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.giron...@u-psud.fr
Web: http://www.ese.u-psud.fr/epc/conservation/Marc.html
Skype: girondot
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