[R-SIG-Mac] Install RNetCDF_1.7-3.tar.gz

[Marc Girondot]

I answer myself to my question just in case someone will search for the 
same problem; he/she will find the solution !
The problem is seen only if MacPorts is used. If the library in 
installed in other way, it works.
The complete solution has been posted here:
http://max2.ese.u-psud.fr/epc/conservation/Girondot/Publications/Blog_r/Entrees/2014/4/7_rgdal_and_other_packages_with_R_3.1.html

Sincerely,

Marc


Le 12/06/2015 15:56, Marc Girondot a écrit :
> Dear list members,
>
> RNetCDF_1.7-3 binaries are not available for OS X Mavericks, so I try 
> install it from sources.
>
> 1- Using MacPorts, I installed netcdf, hdf5, udunits and udunits2 
> libraries. It seems that they are correctly installed with the lastest 
> version:
>
> belinda:~ marc$ port installed
>
> hdf5 @1.8.15-patch1_0+cxx (active)
> netcdf @4.3.3.1_2+dap+netcdf4 (active)
> udunits @1.12.11_2 (active)
> udunits2 @2.1.24_0 (active)
>
> 2- in my .profile, I introduce this line:
> export LD_LIBRARY_PATH=/opt/local:$LD_LIBRARY_PATH
>
> And it seems to work correctly:
>
> belinda:~ marc$ echo $LD_LIBRARY_PATH
> /opt/local:
>
>
> 3- Then I load RNetCDF_1.7-3.tar.gz in the desktop and I run this 
> command:
>
> R CMD INSTALL 
> --configure-args="--with-netcdf-include='/opt/local/include' 
> --with-netcdf-lib='/opt/local/lib' 
> --with-udunits-include='/opt/local/include' 
> --with-udunits-lib='/opt/local/lib' --with-hdf5-lib='/opt/local/lib'" 
> /Users/marc/Desktop/RNetCDF_1.7-3.tar.gz
>
> 4- But I obtain this error (the list of all outputs is shown below. 
> Here I show only the error:
>
> clang -dynamiclib -Wl,-headerpad_max_install_names -undefined 
> dynamic_lookup -single_module -multiply_defined suppress 
> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o 
> RNetCDF.so RNetCDF.o -lnetcdf -ludunits2 -lhdf5_hl -lhdf5 -lexpat 
> -lcurl -lz -ldl -lm -F/Library/Frameworks/R.framework/.. -framework R 
> -Wl,-framework -Wl,CoreFoundation
> ld: library not found for -lnetcdf
>
> Does someone have an idea of the mistake(s) I did ?
>
>
> Thanks a lot
>
> Marc
>
>

-- 
__________________________________________________________
Marc Girondot, Pr

Laboratoire Ecologie, Systématique et Evolution
Equipe de Conservation des Populations et des Communautés
CNRS, AgroParisTech et Université Paris-Sud 11 , UMR 8079
Bâtiment 362
91405 Orsay Cedex, France

Tel:  33 1 (0)1.69.15.72.30   Fax: 33 1 (0)1.69.15.73.53
e-mail: marc.girondot at u-psud.fr
Web: http://www.ese.u-psud.fr/epc/conservation/Marc.html
Skype: girondot