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

Marc Carlson mcarlson at fhcrc.org
Mon Aug 27 19:42:32 CEST 2012


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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