[R] HDF 5 install - how to pass configure flag to the R CMD command

[Raphael Arlitt]

The basic question is: How can I pass configure script command line flags 
from the R CMD command?

Now I try to install the HDF5 package on Linux (SuSE 7.3).
I got hdf5 libraries installed in /usr/local/hdf5   (man/lib/bin).

I understood to install packages the following way:
as root#  R CMD INSTALL   hdf5_1.4.7.tar.gz
Installing source package `hdf5' ...
checking for gcc... gcc
checking for C compiler default output... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
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 library containing inflate... -lz
checking for library containing H5open... no
configure: error: Can't find HDF5
ERROR: configuration failed for package `hdf5'

But how to I tell the install procedure where to look for my hdf libraries?
Changing to the hdf5 package directory I can do a configure and understand 
that I need to give it the flag --with-hdf5=/path/to/the/libraries
That works.

 ./configure --with-hdf5=/usr/local/hdf5
checking for gcc... gcc
checking for C compiler default output... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
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 library containing inflate... -lz
checking for library containing H5open... -lhdf5
checking for sufficiently new HDF5... yes
configure: creating ./config.status
config.status: creating src/Makevars


But how can I give the configure command line flag to the R CMD INSTALL 
command?

Raphael


On Friday 01 March 2002 10:07, you wrote:
> As part of the HDF5 package, you have utilities to convert HDF4 files to
> HDF5, that can be imported in R. Since the conversion program runs on the
> command line, you can call it from R... An perhaps make your own hdf4load()
> function by combining a conversion to hdf5 and the importation of the
> resulting file.
> Best,
>
> Philippe Grosjean

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