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

[Holly]

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


=========================================
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