[R] hdf5 library install issue

Nicola Soranzo nsoranzo at tiscali.it
Wed Jul 6 16:15:25 CEST 2011

On Fri Feb 18 17:48:11 CET 2011 Jérôme wrote:
> I'm trying to install the hdf5 library into R. The HDF5 package is
> installed in a special directory, distributed accross my cluster:
> /share/apps/HDF5
> So i put the args option to the configure command as i read in previous
> post in the list:
> jerome]# R CMD INSTALL --configure-vars='LDFLAGS=-L/share/apps/HDF5/lib'
> --configure-args='--with-hdf5=/share/apps/HDF5' hdf5_1.6.9.tar.gz
> * installing to library '/share/apps/R-core-2.12.1_SHLIB/lib64/R/library'
> * installing *source* package 'hdf5' ...
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> 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
> ** libs
> gcc -std=gnu99 -I/share/apps/R-core-2.12.1_SHLIB/lib64/R/include
> -I/share/apps/HDF5/include -I/usr/local/include    -fpic  -g -O2 -c
> hdf5.c -o hdf5.o
> gcc -std=gnu99 -shared -L/usr/local/lib64 -o hdf5.so hdf5.o
> -Wl,-rpath,/share/apps/HDF5/lib -lhdf5 -lz -lm
> -L/share/apps/R-core-2.12.1_SHLIB/lib64/R/lib -lR
> /usr/bin/ld: cannot find -lhdf5
> collect2: ld returned 1 exit status
> make: *** [hdf5.so] Error 1
> ERROR: compilation failed for package 'hdf5'
> * removing '/share/apps/R-core-2.12.1_SHLIB/lib64/R/library/hdf5'
> So, the problem is that the configure don't use in a correct way the
> option "--with-hdf5", and neither the other configure-vars option.
> How can i do to have this library usable in R?

Dear Jérôme,
I had a similar problem, you can try a patch I developed (and sent to hdf5 
package maintainer with no luck...)



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