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ggtree conflict with Rnexml package!

Open y9c opened this issue 7 years ago • 1 comments
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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"
--

y9c avatar Oct 15 '18 15:10 y9c

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) 

brj1 avatar Oct 15 '18 18:10 brj1