[BioC] Problem in installing Rgraphviz

[Dan Tenenbaum]

On Thu, Jun 6, 2013 at 2:15 AM, Heba [guest] <guest at 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.
>
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