As Dan said, the installation has changed completely; you now just have to
do
  biocLite("Rgraphviz")
and everything should work.  Beside being easier to install, one gain of
the new 2.x version of Rgraphviz was specifically to get it to work on Win
7 and Win Vista.

Now, if you really, really want to use Biconductor 2.9 instead of 2.12, you
are in for a possibly frustrating experience.  It was hard or impossible to
get Rgraphviz to work well under Windows 7 (and there is a big difference
whether you use a 64 bit or 32 bit version of the OS).  As far as I recall,
the binary version of Rgraphviz does _not_ work, but it may be possible to
get it to work if you install from source and are really careful.  However,
if you want to use Rgraphviz you are really much, much better of upgrading
(you are generally always better off by upgrading, but in this case the
gain is rather enormous).

Kasper


On Thu, Jun 6, 2013 at 7:25 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

> On Thu, Jun 6, 2013 at 2:15 AM, Heba [guest] <guest@bioconductor.org>
> wrote:
> >
> > Hello,
> > I am having problems in installing Rgraphviz package on Windows 7. I
> followed the instructions in the read me file @
> http://bioconductor.org/packages/2.9/bioc/readmes/Rgraphviz/README
> >
>
> We strongly recommend upgrading to R-3.0.1 and Bioconductor 2.12;
> recent versions of Rgraphviz are much easier to install because they
> have graphviz bundled into them.
>
> Dan
>
>
>
> > I installed the graphviz 2.20.3.1 to C:\Graphviz2.20 from this link:
> >
> http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1.msi
> >
> > I added C:\Graphviz2.20\bin to my system PATH variable and I can see the
> change in the DOS command window as following
> >
> > C:\Users\acapella>echo %PATH%
> > C:\Python27\Lib\site-packages\PyQt4\bin;C:\Program Files\Common
> Files\Microsoft
> > Shared\Windows Live;C:\Program Files (x86)\Common Files\Microsoft
> Shared\Windows
> >
>  Live;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System3
> > 2\WindowsPowerShell\v1.0\;C:\Program Files (x86)\NTRU Cryptosystems\NTRU
> TCG Sof
> > tware Stack\bin\;C:\Program Files\NTRU Cryptosystems\NTRU TCG Software
> Stack\bin
> > \;C:\Program Files\Wave Systems Corp\Gemalto\Access
> Client\v5\;C:\Program Files
> > (x86)\Windows Live\Shared;C:\Program Files (x86)\Common Files\Roxio
> Shared\DLLSh
> > ared\;C:\Program Files (x86)\Common Files\Roxio
> Shared\OEM\DLLShared\;C:\Program
> >  Files (x86)\Common Files\Roxio Shared\OEM\DLLShared\;C:\Program Files
> (x86)\Com
> > mon Files\Roxio Shared\OEM\12.0\DLLShared\;C:\Program Files
> (x86)\Roxio\OEM\Audi
> > oCore\;C:\Program Files\MATLAB\R2012b\bin;C:\Program
> Files\MATLAB\R2012aNew\bin;
> > C:\Program Files\MATLAB\R2012a\bin;C:\Program
> Files\MATLAB\R2011a\bin;c:\Program
> >  Files (x86)\Microsoft SQL Server\100\Tools\Binn\;c:\Program
> Files\Microsoft SQL
> >  Server\100\Tools\Binn\;c:\Program Files\Microsoft SQL
> Server\100\DTS\Binn\;C:\P
> > rogram Files\Microsoft Windows Performance Toolkit\;C:\Program
> Files\MATLAB\MATL
> > AB Compiler Runtime\v715\runtime\win64;C:\Program Files
> (x86)\QuickTime\QTSystem
> > \;C:\Graphviz2.20\bin
> >
> >
> > Then I installed the package using biocondutor but when try to load the
> library or call specific function it give me the following outputs
> >
> >> biocLite('Rgraphviz')
> > BioC_mirror: 'http://www.bioconductor.org'
> > Using R version 2.14, BiocInstaller version 1.2.1.
> > Installing package(s) 'Rgraphviz'
> > Installing package(s) into
> ‘C:/Users/acapella/Documents/R/win-library/2.14’
> > (as ‘lib’ is unspecified)
> > trying URL '
> http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2.14/Rgraphviz_1.32.0.zip
> '
> > Content type 'application/zip' length 933734 bytes (911 Kb)
> > opened URL
> > downloaded 911 Kb
> >
> > package ‘Rgraphviz’ successfully unpacked and MD5 sums checked
> >
> > The downloaded packages are in
> >
> C:\Users\acapella\AppData\Local\Temp\RtmpUXqbG3\downloaded_packages
> > Warning message:
> > 'boot' cannot be updated, installed directory 'C:/Program
> >   Files/R/R-2.14.0/library' not writeable
> > 'class' cannot be updated, installed directory 'C:/Program
> >   Files/R/R-2.14.0/library' not writeable
> > 'cluster' cannot be updated, installed directory 'C:/Program
> >   Files/R/R-2.14.0/library' not writeable
> > 'foreign' cannot be updated, installed directory 'C:/Program
> >   Files/R/R-2.14.0/library' not writeable
> > 'KernSmooth' cannot be updated, installed directory 'C:/Program
> >   Files/R/R-2.14.0/library' not writeable
> > 'lattice' cannot be updated, installed directory 'C:/Program
> >   Files/R/R-2.14.0/library' not writeable
> > 'MASS' cannot be updated, installed directory 'C:/Program
> >   Files/R/R-2.14.0/library' not writeable
> > 'Matrix' cannot be updated, installed directory 'C:/Program
> >   Files/R/R-2.14.0/library' not writeable
> > 'mgcv' cannot be updated, installed directory 'C:/Program
> >   Files/R/R-2.14.0/library' not writeable
> > 'nlme' cannot be updated, installed directory 'C:/Program
> >   Files/R/R-2.14.0/libra [... truncated]
> >> example(layoutGraph)
> > Warning message:
> > In example(layoutGraph) : no help found for ‘layoutGraph’
> >> library('Rgraphviz')
> > Loading required package: graph
> > Loading required package: grid
> > Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
> >   call: value[[3L]](cond)
> >   error: unable to load shared object
> 'C:/Users/acapella/Documents/R/win-library/2.14/Rgraphviz/libs/x64/Rgraphviz.dll':
> >   LoadLibrary failure:  %1 is not a valid Win32 application.
> >
> >
> >   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’
> >
> >
> >
> >
> > Can you please help me identify the problem?
> >
> > Thanks,
> > Heba
> >
> >
> >  -- output of sessionInfo():
> >
> > R version 2.14.0 (2011-10-31)
> > Platform: x86_64-pc-mingw32/x64 (64-bit)
> >
> > locale:
> > [1] LC_COLLATE=English_United Kingdom.1252
> > [2] LC_CTYPE=English_United Kingdom.1252
> > [3] LC_MONETARY=English_United Kingdom.1252
> > [4] LC_NUMERIC=C
> > [5] LC_TIME=English_United Kingdom.1252
> >
> > attached base packages:
> > [1] grid      stats     graphics  grDevices utils     datasets  methods
> > [8] base
> >
> > other attached packages:
> > [1] graph_1.32.0        BiocInstaller_1.2.1
> >
> > loaded via a namespace (and not attached):
> > [1] tools_2.14.0
> >
> > --
> > Sent via the guest posting facility at bioconductor.org.
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
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> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
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