[BioC] error installing Rgraphviz

[Dan Tenenbaum]

On Mon, May 28, 2012 at 1:36 PM, Mark Miller
<mark.wayne.miller at gmail.com> wrote:
>
> Thanks, Dan.
>
> Unfortunately, that does not solve the problem.
>

Are you getting the same error message? What is the output of R's sessionInfo()
command?

What happens if you type:

 neato -V

at a Windows command prompt?

Dan


> Mark
>
>
>
>
> On Mon, May 28, 2012 at 12:24 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>> [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]]
>> >> >
>> >> >
>> >> > _______________________________________________
>> >> > Bioconductor mailing list
>> >> > Bioconductor at r-project.org
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>> >> > Search the archives:
>> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>> >
>
>