Hi Wolfang 

Thanks for the warning: I am trying to be a better BioC poster every day!
I thought that the function error I am getting is independent of the graphNEL object, 
which I should not have assumed??

The error message that I am getting is the same for all types of networks.
As an example, I have used a sample network that comes with the 'RBGL' package.
The commands and the sessionInfo is below. All this was done on a Linux Box.

In the meantime, I have used an up-to-date version of R and RBCF package on my Windows machine
and I get the same error with the identical commands. The example is the same for my linux machine. Error and sessionInfo is below.

Thanks again.
-burak

####### Begin: Commands and SessionInfo() Windows machine ##########

> library(graph)
> utils:::menuInstallLocal()
package 'XML' successfully unpacked and MD5 sums checked
package 'RBGL' successfully unpacked and MD5 sums checked
updating HTML package descriptions
>  net1 <- fromGXL(file(system.file("XML/simpleExample.gxl",package="RBGL")))
> 
> net1
A graphNEL graph with directed edges
Number of Nodes = 4 
Number of Edges = 3 
> 
> highlyConnSG(net1)
Error: could not find function "highlyConnSG"
> 
> sessionInfo()
R version 2.6.1 (2007-11-26) 
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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] graph_1.16.1

loaded via a namespace (and not attached):
[1] cluster_1.11.9 tools_2.6.1    XML_1.9-0     



####### End: Commands and SessionInfo() Windows machine ##########



####### Begin: Commands and SessionInfo() Linux machine ##########

> library(RBGL)
Loading required package: graph
> net1 <- fromGXL(file(system.file("XML/simpleExample.gxl",package="RBGL")))
Loading required package: XML

Attaching package: 'XML'


        The following object(s) are masked from package:graph :

         addNode

> net1
A graphNEL graph with directed edges
Number of Nodes = 4
Number of Edges = 3
> highlyConnSG(net1)
Error: could not find function "highlyConnSG"
>
> sessionInfo()
R version 2.5.0 (2007-04-23)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
[7] "base"

other attached packages:
     XML     RBGL    graph
 "1.9-0" "1.3.13" "1.14.2"


####### End: Commands and SessionInfo() Linux machine ##########






Burak,

you will get better answers if you provide a complete set of commands 
that, starting from a fresh R session, lead to your error. You didn't 
tell us what net1 is nor which expressions you have evaluated before. If 
you expect others to guess, they may not be able or willing to do it.

  Best wishes
	Wolfgang

Tony Chiang ha scritto:
> Hi Burak,
> 
> First thing to do is to update your R and RBGL. The current released version
> is 2.6 though the latest is a patched version (someone will correct me if I
> am wrong). If the trouble still persists, let us know.
> 
> Cheers,
> --Tony
> 
> On Dec 19, 2007 9:17 AM, burak kutlu <burak_kutlu@...> wrote:
> 
>> Hi
>> I am trying to understand why 'highlyConnSG' does not work for me. Other
>> RBGL functions seem to work fine.
>> Error message and sessionInfo is below, any ideas?
>> Thanks a lot
>> -burak
>>
>>
>>> highlyConnSG(net1)
>> Error: could not find function "highlyConnSG"
>>>
>>> sessionInfo()
>> R version 2.5.0 (2007-04-23)
>> i686-pc-linux-gnu
>>
>> locale:
>>
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
>> [7] "base"
>>
>> other attached packages:
>>  gaggle    rJava     RBGL    graph
>>  "1.4.0" "0.4-16" "1.3.13" "1.14.2"
>>



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