[BioC] error installing Rgraphviz

[Dan Tenenbaum]

[cc'ing Bioconductor again]

Hi Mark,

On Mon, May 28, 2012 at 1:45 PM, Mark Miller
<mark.wayne.miller at gmail.com> wrote:
>
> Dan,
>
> Just saw your earlier request for sessioninfo().
>
> I have never used that command before, but here is the output when I just
> tried it.
>
> The result when I type:
>
> C:\>neato -V
>
> is:
>
> neato - Graphviz version 2.20.3 (Wed Oct 8 06:02:12 UTC 2008)
>
> Mark
>
>
>
>
> R version 2.15.0 (2012-03-30)
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>   Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit 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\RtmpyQNH4k\downloaded_packages
> Warning message:
> installed directory not writable, cannot update packages 'foreign', 'MASS',
>   'mgcv', 'nlme', 'survival'
>> 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:  %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’
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> 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_1.34.0        BiocInstaller_1.4.4
>
> loaded via a namespace (and not attached):
> [1] BiocGenerics_0.2.0 stats4_2.15.0      tools_2.15.0
>>
>


It looks like you are running 64-bit R. Try running 32-bit R by executing:

"C:\Program Files\R\R-2.15\bin\i386\R.exe"

Does that work?

If you don't really need to be running 64-bit R, then just use 32-bit
R with Rgraphviz.
If you really want to use 64-bit R woth Rgraphviz, install this file:

http://www.stats.ox.ac.uk/pub/Rtools/goodies/Win64No_/graphviz64.zip

Unzip it in some directory, say c:\graphviz64, then remove the
existing graphviz\bin directory from your PATH and add
c:\graphviz64\bin. Note that this is not a full version of graphviz,
just enough to support Rgraphviz.

Dan



>
>
>
>
>
>
>
> On Mon, May 28, 2012 at 12:39 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>> 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
>> >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >> >> > Search the archives:
>> >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >> >
>> >> >
>> >
>> >
>
>