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

[Holly]

Thanks Dan. It works now.
Holly

On 04/06/2012 07:09 PM, Dan Tenenbaum wrote:
> 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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