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

[Marc Carlson]

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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