[BioC] package(graph)

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Wed Aug 6 10:26:25 MEST 2003

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 :-(


-----Original Message-----
From: Ivan Borozan [mailto:ivan at ebi.ac.uk]
Sent: 05 August 2003 17:36
To: bioconductor at 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

./configure --enable-cxx --enable-threadsafe --with-pthread


(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
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,

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