Problems running phyloscanner_analyse_trees.R

[thednainus]

Hello,

I am doing the tutorial here and I get an error message when running the code below:

Code

~/phyloscanner/phyloscanner_analyse_trees.R RAxMLfiles/RAxML_bestTree.InWindow_  
RunWithoutBlacklisting s,20 --outgroupName C.BW.00.00BW07621.AF443088  
--multifurcationThreshold g

Error message:

Error in DataMask$new(.data, caller_env) : 
  argument "caller_env" is missing, with no default
Calls: sapply ... mutate.data.frame -> mutate_cols -> <Anonymous> -> initialize
Execution halted

I did find some similar error message in google (https://www.gitmemory.com/issue/YuLab-SMU/ggtree/395/836076062). And indeed my dplyr and ggtree is the same version as in the google search.

I use a mac OS 10.3.6. My R version is 4.0.3 dplyr version is 1.0.6 and ggtree version is 2.4.2

Is the error message caused by the new dplyr version or is it something else?

Thanks! Fabricia.

[mdhall272]

If you update to R 4.1.0 and the latest ggtree, it runs fine on my machine.

[thednainus]

Hi Matthew, it did run in my computer too when I updated to R 4.1.0. Thanks. I just get a few warning messages. Do you get those too? I still get the results despite the warning messages.

[mdhall272]

Have you updated phyloscannerR? I got rid of a lot of the warnings last night.

[thednainus]

Just updated it now. No more warnings. Thanks!