Jitao David Zhang authored on 11/02/2019 14:53:00
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+library(testthat) |
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+library(KEGGgraph) |
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+ |
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+## Alexander Gulliver Bjornholt Gronning reported that this file cannot be exported as data.frame |
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+## when reactions=TRUE |
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+## It turned out the reason is that KEGGedgeData is not necessarily of the same length as edgeData |
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+## Now it is fixed |
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+kgmlFile <- system.file("extdata/hsa05210.xml", package="KEGGgraph")
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+kgmlDf <- parseKGML2DataFrame(kgmlFile, reactions=TRUE, genesOnly=FALSE) |
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+ |
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+## Alexander Gulliver Bjornholt Gronning reported that the following file reported error |
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+## Error in (function (classes, fdef, mtable) : |
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+## unable to find an inherited method for function ‘getName’ for signature ‘"NULL"’ |
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+## when reactions=TRUE |
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+## It was found to be caused by compound nodes (e.g. nodes containing more than one nodes), and |
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+## nodes that are not annotated (e.g. glycans) |
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+## it was fixed in 1.43.3 |
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+compoundKgml <- system.file("extdata/hsa00062.xml", package="KEGGgraph")
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+compoundKgmlDf <- parseKGML2DataFrame(compoundKgml, reactions=TRUE, genesOnly=FALSE) |
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