[Bioc-devel] Error in .get_entry_index(name, stop_if_missing)

[Zhezhen Wang]

Hi I had the following error while checking the package https://github.com/xyang2uchicago/BioTIP

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getCluster_methods
> ### Title: Clustering Network Nodes
> ### Aliases: getCluster_methods
>
> ### ** Examples
>
> test = list('state1' = matrix(sample(1:10,6),3,3),'state2' =
+ matrix(sample(1:10,6),3,3),'state3' = matrix(sample(1:10,6),3,3))
> #assign colnames and rownames to the matrix
>
> for(i in names(test)){
+ colnames(test[[i]]) = 1:3
+ row.names(test[[i]]) = 1:3}
>
> #using 'rw' or 'natural' method
> igraphL <- getNetwork(test, fdr=1)
[1] "state1:3 nodes"
[1] "state2:3 nodes"
[1] "state3:3 nodes"
> #[1] "state1:3 nodes"
> #[1] "state2:3 nodes"
> #[1] "state3:3 nodes"
>
> cl <- getCluster_methods(igraphL)
>
> #using 'km', 'pam' or 'hcm'
> cl <- getCluster_methods(test, method = 'pam', cutoff=2)
Error in .get_entry_index(name, stop_if_missing) :
  Entry TSDistances not in registry.
Calls: getCluster_methods ... TSDatabaseDistances -> dist -> <Anonymous> -> f -> .get_entry_index
Execution halted

It seems the problem is because the required library 'TSdist' not load successfully. However, import(TSdist) is written in both DESCRIPTION and NAMESPACE.

Zhezhen

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