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...) http://biowiki.crs4.it/biowiki/NicolaSoranzo#Patches_for_R_packages Regards, Nicola ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
