[BioC] RBGL function highlyConnSG not recognized

[Wolfgang Huber]

Dear Burak,

to supplement what Robert said, please check
http://www.stats.bris.ac.uk/R/doc/manuals/R-intro.html
and particular Chapter 13 "Packages".

Best wishes
   Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

Robert Gentleman wrote:
> 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"