[BioC] Rgraphviz installation failure with R 2.12.0

Martin Morgan mtmorgan at fhcrc.org
Mon Dec 20 19:38:40 CET 2010


On 12/20/2010 6:29 AM, Mary Putt wrote:
> 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:/"

Hi Mary --

Follow the instructions in the original error message

 > 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

The README file says that you need to download and install

       
http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1.msi

and then add the path to the 'bin' directory of the installation to your 
system's PATH variable (Control Panels -> System -> Advanced Settings -> 
Environment Variables, then 'new' or 'edit' a user variable to be named 
PATH as a semi-colon separated list of directory paths. When I did this 
and restarted R, I saw in part

 > Sys.getenv("PATH")
"<...>;C:\\Program Files (x86)\\Graphviz2.20\\bin;<...>"

where <...> are other paths not relevant to Rgraphviz, the the path that 
I have might differ from the path that you have. To ensure that I had 
entered the right PATH, I then did

 > list.files("C:\\Program Files (x86)\\Graphviz2.20\\bin")
  [1] "acyclic.exe"                    "bcomps.exe"
  [3] "ccomps.exe"                     "circo.exe"
  [5] "comdlg32.ocx"                   "diffimg.exe"
  [7] "dijkstra.exe"                   "dot.exe"
  [9] "dot2gxl.exe"                    "dotty.exe"

and so on. With graphviz correctly installed, I was then able to

 > biocLite('Rgraphviz')

Best of luck,

Martin


>
>
>
> 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
>
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-- 
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109



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