      
Hi Agus,

I have just installed rgdal package on MacOSX 10.6.5 yesterday. It is
very simple.
What you should do is two steps.
1. install rgdal and proj
2. install rgdal as source

If you use MacPorts, you may just do the followings:
$ sudo port install gdal proj
then run 64-bit R. Inside R, you may execute the followings:

            

      
      
      
    

        
'--with-proj-lib=/opt/local/lib')

            

      
      
      
    

        
If you run 32-bit R, you will fail because ports were complied as 64-bit.

Hope it helps you.



2010/12/30 Roger Bivand <Roger.Bivand at nhh.no>: