[BioC] Rgraphviz installation failure with R 2.12.0

[Mary Putt]

Thank you Martin I very much appreciate your help. 

Here are the results of your suggestion. 


> Sys.getenv("PATH")
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               PATH 
"C:\\Program Files\\Insightful\\splus80\\;C:\\Program Files\\Business Objects\\common\\3.5\\bin\\NOTES\\;C:\\Program Files\\Business Objects\\common\\3.5\\bin\\NOTES\\DATA\\;\"C:\\Program Files\\Symantec\\Norton Ghost 2003\\\";C:\\Program Files\\Microsoft SQL Server\\80\\Tools\\Binn\\;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\Program Files\\Kerberos\\;C:\\Program Files\\QuickTime\\QTSystem\\;C:\\Program Files\\Common Files\\Roxio Shared\\DLLShared\\;C:\\Program Files\\Common Files\\Roxio Shared\\9.0\\DLLShared\\;C:\\Program Files\\SAS\\SharedFiles\\Formats;C:\\Program Files\\MATLAB\\R2009b\\runtime\\win32;C:\\Program Files\\MATLAB\\R2009b\\bin;\"C:\\Program Files\\Mplus\\\"" 

> list.files()
 [1] "Default.rdp"                   "desktop.ini"                   "Downloads"                     "Enterprise Guide Sample.lnk"   "HP LJ 3005"                    "HP LJ 4250"                   
 [7] "kaplan"                        "log"                           "MATLAB"                        "My Albums"                     "My Business Objects Documents" "My Cytel Files"               
[13] "My Music"                      "My Pictures"                   "My SAS Files"                  "My Videos"                     "NCSS"                          "New Folder"                   
[19] "output_remove_11.Rdata"        "output_single_11.Rdata"        "RECYCLER"                      "S-PLUS Projects"               "SafeNet Sentinel"              "System Volume Information"    
[25] "VIM_8.pdf"                    

> getwd()
[1] "D:/"



To: Mary Putt <mputt at mail.med.upenn.edu>
Cc: bioconductor at r-project.org
Subject: Re: [BioC] Rgraphviz installation failure with R 2.12.0
Message-ID: <4D0B8FB8.1010605 at fhcrc.org>
Content-Type: text/plain; charset=ISO-8859-1

On 12/17/2010 06:48 AM, Mary Putt wrote:

> > I have the same installation problems on two 32 bit computers running
> > Windows 7 or Windows XP. and R 2.12.0
> > 
> > The shared object RGraphviz.dll is where it is supposed to be.
> > 
> > Any suggestions greatly appreciated.
> > 
> > Thank you
> > 
> > Mary
> > 
>   
>> >>   biocLite("Rgraphviz")
>>     
> > Using R version 2.12.0, biocinstall version 2.7.4.
> > Installing Bioconductor version 2.7 packages:
> > [1] "Rgraphviz"
> > Please wait...
> > 
> > trying URL
> > 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contrib/2.12/Rgraphviz_1.28.0.zip'
> > 
> > Content type 'application/zip' length 1065188 bytes (1.0 Mb)
> > opened URL
> > downloaded 1.0 Mb
> > 
> > package 'Rgraphviz' successfully unpacked and MD5 sums checked
> > 
> > The downloaded packages are in
> >       C:\Documents and Settings\mputt\Local
> > Settings\Temp\Rtmpi20FRB\downloaded_packages
> > 
>   
>> >> library("Rgraphviz")
>>     
> > Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
> > call: value[[3L]](cond)
> > error: unable to load shared object
> > 'C:/PROGRA~1/R/R-212~1.0/library/Rgraphviz/libs/i386/Rgraphviz.dll':
> > LoadLibrary failure:  The specified module could not be found.
>   

Hi Mary -- the cryptic error message is saying that "I tried to load
Rgraphviz.dll, but could not, because something Rgraphviz.dll depends on
could not be found'. Can you show us (e.g., Sys.getenv('PATH') and
list.files()) that you've done these things correctly:


> > Check that (1) graphviz is installed on your system; (2) the installed
> > version of graphviz matches '2.20.3'; this is the version used to build
> > this Rgraphviz package; (3)
> > graphviz is accessible to R, e.g., the path to the graphviz 'bin'
> > directory is in the system 'PATH' variable.  See additional instructions
> > in the 'README' file of the
> > Rgraphviz 'source' distribution, available at
> > 
> > http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html
> > 
> > Ask further questions on the Bioconductor mailing list
> > 
> > http://bioconductor.org/docs/mailList.html
> > 
> > 
> > Error: package/namespace load failed for 'Rgraphviz'
>   

I think this should be sufficient on 32-bit systems; for 64-bit systems
you'll have to read the README file indicated above.

Martin