[BioC] error installing Rgraphviz

[Dan Tenenbaum]

Hi Mark,

On Sun, May 27, 2012 at 4:13 PM, Mark Miller
<mark.wayne.miller at gmail.com> wrote:
> I am attempting to install the package 'Rgraphviz' in R version 2.15.0 on a
> PC running Windows 7, Platform: x86_64-pc-mingw32/x64 (64-bit).  However,
> when I type 'library('Rgraphviz')' I keep getting a pop-up error message
> stating 'DP_LocalAvatar: Rgui.exe - System Error' 'The program can't start
> because libcdt-4.dll is missing from your computer. Try reinstalling the
> program to fix the problem.' Within R I get an error message stating that
> there is no package 'Rgraphviz'.
>
> I installed Graphviz using a file called 'graphviz-2.20.3.1.msi' which I
> believe I downloaded from the link in an R post found here:
>
> http://r.789695.n4.nabble.com/Rgraphviz-install-td878526.html
>
> The actual link within the above R post was:
>
> http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1.msi
>
>
>
> The directory to Graphviz on my computer is 'c:\Program Files
> (x86)\Graphviz2.20' and the file 'libcdt-4.dll' is located in the folder
> 'c:\Program Files (x86)\Graphviz2.20\bin'.  The following appears at the
> end of my path statement 'Program Files (x86)\Graphvis2.20\bin' and is also
> displayed when I type 'C:\echo %PATH%' in a command window.
>

Can you send the full output of the echo %PATH% command?
Note that "Graphviz" is mis-spelled above. Could that be the problem?


Also note that if you set your PATH in Control Panel, you need to
start a new command window after making the change, because the change
will not be reflected in any currently open command windows.

> The directory to R on my computer is 'c:\Program Files\R\R-2.15.0\'.
>
> When I try to install 'Rgraphviz' I get the following messages within R:
>
>
>> source("http://bioconductor.org/biocLite.R")
>
> BiocInstaller version 1.4.4, ?biocLite for help
>
>> biocLite("Rgraphviz")
>
> BioC_mirror: http://bioconductor.org
> Using R version 2.15, BiocInstaller version 1.4.4.
> Installing package(s) 'Rgraphviz'
> trying URL '
> http://www.bioconductor.org/packages/2.10/bioc/bin/windows/contrib/2.15/Rgraphviz_1.34.0.zip
> '
> Content type 'application/zip' length 936601 bytes (914 Kb)
> opened URL
> downloaded 914 Kb
>
> package ‘Rgraphviz’ successfully unpacked and MD5 sums checked
>
> The downloaded binary packages are in
>        C:\Users\Mark W
> Miller\AppData\Local\Temp\Rtmpqyh1A3\downloaded_packages
> Warning message:
> installed directory not writable, cannot update packages 'foreign', 'MASS',
>  'mgcv', 'nlme', 'survival'
>
>>
>
>
> The file 'Rgraphviz_1.34.0.zip' is placed in 'C:\Users\Mark W
> Miller\AppData\Local\Temp\Rtmpqyh1A3\downloaded_packages' and the package
> 'Rgraphviz' does not appear in the R library in 'c:\Program
> Files\R\R-2.15.0\library'.  Rather 'Rgraphviz' appears in 'C:\users\Mark W
> Miller\Documents\R\win-library\2.15'
>

This is ok.


> I have copied and pasted the 'Rgraphviz' folder from 'C:\users\Mark W
> Miller\Documents\R\win-library\2.15' into 'C:\Program
> Files\R\R-2.15.0\library\'.


You do not need to do this.

>
> Then inside R I type 'library('Rgraphviz')' and get the following message
> in a pop-up window:
>
> 'DP_LocalAvatar: Rgui.exe - System Error' 'The program can't start because
> libcdt-4.dll is missing from your computer. Try reinstalling the program to
> fix the problem.'
>
> and the following messages within R:
>
>
>> 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/Mark W
> Miller/Documents/R/win-library/2.15/Rgraphviz/libs/x64/Rgraphviz.dll':
>  LoadLibrary failure:  The specified module could not be found.
>
>
>  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’
>
>>
>
>
> The file 'C:\Users\Mark W
> Miller\Documents\R\win-library\2.15\Rgraphviz\libs\x64\Rgraphviz.dll' does
> exist in that folder and in the folder where I copied and pasted it
> into: 'c:\Program Files\R\r-2.15.0\library\Rgraphviz\libs\x64\'.
>
>
> In addition to the steps described above I have tried countless variations
> over approximately 8 hours, including uninstalling R and re-installing it.
>
> During one reboot maybe 4 hours into this process I even got an error
> message on start-up and almost everything on my desktop had disappeared.  I
> restarted the computer again and my normal desktop was restored.  (I found
> a post on the internet describing something similar when trying to install
> 'Rgraphviz' but I do not know whether my experience was related to that
> previous incident.)
>
> I am hoping someone can provide detailed step-by-step instructions on how
> to install the package Rgraphviz and/or identify where I am making a
> mistake based on the information I have provided.  I have tried to include
> here as much information as I can think of.  If I can include additional
> helpful information please let me know.
>
> I wonder whether the above warning message is related to why I cannot
> install 'Rgraphviz': 'Warning message: installed directory not writable,
> cannot update packages 'foreign', 'MASS', 'mgcv', 'nlme', 'survival''.
>

No. That is just biocLite() telling you that those packages couldn't
be updated because they live in a directory that you can't write to.
If you log in as an admin user you can update those packages and make
that message go away, or you can just ignore it.

Dan


> I have not previously posted on this forum.  Hopefully I am following
> protocol.
>
> Thank you for any advice.
>
> Mark W. Miller
>
>        [[alternative HTML version deleted]]
>
>
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