[BioC] rBiopaxParser error

[Frank Kramer]

Hi Suzy,

thank you for the report. I was able to reproduce the problem and am 
looking into this.

Best wishes,
Frank


University Medical Center Göttingen
Department of Medical Statistics
Humboldtallee 32
37073 Göttingen
Germany

Phone: +49 (0) 551 39-10710
Fax: +49 (0) 551 39-4995

http://www.ams.med.uni-goettingen.de/kramer-en.shtml

On 03.06.2013 23:56, Dan Tenenbaum wrote:
> 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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