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

[Martin Morgan]

On 03/21/2012 05:18 PM, Amit Kumar Kashyap wrote:
> Hello Steve ,
>
>   Thanks for the information .  It was helpful to read to README ..I
> followed the instructions in README  but still unsuccessful to run it
> RGraphviz .
>
> it says
>
> program can't start because MSVCR80.dll is missing from your computer..
> I am using windows7 and Latest R version 14.2

Hi Amit -- google for MSVCR80.dll, download and install; I'm surprised 
it's needed. Martin

>
>
> Thanks
>
>   - Amit
>
>
>
> On Thu, Mar 15, 2012 at 4:35 PM, Steve Lianoglou<
> mailinglist.honeypot at gmail.com>  wrote:
>
>> 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]]
>>>
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
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>>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>>
>> --
>> 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
>>
>
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