[R] problem installing RNetCDF

Prof Brian Ripley ripley at stats.ox.ac.uk
Thu Mar 9 10:24:11 CET 2006

You forgot to tell us you are running MacOS X.  Looks like a problem with 
your compiler installation (and are you using a pre-compiled R from CRAN 
and an incompatible compiler?).

The installation procedure is complicated because the system dependencies 
need to be checked.  It works well under Unix and not well under Windows. 
Some MacOS X users seem to think MacOS X is 'Unix-alike', but it vies with 
AIX as being the most extreme outlier in that set.  (For a start, it is 
based on BSD, not the Single Unix specification, and no other (recent) 
Unix-alike has bundles.)

On Wed, 8 Mar 2006, Zepu Zhang wrote:

> Hello all,
> I set 'UDUNITS_PATH' and 'NETCDF_PATH' successfully to my custom places and
> then
> % R CMD INSTALL RNetCDF_1.1-3.tar.gz
> and got this:
> ...
> checking for executable suffix...
> checking for object suffix... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for main in -lnetcdf... yes
> checking for main in -ludunits... yes
> checking for /Users/zpzhang/research/library/include/netcdf.h... yes
> checking for /Users/zpzhang/research/library/include/udunits.h... yes
> configure: creating ./config.status
> config.status: creating R/load.R
> config.status: creating src/Makevars
> ** libs
> gcc -no-cpp-precomp -I/sw/Library/Frameworks/R.framework/Resources/
> include -I/Users/zpzhang/research/library/include -I/Users/zpzhang/research/
> library/include -I/sw/include   -fno-common  -g -O2 -c RNetCDF.c -o
> RNetCDF.o
> gcc: unrecognized option '-no-cpp-precomp'
> gcc -bundle -flat_namespace -undefined suppress -lcc_dynamic -L/sw/lib -o
> RNetCDF.so RNetCDF.o -L/Users/zpzhang/research/library/lib -lnetcdf -L/
> Users/zpzhang/research/library/lib -ludunits  -lcc_dynamic -F/sw/Library/
> Frameworks -framework R
> gcc: couldn't run 'undle-gcc-4.0.2': No such file or directory
> make: *** [RNetCDF.so] Error 1
> ERROR: compilation failed for package 'RNetCDF'
> ....
> Does anyone have any insight to this 'undle-gcc-4.02' problem?
> By the way, the package contains one C source file only but the installation
> seems quite complicated. I understand it uses 'standard' procedures---
> configure, etc.---but wouldn't a simple Makefile be much easier to cope with? I
> would be pretty straightfoward what variables and paths to change, etc.
> By the way again, any comments on ncdf vs RNetCDF? I just couldn't like the
> inconsistent naming in ncdf (put.var.ncdf, att.put.ncdf, dim.get.ncdf,
> get.var.ncdf, ...), otherwise its very recent update would have attracted me to it.
> Anyway these are not big packages and should be all fine.
> Thanks for the help!
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Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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