[BioC] error installing Rgraphviz

[Dan Tenenbaum]

On Mon, May 28, 2012 at 2:13 PM, Mark Miller
<mark.wayne.miller at gmail.com> wrote:
>
> Dan,
>
> I found the *.exe file needed to open the 32-bit version of R and was able
> to install 'Rgraphviz'!
>
> Thanks for your help with this.  I hope this helps others.
>

Glad it works.
Dan


> Mark
>
>
>
> On Mon, May 28, 2012 at 1:09 PM, Mark Miller <mark.wayne.miller at gmail.com>
> wrote:
>>
>>
>> Hi Dan,
>>
>> When I click on "C:\Program Files\R\R-2.15\bin\i386\R.exe" R opens in a
>> command window as a command-line program.  I have never used R that way.
>>
>> When I installed R I think it installs both 32-bit and 64-bit versions and
>> places desktop icons for both versions.  I just remove the desktop icon for
>> the 32-bit version.  Would it be okay if I re-install R and try running the
>> 32-bit version from the desktop icon?  Do you think Rgraphviz would work
>> that way?  Or must the 32-bit version of R operate from a command window for
>> Rgraphviz to function?
>>
>> I am sure the 32-bit version is still installed on my machine.  I just do
>> not know how to open the GUI I am used to without the desktop icon present
>> given that clicking on R.exe above opened a command window.
>>
>> Mark
>>
>>
>>
>> On Mon, May 28, 2012 at 12:54 PM, Dan Tenenbaum <dtenenba at fhcrc.org>
>> wrote:
>>>
>>> [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
>>> >> >> >
>>> >> >> >
>>> >> >
>>> >> >
>>> >
>>> >
>>
>>
>