[BioC] Help - Rgraphviz install error for R 2.15 on Ubuntu 11.10

[Dan Tenenbaum]

Hi Holly,


On Fri, Apr 6, 2012 at 1:20 PM, Holly <xyang2 at uchicago.edu> wrote:
> Hi,
>
> I recently reinstall my machine and cannot figure out how to make Rgraphviz
> work. Following is the information, Please help!
>
> Thanks.
>
>
> $ sudo apt-get install graphviz
> # it installed the by default the 2.26.3-5ubuntu4
> $ whereis graphviz
> graphviz: /usr/lib/graphviz /usr/share/graphviz
> /usr/share/man/man7/graphviz.7.gz
>
>
> $R
>> source("http://bioconductor.org/biocLite.R")
> BiocInstaller version 1.4.3, ?biocLite for help
>> biocLite("Rgraphviz")
> BioC_mirror: http://bioconductor.org
> Using R version 2.15, BiocInstaller version 1.4.3.
> Installing package(s) 'Rgraphviz'
> trying URL
> 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Rgraphviz_1.34.0.tar.gz'
> Content type 'application/x-gzip' length 694533 bytes (678 Kb)
> opened URL
> ==================================================
> downloaded 678 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 ‘/usr/local/lib/R/site-library/Rgraphviz’
>
> The downloaded source packages are in
> ‘/tmp/Rtmp8PFzCV/downloaded_packages’
> Warning message:
> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> installation of package ‘Rgraphviz’ had non-zero exit status
>
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BiocInstaller_1.4.3
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.0
>

I think you need the graphviz-dev package as well:

sudo apt-get install graphviz-dev

Dan


>
> =========================================
> Xinan "Holly" Yang, Ph.D.
> Research Associate (Assistant Professor)
> The University of Chicago Departments of Pediatrics
> Section of Hematology/Oncology
> 900 East 57th Street, KCBD Room 5121
> Chicago, Illinois 60637
> Phone: 773/702-5960
> FAX: 773/834-1329
> xyang2 at uchicago.edu
>
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