[BioC] Please help : RGraphviz installation problem version 1.32 in Ubuntu and Windows 7

[Steve Lianoglou]

Hi,

On Thu, Mar 15, 2012 at 11:21 AM, Amit Kumar Kashyap
<amitonbiochem at gmail.com> wrote:
> hello All ,
> I was trying to install RGrphaviz packge in R from :
> http://www.bioconductor.org/packages/release/bioc/html/Rgraphviz.html
>
> but could not successfully either in Linux or windows
>
> In windows it says :
> *The program can not start because libctd-4.dll missing *
> *
> *
> In Linnux (Ubuntu 11 .10 ) it says :
>
> ERROR: configuration failed for package ‘Rgraphviz’v ..
>
> Can anyone please explain what exactly the problem  : Is tha correct
>  version of the program .. ?   or do we need
> to additional configuration setting  ?
>
> I Google it but the discussion posts are quite old .. so please help me

Did you read this?

http://www.bioconductor.org/packages/release/bioc/readmes/Rgraphviz/README

Also, you might consider updating your version of the R to the newest ...

-steve

>
> Thanks
>
> Regards
> -Amit Kumar
>
>
>
>
>
>>     source("http://bioconductor.org/biocLite.R")
> BioC_mirror = http://bioconductor.org
> Change using chooseBioCmirror().
> Warning messages:
> 1: In safeSource() : Redefining ‘biocinstall’
> 2: In safeSource() : Redefining ‘biocinstallPkgGroups’
> 3: In safeSource() : Redefining ‘biocinstallRepos’
>>     biocLite("Rgraphviz")
> Using R version 2.13.1, biocinstall version 2.8.4.
> Installing Bioconductor version 2.8 packages:
> [1] "Rgraphviz"
> Please wait...
>
> Installing package(s) into ‘/home/amit/R/x86_64-pc-linux-gnu-library/2.13’
> (as ‘lib’ is unspecified)
> trying URL '
> http://bioconductor.org/packages/2.8/bioc/src/contrib/Rgraphviz_1.30.1.tar.gz
> '
> Content type 'application/x-gzip' length 730304 bytes (713 Kb)
> opened URL
> ==================================================
> downloaded 713 Kb
>
> * installing *source* package ‘Rgraphviz’ ...
> 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 ISO C89... none needed
> checking how to run the C preprocessor... gcc -E
> checking for grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking for stdbool.h that conforms to C99... yes
> checking for _Bool... yes
> checking for whether compiler has bool... yes
> configure: No --with-graphviz option was specified. Trying to find Graphviz
> using other methods.
> checking for pkg-config... /usr/bin/pkg-config
> Package libgvc was not found in the pkg-config search path.
> Perhaps you should add the directory containing `libgvc.pc'
> to the PKG_CONFIG_PATH environment variable
> No package 'libgvc' found
> configure: pkg-config was not able to find the Graphviz library libgvc.
> This either indicates that Graphviz is old or that something is wrong.
> Verify Graphviz is installed and that PKG_CONFIG_PATH is correct.
> checking for dotneato-config... no
> configure: dotneato-config not found in PATH.
> configure: Using default directory /usr/local, consider specifiying
> --with-graphviz
> configure: error: /usr/local/bin/dot not found.  Check Graphviz
> installation.
> ERROR: configuration failed for package ‘Rgraphviz’
> * removing ‘/home/amit/R/x86_64-pc-linux-gnu-library/2.13/Rgraphviz’
>
> The downloaded packages are in
> ‘/tmp/RtmpyHrdSv/downloaded_packages’
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package 'Rgraphviz' had non-zero exit status
>
>        [[alternative HTML version deleted]]
>
>
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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact