installatioin problem
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Jin, Ying ▴ 20
@jin-ying-402
Last seen 7.2 years ago
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@stat.math.ethz.ch <mailto:bioconductor@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@renaltools graph]# ls CONTENTS data DESCRIPTION doc GXL help html INDEX latex man Meta R R-ex Scripts [root@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@jimmy.harvard.edu <mailto:rgentlem@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! [[alternative HTML version deleted]]
rhdf5 reposTools graph Rgraphviz rhdf5 reposTools graph Rgraphviz • 647 views
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Entering edit mode
Jeff Gentry ★ 3.9k
@jeff-gentry-12
Last seen 7.2 years ago
> it's said "loading required package: graph" failed with no DESCRIPTION, > but the actually the package is existing: If you do 'library(graph)' in R, what happens?
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