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ggtree conflict with Rnexml package!
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Code to reproduce the bug with error log:
> library("tidyverse")
> library("RNeXML")
Loading required package: ape
> library("treeio")
Attaching package: ‘treeio’ The following object is masked from ‘package:ape’: drop.tip
> library("ggtree")
ggtree v1.13.5 For help: https://guangchuangyu.github.io/software/ggtree If you use ggtree in published research, please cite: Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628
Attaching package: ‘ggtree’ The following object is masked from ‘package:ape’: rotate The following object is masked from ‘package:tidyr’: expand
> f <- system.file("examples", "comp_analysis.xml", package="RNeXML")
> nexml <- nexml_read(f)
Found more than one class "tree" in cache; using the first, from namespace 'cli' Also defined by ‘RNeXML’
Found more than one class "tree" in cache; using the first, from namespace 'cli' Also defined by ‘RNeXML’
Found more than one class "tree" in cache; using the first, from namespace 'cli' Also defined by ‘RNeXML’
Error in validObject(.Object) :
invalid class “MethodWithNext” object:
invalid object for slot "nextMethod" in class "MethodWithNext": got class "NULL", should be or extend class "PossibleMethod"
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The conflict appears to be with tidyverse not ggtree as the following code gives the same error:
library("tidyverse")
library("RNeXML")
f <- system.file("examples", "comp_analysis.xml", package="RNeXML")
nexml <- nexml_read(f)