Question: KEGGSOAP: list.pathways(org) or alternative way
0
gravatar for Jenny Kar
7.2 years ago by
Jenny Kar30
Greece
Jenny Kar30 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]]
pathways organism keggsoap • 525 views
ADD COMMENTlink modified 7.2 years ago by Marc Carlson7.2k • written 7.2 years ago by Jenny Kar30
Answer: KEGGSOAP: list.pathways(org) or alternative way
0
gravatar for Marc Carlson
7.2 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k 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]] > > _______________________________________________ > 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 7.2 years ago by Marc Carlson7.2k
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]] >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 7.1 years ago by Marc Carlson7.2k
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