Dear all
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 taht 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?
Regards
--
-- Jérôme
Si quelqu'un vous dit : "Je me tue à vous le répéter",
laissez-le mourir.
(Jacques Prévert)
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