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Question: rBiopaxParser error
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gravatar for suzy.stiegelmeyer@syngenta.com
5.7 years ago by
United States
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@syngenta.com<mailto:suzy.stiegelmeyer@syngenta.com> www.syngenta.com<http: www.syngenta.com=""/> This message may contain confidential information. If yo...{{dropped:7}}
rbiopaxparser • 584 views
ADD COMMENTlink modified 5.7 years ago by Dan Tenenbaum8.2k • written 5.7 years ago by suzy.stiegelmeyer@syngenta.com40
Answer: rBiopaxParser error
0
gravatar for Dan Tenenbaum
5.7 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k 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=""/> > > > > > This message may contain confidential information. If yo...{{dropped:7}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 5.7 years ago by Dan Tenenbaum8.2k
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 G?ttingen Department of Medical Statistics Humboldtallee 32 37073 G?ttingen 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=""/> >> >> >> >> >> This message may contain confidential information. If yo...{{dropped:7}} >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 5.7 years ago by Frank Kramer60
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