[BioC] error installing Rgraphviz

[Dan Tenenbaum]

[cc'ing bioconductor list so others can benefit from this]

On Mon, May 28, 2012 at 1:16 PM, Mark Miller
<mark.wayne.miller at gmail.com> wrote:
>
> Hi Dan,
>
> Thank you for the reply.
>
> Below is my current PATH statement:
>
> C:\Program Files\Common Files\Microsoft Shared\Windows Live;C:\Program Files
> (x86)\Common Files\Microsoft Shared\Windows Live;C:\Program Files\Dell\DW
> WLAN Card;;C:\Program Files (x86)\AMD APP\bin\x86_64;C:\Program Files
> (x86)\AMD
> APP\bin\x86;%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32\Wbem;%SYSTEMROOT%\System32\WindowsPowerShell\v1.0\;C:\Program
> Files (x86)\ATI Technologies\ATI.ACE\Core-Static;C:\Program
> Files\WIDCOMM\Bluetooth Software\;C:\Program Files\WIDCOMM\Bluetooth
> Software\syswow64;C:\Program Files (x86)\Windows
> Live\Shared;c:\MinGW\bin;C:\Program Files (x86)\Graphviz2.20
>

The directory that should be in your PATH is:

C:\Program Files (x86)\Graphviz2.20\bin

(note the \bin at the end). That is where the DLL is located that
Rgraphviz is complaining about, as well as other files it needs.



> You are correct that I had misspelled 'Graphviz' earlier.  I think I have
> spelled it correctly now.  I tried to check whether that was the problem by
> first correcting the spelling in the PATH statement and then trying to
> re-install Rgraphviz.  However, I still received errors.
>
> Next I uninstalled Graphviz.  I noted that I had to manually remove Graphviz
> from the PATH statement.  Then I re-installed Graphviz and added it back to
> the PATH statement.  I still receive the pop-up error message described
> earlier after re-installing Rgraphviz.
>
> In between uninstalling and re-installing or between correcting, removing
> and adding text to the PATH statement I performed frequent reboots followed
> by use of the 'echo %PATH%' command statement to check the PATH.
>

You do not need to reboot your machine after chaning the PATH. You
just need to close and reopen the command prompt window.

> I think this covers your earlier suggestions.  Sorry if I overlooked any.
>
> I was hoping to install Rgraphviz because I was hoping to explore R's
> ability to act as a GIS system and a reference book on the subject used
> Rgraphviz in at least one example file.  I do not know how frequently
> Rgraphviz is used by that reference, so I do not yet know how critical
> Rgraphviz will be for me in pursuing that exploration.
>
> Regardless, thank you for your help.  Let me know if I can provide
> additional useful information.
>

If the above suggestions do not help, please send the output of the
sessionInfo() command. I'm wondering if you are running 32- or 64-bit
R. If 64, then you'll need to install a different version of Graphviz.

Dan


> Mark
>
>
>
>
>
>
> On Mon, May 28, 2012 at 9:35 AM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>> 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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>
>