[BioC] Rgraphviz: .onLoad error

Patrick Aboyoun paboyoun at fhcrc.org
Wed May 6 04:01:24 CEST 2009

First to your point on the DESCRIPTION file. The SystemRequirements 
field in the DESCRIPTION file is intended to describe system 
requirements above what R expects in order to install/build the package 
from source. As such the Rgraphviz package claims it can be built from 
source against Graphviz version 2.2 or greater. We can bump that number 
up to something more recent since we aren't testing it against Graphviz 
2.2 anymore, but that wouldn't make your life any easier.

Over the last development cycle Kasper and others (including me) worked 
to make Rgraphviz easier to use on Windows. I can't speak about non BioC 
packages, but all BioC 2.4 packages (running on R 2.9.x) are stable. One 
of the changes Kasper made to the Rgraphviz package in BioC 2.4 is 
improving the graphvizVersion function to print out both the version of 
Graphviz that Rgraphviz was built against alongside the version that 
Rgraphviz is currently linking to.

 > library(Rgraphviz)
Loading required package: graph
Loading required package: grid
 > graphvizVersion()
[1] '2.20.3'

[1] '2.20.3'

In addition, when you load the Rgraphviz library, it will produce a 
warning like

Warning message:
Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.22.2. This _may_ cause problems.

if something looks squirrelly. It is enhancements like these that make 
it worth upgrading your version of R.

 > sessionInfo()
R version 2.9.0 (2009-04-17)

LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United States.1252;LC_NUME
RIC=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

> Kasper Daniel Hansen wrote:
>> You are using R-2.8.1, so the easiest fix would be for you to upgrade 
>> to R-2.9. I am not sure we can be too helpfull with older version.
>> Nevertheless, from
>> http://bioconductor.org/checkResults/2.3/bioc-LATEST/Rgraphviz/liverpool-checksrc.html 
>> it seems that this version of graphviz was build using 2.21, which is 
>> a development version (based on the directory name). You will not be 
>> able to find that archived anywhere. I suggest building from source 
>> yourself. Or perhaps try Graphviz 2.22 which we still have some 
>> hiccups with.
>> So, you should upgrade....
> Thanks very much for the this information Kasper.  Unfortunately, 
> upgrading to R-2.9.0 is a largish job
> because it entails upgrading some other packages that don't yet work 
> with 2.9.0 and modifying my
> eclipse development environment as well.  I was hoping to wait until 
> 2.9.0-patched and other
> packages settled down.
> Because graphviz and Rgraphviz seem to have a long history of 
> incompatibility problems, could I suggest
> that the DESCRIPTION file for Rgraphviz be more explicit about exactly 
> which version of graphviz it
> was built with?
> The present System Requirements,
> Graphviz version >= 2.2
> is insufficiently precise (I have Graphviz 2.20).    Such information 
> could be also be maintained in an
> Rgraphvis-package.Rd file, (with a link to
> the graphviz version.) but that doesn't seem to be part of the package
> That might forestall a lot of traffic on the bioc list on this topic, 
> though I realize it creates an extra
> maintenance step.

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