Issue Installing RGraphviz in Windows

Question

I have read the README on the RGraphviz page and have looked at numerous question on the R help list and here, but I'm still not finding a reason for why I am unable to install the Rgraphviz package on R 2.14.0.

1. I have downloaded and installed Graphviz 2.20.3 (although the start menus says it's 2.21)

2. I've added the Graphviz bin folder to my user path.

   strsplit(Sys.getenv("PATH"), ";") [[1]] [1] "C:\Program Files\R\R-2.14.0\bin\x64"
   [2] "C:\Program Files\Common Files\Microsoft Shared\Windows Live"
   [3] "C:\Program Files (x86)\Common Files\Microsoft Shared\Windows Live"
   [4] "C:\Windows\system32"
   [5] "C:\Windows"
   [6] "C:\Windows\System32\Wbem"
   [7] "C:\Windows\System32\WindowsPowerShell\v1.0\"
   [8] "C:\Program Files\Intel\WiFi\bin\"
   [9] "C:\Program Files\Common Files\Intel\WirelessCommon\"
   [10] "C:\Program Files\Intel\DMIX"
   [11] "C:\Program Files (x86)\NTRU Cryptosystems\NTRU TCG Software Stack\bin\"
   [12] "C:\Program Files\NTRU Cryptosystems\NTRU TCG Software Stack\bin\"
   [13] "C:\Program Files (x86)\Intel\Services\IPT\"
   [14] "C:\Program Files\Dell\Dell Data Protection\Access\Advanced\Wave\Gemalto\Access Client\v5\" [15] "C:\Program Files (x86)\Windows Live\Shared"
   [16] "c:\Program Files (x86)\Microsoft SQL Server\100\Tools\Binn\"
   [17] "c:\Program Files\Microsoft SQL Server\100\Tools\Binn\"
   [18] "c:\Program Files\Microsoft SQL Server\100\DTS\Binn\"
   [19] "C:\Program Files (x86)\Graphviz2.20\bin"

3. Used bioconductor to install the Rgraphviz package.

   source("http://bioconductor.org/biocLite.R") 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/Abraham/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\Abraham\AppData\Local\Temp\RtmpYNFDxs\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/library' not writeable 'n [... truncated]

Now it states that Rgraphviz was successfully unpacked. However, when I attempt to import the package with library, I get an error message.

> library("Rgraphviz")
Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
  call: value[[3L]](cond)
  error: unable to load shared object 'C:/Users/Abraham/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’

Anyone have an idea what could be wrong? I've tried this on different versions of R and same problem happened.

And FYI:

> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   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

Answer 1

Personally, I'd suggest (a) updating to R-2.15.1 and then (b) using the 'devel' version of Bioconductor (the 'devel' version will become the release version on October 2, so for the patient the recommendation is to wait until then). Do (b) in a fresh R installation with

source("http://bioconductor.org/biocLite.R")
BiocInstaller::useDevel()

More detailed instructions cover the situation where you wish to use both release and development versions of Bioconductor. Then install Rgraphviz as

biocLite("Rgraphviz")

end of story, no graphviz to install, etc.