[BioC] installatioin problem

[Jin, Ying]

Greetings-
 
I'm having difficulty in installing the 'Rgrpahviz' and 'rhdf5' packages in the installation of Bioconductor. In the first-time installation, I called the "getBioC()" function try to install all the packages. Other packages except the above two are installed in "/usr/lib/R/library" directory, however, after I installed the special library 'GraphViz' for the 'Rgraphviz' package, I still can't install 'Rgraphviz' after calling "getBioC()" again.
Please take a look at the following output: 
> source("http://www.bioconductor.org/getBioC.R <http://www.bioconductor.org/getBioC.R> ")
> getBioC()
Running getBioC version 1.2.40....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found at: www.bioconductor.org/getBioC.R <http://www.bioconductor.org/getBioC.R> 
Please direct any concerns or questions to bioconductor at stat.math.ethz.ch <mailto:bioconductor at stat.math.ethz.ch> .
[1] "Installing reposTools ..."
Creating a new generic function for "summary" in package 
reposTools 
Synching your local package management information ...
Packages which have been removed:
        Rgraphviz
        rhdf5
 
Synching your local package management information ...
[1] "Attempting to download Rgraphviz from http://www.bioconductor.org/repository/release1.2/package/Source <http://www.bioconductor.org/repository/release1.2/package/Source> "
[1] "Download complete."
[1] "Installing Rgraphviz"
* Installing *source* package 'Rgraphviz' ...
** libs
gcc -I/usr/lib/R/include `dotneato-config --cflags`  -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -O2 -m486 -fno-strength-reduce -g -c Rgraphviz.c -o Rgraphviz.o
In file included from /usr/local/include/graphviz/types.h:11,
                 from /usr/local/include/graphviz/render.h:28,
                 from common.h:19,
                 from Rgraphviz.c:1:
/usr/local/include/graphviz/pathplan.h:11: warning: ignoring pragma: 
In file included from /usr/local/include/graphviz/pathplan.h:16,
                 from /usr/local/include/graphviz/types.h:11,
                 from /usr/local/include/graphviz/render.h:28,
                 from common.h:19,
                 from Rgraphviz.c:1:
/usr/local/include/graphviz/pathgeom.h:11: warning: ignoring pragma: 
In file included from /usr/local/include/graphviz/render.h:29,
                 from common.h:19,
                 from Rgraphviz.c:1:
/usr/local/include/graphviz/graph.h:11: warning: ignoring pragma: 
In file included from common.h:20,
                 from Rgraphviz.c:1:
/usr/local/include/graphviz/graph.h:11: warning: ignoring pragma: 
In file included from common.h:23,
                 from Rgraphviz.c:1:
/usr/local/include/graphviz/adjust.h:11: warning: ignoring pragma: 
gcc -shared -L/usr/local/lib -o Rgraphviz.so Rgraphviz.o -Wl,`dotneato-config --libs` -lm  
** R
** inst
** save image
Loading required package: graph 
Error in library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts,  : 
        This is not a valid package -- no DESCRIPTION exists
[1] FALSE
Loading required package: graph 
Error in library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts,  : 
        This is not a valid package -- no DESCRIPTION exists
Error: Rgraphviz requires package graph
Execution halted
/usr/lib/R/bin/INSTALL: line 337: 16941 Broken pipe             cat "${R_PACKAGE_DIR}/R/${pkg}"
ERROR: execution of package source for 'Rgraphviz' failed
[1] "Attempting to download rhdf5 from http://www.bioconductor.org/repository/release1.2/package/Source <http://www.bioconductor.org/repository/release1.2/package/Source> "
[1] "Download complete."
[1] "Installing rhdf5"
* 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'
>From URL:  http://www.bioconductor.org/repository/release1.2/package/Source <http://www.bioconductor.org/repository/release1.2/package/Source> 
        Rgraphviz version 1.0
        rhdf5 version 1.0.1
Packages that were not updated:
        AnnBuilder
        Biobase
        DynDoc
        RBGL
        ROC
        Ruuid
        SAGElyzer
        affy
        affycomp
        affydata
        annotate
        edd
        genefilter
        geneplotter
        graph
        hexbin
        limma
        makecdfenv
        marrayClasses
        marrayInput
        marrayNorm
        marrayPlots
        marrayTools
        multtest
        reposTools
        tkWidgets
        vsn
        widgetTools
Packages Rgraphviz and rhdf5 require special libraries to be installed.
Please see the URL http://www.bioconductor.org/faq/#Other <http://www.bioconductor.org/faq/#Other>  Notes for
more details on installing these packages if they fail
to install properly
Warning messages: 
1: Installation of package Rgraphviz had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 
2: Installation of package rhdf5 had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 
> 

it's said "loading required package: graph" failed with no DESCRIPTION, but the actually the package is existing:
 
[root at renaltools graph]# ls
CONTENTS  data  DESCRIPTION  doc  GXL  help  html  INDEX  latex  man  Meta  R  R-ex  Scripts
[root at renaltools graph]# more DESCRIPT* 
Package: graph
Title: graph: A package to handle graph data structures
Version: 1.1.9
Author: R. Gentleman, Elizabeth Whalen
Description: A package that implements some simple graph handling
        capabilities.
Maintainer: R. Gentleman <rgentlem at jimmy.harvard.edu <mailto:rgentlem at jimmy.harvard.edu> >
License: LGPL
Depends: R (>= 1.7), cluster, XML
Built: R 1.7.1; ; 2003-08-08 15:26:26

Thanks advance for your great help!

 



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