[BioC] KEGGSOAP: list.pathways(org) or alternative way

[Marc Carlson]

So bug fixes for this package should now have propagated to both release 
and devel.  Updating the package via biocLite() should be all you need 
to do.

biocLite("KEGGSOAP")

   Marc


On 08/23/2012 10:55 AM, Marc Carlson wrote:
> Hi Jenny,
>
> It seems that you have found a bug in KEGGSOAP that has crept in from 
> changes in one of it's dependencies.  I have patched it in the devel 
> branch and will propagate those changes to release as soon as I can 
> verify that there will not be other fallout for packages that depend 
> on KEGGSOAP.  I have also added unit tests to prevent this kind of 
> nasty surprise from staying hidden in the future.
>
>  Marc
>
>
> On 08/21/2012 07:05 AM, Jenny Kartsaki wrote:
>> Hello,
>>
>> I am a beginner user of KEGGSOAP and for my application i need the 
>> function
>> list.pathways(org) for human organism.
>> I have noticed that there are some problems with this function and i
>> wanted to know if
>> it provides all of the pathways that are on KEGG Pathway database or if
>> there is an alternative
>> way to take all the pathways.
>>
>> Furthermore , i want to ask what this warning message means:
>>
>> Warning message:
>> In matrix(unlist(.SOAP(KEGGserver, "list_pathways", .soapArgs = 
>> list(org = org),  :
>>     data length [255] is not a sub-multiple or multiple of the number 
>> of rows [128]
>>
>>
>> Thank you ,
>>
>> Jenny
>>
>> ######################################
>>
>> R version 2.15.1 (2012-06-22)
>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=Greek_Greece.1253  LC_CTYPE=Greek_Greece.1253    
>> LC_MONETARY=Greek_Greece.1253
>> [4] LC_NUMERIC=C                  LC_TIME=Greek_Greece.1253
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>>    [1] KEGGSOAP_1.30.0      KEGGgraph_1.12.0     graph_1.34.0         
>> XML_3.9-4.1
>>    [5] KEGG.db_2.7.1        RSQLite_0.11.1       DBI_0.2-5            
>> AnnotationDbi_1.18.1
>>    [9] Biobase_2.16.0       BiocGenerics_0.2.0   BiocInstaller_1.4.7
>>
>> loaded via a namespace (and not attached):
>> [1] codetools_0.2-8 IRanges_1.14.4  RCurl_1.91-1.1  SSOAP_0.8-0     
>> stats4_2.15.1
>> [6] tools_2.15.1    XMLSchema_0.7-2
>>
>>
>>
>>     [[alternative HTML version deleted]]
>>
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>
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