[BioC] RBGL function highlyConnSG not recognized

[Robert Gentleman]

Hi,

burak kutlu wrote:
> 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

So, now why are you installing these packages and why from local zip 
files? The advice given very often here is to use biocLite for all 
installing, please use it.  But most importantly, there is no reason to 
reinstall these (your previous posts suggest that you have already 
installed them).  And you seem to be very confused about the difference 
between installing (which you do once) and loading, which you do often.

  I suspect that all you want here is

  library(XML)
  library(RBGL)


>>  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     
> 

  well - since you did not load the RBGL package it is not there
  and R cannot find the functions.

  use
  library(RBGL)

> 
> 
> ####### 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 at ...> 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"
>>>
> 
> 
> 
>       ____________________________________________________________________________________
> Looking for last minute shopping deals?  
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org