Hi,
I tried to install RNetCDF binary package but when I try to load it
after installation, it gives this message
> library("RNetCDF")
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library '/Library/Frameworks/R.framework/
Versions/2.3/Resources/library/RNetCDF/libs/ppc/RNetCDF.so':
dlopen(/Library/Frameworks/R.framework/Versions/2.3/Resources/
library/RNetCDF/libs/ppc/RNetCDF.so, 6): Symbol not found: _nc_inq_dimid
Referenced from: /Library/Frameworks/R.framework/Versions/2.3/
Resources/library/RNetCDF/libs/ppc/RNetCDF.so
Expected in: flat namespace
Error in library("RNetCDF") : .First.lib failed for 'RNetCDF'
So I tried to install it from source, through the interface (i.e.
with default parameters). It issues the command:
install.packages(c("RNetCDF"),lib="/Library/Frameworks/Resources/
library/",contriburl=contrib.url(getOption
("repos"),"source"),type='source',dependencies=FALSE)
and the compilation stops because it cannot find netcdf libraries.
These libraries are installed through fink and hence are in /sw/lib/
and the headers in /sw/include/:
[EMAIL PROTECTED]:RNetCDF$ ll /sw/lib/libnetcdf*
lrwxr-xr-x 1 root admin 29 Jul 18 14:59 /sw/lib/libnetcdf.
3.5.0.dylib -> /sw/lib/libnetcdf.3.6.1.dylib
-rwxr-xr-x 1 root admin 1152056 Jul 18 14:59 /sw/lib/libnetcdf.
3.6.1.dylib
lrwxr-xr-x 1 root admin 29 Jul 18 14:59 /sw/lib/libnetcdf.
3.dylib -> /sw/lib/libnetcdf.3.6.1.dylib
-rwxr-xr-x 1 root admin 779952 Jul 18 14:59 /sw/lib/libnetcdf.a
lrwxr-xr-x 1 root admin 25 Jul 18 14:59 /sw/lib/
libnetcdf.dylib -> /sw/lib/libnetcdf.3.dylib
-rw-r--r-- 1 root admin 131532 Jul 18 14:59 /sw/lib/libnetcdf_c+
+.3.6.1.dylib
lrwxr-xr-x 1 root admin 33 Jul 18 14:59 /sw/lib/libnetcdf_c+
+.3.dylib -> /sw/lib/libnetcdf_c++.3.6.1.dylib
-rwxr-xr-x 1 root admin 169032 Jul 18 14:59 /sw/lib/libnetcdf_c+
+.a
lrwxr-xr-x 1 root admin 29 Jul 18 14:59 /sw/lib/libnetcdf_c+
+.dylib -> /sw/lib/libnetcdf_c++.3.dylib
[EMAIL PROTECTED]:RNetCDF$ ll /sw/include/netcdf*
-rwxr-xr-x 1 root admin 31574 Jul 18 14:59 /sw/include/netcdf.h
-rwxr-xr-x 1 root admin 23 Jul 18 14:59 /sw/include/netcdf.hh
-rwxr-xr-x 1 root admin 49501 Jul 18 14:59 /sw/include/netcdf.inc
-rwxr-xr-x 1 root admin 166532 Jul 18 14:59 /sw/include/netcdf.mod
-rwxr-xr-x 1 root admin 18793 Jul 18 14:59 /sw/include/netcdfcpp.h
But these are non-standard paths. So I looked at ./configure --help
which gives me the options to set:
--with-netcdf-include=INCLUDE_PATH
the location of netcdf header files
--with-netcdf-lib=LIB_PATH
the location of netcdf libraries
Therefore I tried the command:
install.packages(c("RNetCDF"),lib="/Library/Frameworks/Resources/
library/",contriburl=contrib.url(getOption
("repos"),"source"),type='source',dependencies=FALSE,configure.args="--w
ith-netcdf-include=/sw/include/ --with-netcdf-lib=/sw/lib/")
but to no avail, I still get the same error message:
checking for main in -lnetcdf...
The downloaded packages are in
/private/tmp/RtmpakpDoj/downloaded_packages
no
configure: error: netcdf library not found
ERROR: configuration failed for package 'RNetCDF'
** Removing '/Library/Frameworks/Resources/library/RNetCDF'
Warning message:
installation of package 'RNetCDF' had non-zero exit status in:
install.packages(c("RNetCDF"), lib = "/Library/Frameworks/Resources/
library/",
Does somebody know what I am doing wrong and what could be the
solution (apart from installing netcdf libraries in classic system
directories: I prefer them to be managed by Fink)? Thanks in advance.
JiHO
---
http://jo.irisson.free.fr/
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