[BioC] rBiopaxParser error

[Dan Tenenbaum]

I can reproduce this. CC'ing the rBiopaxParser maintainer.

Dan


On Mon, Jun 3, 2013 at 2:38 PM,  <suzy.stiegelmeyer at syngenta.com> wrote:
> Hi,
> Does anyone know a workaround for the following error I'm getting using the rBiopaxParser package?  In case you want to try it yourself, download the ricecyc file from here:
> ftp://ftp.gramene.org/pub/gramene/pathways/ricecyc/v_3_3/
> Thanks in advance for your help,
> Suzy
>
> R session:
>
>> ricecyc=readBiopax("C:/Data/rice/ricecyc/v_3_3/ricecyc_v3_3_biopax-level2.owl")
> Found a BioPAX level 2 OWL. Parsing...
>
> [Info Verbose] Parsing Biopax-Model as a data.frame...
> [Info Verbose] Estimating up to 351239 entries. This will roughly need 78 MB of RAM.
> [Info Verbose] Where I came from this would've taken at least 1054 seconds!
> Error: internal_XMLInstance2DF - NewInstance: x= 1  instance: bp:bioSource bioSource1694 bp:TAXON-XREF
> ret: bp:unificationXref newInstance: bp:unificationXref 2ret: bp:unificationXref newInstance: bp:unificationXref 2ret: unificationXref1695 newInstance: unificationXref1695 2ret: unificationXref1695 newInstance: unificationXref1695 2ret: bp:ID newInstance: bp:ID 2ret: bp:DB newInstance: bp:DB 2ret: rdf:datatype newInstance: rdf:datatype 2ret: rdf:datatype newInstance: rdf:datatype 2ret: http://www.w3.org/2001/XMLSchema#string newInstance: http://www.w3.org/2001/XMLSchema#string 2ret: http://www.w3.org/2001/XMLSchema#string newInstance: http://www.w3.org/2001/XMLSchema#string 2ret: 39947 newInstance: 39947 2ret: NCBI Taxonomy newInstance: NCBI Taxonomy 2
> Error in paste("Something went wrong parsing:", class, id, ". Parsed ",  :
>   cannot coerce type 'closure' to vector of type 'character'
> In addition: Warning message:
> In internal_getBiopaxModelAsDataFrame(ret, biopaxxml, verbose = verbose) :
>   Something went wrong parsing: owl:Ontology   Parsed  owl:Ontology . Debug: i= 1  p= 2Something went wrong parsing: owl:Ontology   Parsed   . Debug: i= 1  p= 2Something went wrong parsing: owl:Ontology   Parsed  rdfs:comment . Debug: i= 1  p= 2Something went wrong parsing: owl:Ontology   Parsed  RiceCyc%32Version%323%462%46 . Debug: i= 1  p= 2
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] Rgraphviz_2.5.3     graph_1.39.1        rBiopaxParser_1.1.0
>
> loaded via a namespace (and not attached):
> [1] BiocGenerics_0.7.2 parallel_3.0.1     stats4_3.0.1       tools_3.0.1        XML_3.96-1.1
>
>
> _________________________________
>
> Suzy Stiegelmeyer, PhD
> Computational Biologist
> Bioinformatics
>
> Syngenta Biotechnology, Inc.
> 3054 Cornwallis Rd
> Research Triangle Park, NC
> 27709
> USA
>
> phone +1 919 281 7472
>
> suzy.stiegelmeyer at syngenta.com<mailto:suzy.stiegelmeyer at syngenta.com>
> www.syngenta.com<http://www.syngenta.com/>
>
>
>
>
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