Hi all, I've downloaded hdf5-1.6.0.tar.gz and installed it on my linux RH 8.0 using ./configure --enable-cxx --enable-threadsafe --with-pthread --prefix=/opt/gnu/hdf5 make #Install (rm -rf /opt/gnu/hdf5) cd /usr/local/src/hdf5-1.6.0 make install #User's Setting export PATH="/opt/gnu/hdf5/bin:$PATH" export LD_LIBRARY_PATH="/opt/gnu/hdf5/lib:$LD_LIBRARY_PATH" and still got R CMD INSTALL -l ../../../usr/lib/R/library/ rhdf5_1.0.1.tar.gz * Installing *source* package 'rhdf5' ... 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 how to run the C preprocessor... gcc -E checking for hdf5... yes checking for H5Fopen in -lhdf5... no checking for hdf5.h... no checking hdf5 in /sw... failed configure: error: please specify a valid hdf5 installation with --with-hdf5=DIR ERROR: configuration failed for package 'rhdf5' any help would be appreciated ...also has anyone tried to install graphviz on a Linux RH 8.0 machine if yes could he/she inform me of the exact procedure ? 2) On uploading the package {graph} i get Error in library(graph) : .First.lib failed although the package {graph} seems to install properly ? all the best, ivan

Hi Ivan I struggled with this for a while, and the only help I can give you is that if you don't need rhdf5, simply don't install it - and get all the other Bioconductor modules from the website :-( Thanks Mick -----Original Message----- From: Ivan Borozan [mailto:ivan@ebi.ac.uk] Sent: 05 August 2003 17:36 To: bioconductor@stat.math.ethz.ch Subject: [BioC] package(graph) Hi all, I've downloaded hdf5-1.6.0.tar.gz and installed it on my linux RH 8.0 using ./configure --enable-cxx --enable-threadsafe --with-pthread --prefix=/opt/gnu/hdf5 make #Install (rm -rf /opt/gnu/hdf5) cd /usr/local/src/hdf5-1.6.0 make install #User's Setting export PATH="/opt/gnu/hdf5/bin:$PATH" export LD_LIBRARY_PATH="/opt/gnu/hdf5/lib:$LD_LIBRARY_PATH" and still got R CMD INSTALL -l ../../../usr/lib/R/library/ rhdf5_1.0.1.tar.gz * Installing *source* package 'rhdf5' ... 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 how to run the C preprocessor... gcc -E checking for hdf5... yes checking for H5Fopen in -lhdf5... no checking for hdf5.h... no checking hdf5 in /sw... failed configure: error: please specify a valid hdf5 installation with --with-hdf5=DIR ERROR: configuration failed for package 'rhdf5' any help would be appreciated ...also has anyone tried to install graphviz on a Linux RH 8.0 machine if yes could he/she inform me of the exact procedure ? 2) On uploading the package {graph} i get Error in library(graph) : .First.lib failed although the package {graph} seems to install properly ? all the best, ivan _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

On Tue, 5 Aug 2003, Ivan Borozan wrote: > R CMD INSTALL -l ../../../usr/lib/R/library/ rhdf5_1.0.1.tar.gz > configure: error: please specify a valid hdf5 installation with > --with-hdf5=DIR > ERROR: configuration failed for package 'rhdf5' I'm not certain that the configure script from rhdf5 picks up the LD_LIBRARY_PATH. Try adding '--configure-args=--with-hdf=<dir>' to your R INSTALL command and see if that helps. > any help would be appreciated ...also has anyone tried to install graphviz > on a Linux RH 8.0 machine if yes could he/she inform me of the exact > procedure ? I've not installed on 8.0 but several 7.X machines. In all cases it was as simple as downloading graphviz-current from www.graphviz.org (follow the 'most recent developmental release' link), and then the standard install (./configure; make; make install). > 2) On uploading the package {graph} i get > Error in library(graph) : .First.lib failed > although the package {graph} seems to install properly ? Is there no other output between library(graph) and that error message?