[BioC] How to install Rgraphviz on Windows - REALLY!

Wed Jun 24 08:09:42 CEST 2009

Hi There

Many thnx for coming back to me & so quickly!

Just to add to the plot:
1. I have R2.8.1 also fully loaded on this laptop, but did not bother to populate packages as R2.9.0 was out so quickly - and once loaded I tried to load Rgraphviz on R2.9.0 ~ to no avail
2. However, I have Rgraphviz running on my home laptop also on Windows XP on R2.8.1, and yesterday boldly copied all library files on Rgraphviz to my work laptop (Windows XP) now under R2.8.1 and voila it's running and also tested the R> example(layoutGraph)

> example(layoutGraph)

lytGrp> library(graph)

lytGrp> set.seed(123)

lytGrp> V <- letters[1:10]

lytGrp> M <- 1:4

lytGrp> g1 <- randomGraph(V, M, 0.8)

lytGrp> x <- layoutGraph(g1)

lytGrp> library(graph)

3. No same luck on R2.9.0!

BR Ernest

-----Original Message-----
From: Kasper Daniel Hansen [mailto:khansen at stat.berkeley.edu]
Sent: 24 June 2009 12:52 AM
To: Jenny Drnevich
Cc: Ernest Hobson; bioconductor at stat.math.ethz.ch; Patrick Aboyoun; Martin Morgan; Sim, Fraser
Subject: Re: [BioC] How to install Rgraphviz on Windows - REALLY!

1) I agree that the use of the README file is pretty inconvenient.
2) Clearly, the README file is wrong. The way you can always check
what you need is the following, read
http://bioconductor.org/checkResults/2.4/bioc-LATEST/Rgraphviz/liverpool-checksrc.html
(this is the windows build server), where you will see that Rgraphviz
(for windows) is build using Graphviz 2.20.3 (But OS X Leopard uses
2.22.2). This is of course really irritating, and I have attempted to
remedy this by the install/build message (but see 4) below - it really
does not work as well as I thought).
3) The way Graphviz version is set on Windows is pretty unstable...
4) While I have added the build/install check, it currently fails if
you are using Graphviz 2.22 because the DLL fails to load. I have some
ideas on how to fix this, but I need to brush up on my knowledge on
exactly how DLLs are loaded, to see if it is possible to catch this at
an earlier stage.

Essentially, I need to fix this in the coming days (weeks). There has
been (too many) emails on this in the last couple of days, so it has
certainly been pushed up my priority schedule.

Finally, I have no idea why you get the error when you load Rgraphviz.
If you can successfully run
R> example(layoutGraph)
then everything should be working.

Kasper

On Jun 23, 2009, at 10:10 , Jenny Drnevich wrote:

> Hi Ernest, Kasper and others from previous threads of installing
> Rgraphviz...
>
> As noted many times in different threads on this list, there are
> always problems with Windows users being able to successfully
> install and use Rgraphviz because of an outside program, Graphviz. I
> just went through 2 recent threads (links below) after the R 2.9/
> BioC 2.4 releases, and I still don't have Rgraphviz loading
> completely without errors (although I think it's functional). First
> of all, somewhere in one of the threads, Kasper (I think) said he
> needed to getting around to writing a vignette on how to install
> everything properly, which would be nice to have in the
> Documentation section of the Rgraphviz page:
> http://www.bioconductor.org/packages/release/bioc/html/Rgraphviz.html
>
> Instead, the text at the top says to see the README file, which is
> in the source distribution (probably difficult for the average
> Windows user to actually get this file!). The instructions in the
> README file for using the Windows binary of Rgraphviz say to
> download the Graphviz ***2.22.2*** binary file. However, this is not
> the correct version, as indicated in the links below. I just tried
> the  Graphviz 2.22.2, and got all the same errors documented before.
> Then I followed Patrick's suggestion on 4/29/09 to use Graphviz 2.20
> available from here:
>
> http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1.msi
>
> So here are the step I went through:
> 1. No other Graphviz version installed on my computer, no C:\Program
> Files\GraphvizX.XX\bin in my PATH, R not running.
> 2. Installed Graphviz 2.20 using the file from the link above.
> 3. Made sure C:\Program Files\Graphviz2.20\bin is in my PATH.
> 4. Started R, downloaded and installed Rgraphviz using:
> > source("http://bioconductor.org/biocLite.R")
> > biocLite("Rgraphviz")
>
> Now, according to everything I can find in the archives, this
> *should* have worked. But when I try:
> > library(Rgraphviz)
>
> I still am getting a Windows error box that pops up. The top says "R
> Console: Rgui.exe - Entry Point Not Found" and the text in the box
> says "The procedure entry point g_intern_static_string could not be
> located in the dynamic link library libglib-2.0-0.dll."  However,
> when I then click OK on this error box, Rgraphviz appears to finish
> loading fine:
>
> > library(Rgraphviz)
> Loading required package: graph
> Loading required package: grid
> > sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.
> 1252;LC_MONETARY=English_United States.
> 1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets
> methods
> [8] base
>
> other attached packages:
> [1] Rgraphviz_1.22.1 graph_1.22.2
>
> loaded via a namespace (and not attached):
> [1] tools_2.9.0
>
>
> > graphvizVersion()
> $installed_version
> [1] '2.20.3'
>
> $build_version
> [1] '2.20.3'
>
>
> I don't really use Rgraphviz, so I don't have any code to see if
> works completely. I had gotten to this same point a couple of R
> versions ago, which is where Ernest found my e-mail. I still think I
> had the Windows error message, which I guess I just ignored as
> everything I needed to do back then seemed to work. So, should I and
> others continue to ignore it now if we get to this point? Anything
> else to try?
>
> Writing the "how to install" vignette would really come in handy!!!
>
> Thanks,
> Jenny
>
>
>
>
>
>
> Recent threads on installing Rgraphviz:
> https://stat.ethz.ch/pipermail/bioconductor/2009-April/027374.html
>
> https://stat.ethz.ch/pipermail/bioconductor/2009-May/027495.html
>
>
>
> At 05:10 AM 6/23/2009, Ernest Hobson wrote:
>> Hi There Jenny
>>
>> I've tried your steps a number of times, but keep getting the same
>> error below!
>>
>> Could you kindly help?
>>
>> Thnx Ernest
>>
>> Loading required package: graph
>> Loading required package: grid
>> Error in inDL(x, as.logical(local), as.logical(now), ...) :
>>  unable to load shared library 'C:/PROGRA~1/R/R-29~1.0/library/
>> Rgraphviz/libs/Rgraphviz.dll':
>>  LoadLibrary failure:  The specified module could not be found.
>>
>>        [[alternative HTML version deleted]]
>>
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>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at illinois.edu