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emvolz / treedater

Scalable relaxed clock phylogenetic dating
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Error in if (cv > 1) { : missing value where TRUE/FALSE needed message #22

Open Dhihram opened 1 month ago

Dhihram commented 1 month ago

time.data <- treedater::dater(tree, sts=sts, s = seqlen, clock ="uncorrelated", searchRoot=TRUE) Note: Initial guess of substitution rate not provided. Will attempt to guess starting conditions. Provide initial guesses of the rate using omega0 parameter. Note: Minimum temporal branch length (minblen) set to 0.0186331312223994. Increase minblen in the event of convergence failures. Tree is rooted. Not estimating root position. Initial guesses of substitution rate: 0.0223656181040256,0.0223811368102775,0.0367202750598568,0.0369537668001815,0.0510749320156881,0.0515263967900855 Error in if (cv > 1) { : missing value where TRUE/FALSE needed

I found the error message when I want to running treedater.

This is a brief of my data:

sts WT-NORO-0324 WT-NORO-0325 WT-NORO-0326 WT-NORO-0331 WT-NORO-0693 WT-NORO-0989 2003.819 2003.816 2003.816 2003.934 2004.194 2004.934

summary(tree)

Phylogenetic tree: tree

Number of tips: 6 Number of nodes: 5 Branch lengths: mean: 0.006128069 variance: 0.0001479546 distribution summary: Min. 1st Qu. Median 3rd Qu. Max. 0.000000e+00 3.844413e-05 4.141834e-04 6.424393e-03 3.920875e-02 No root edge. Tip labels: WT-NORO-0989 WT-NORO-0693 WT-NORO-0331 WT-NORO-0325 WT-NORO-0324 WT-NORO-0326 Node labels: Root 97 94 57 100

emvolz commented 1 month ago

Can you show the output of this? 

installed.packages()['treedater', ]

If you have not installed the development version, can you try 

remotes::install_github('emvolz/treedater')
Dhihram commented 1 month ago

installed.packages()['treedater', ] Package "treedater" LibPath "C:/Users/dhihr/AppData/Local/R/win-library/4.3" Version "0.5.0" Priority NA Depends "ape (>= 5.0),limSolve (>= 1.5.5.0)" Imports NA LinkingTo NA Suggests "lubridate,ggplot2,foreach,iterators,mgcv,knitr,rmarkdown" Enhances NA License "GPL-2" License_is_FOSS NA License_restricts_use NA OS_type NA MD5sum NA NeedsCompilation "no" Built "4.3.2"

Dhihram commented 1 month ago

When I try to install, this is the result

Warning messages: 1: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\dhihr\AppData\Local\R\win-library\4.3\00LOCK\digest\libs\x64\digest.dll to C:\Users\dhihr\AppData\Local\R\win-library\4.3\digest\libs\x64\digest.dll: Permission denied 2: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\dhihr\AppData\Local\R\win-library\4.3\00LOCK\Rcpp\libs\x64\Rcpp.dll to C:\Users\dhihr\AppData\Local\R\win-library\4.3\Rcpp\libs\x64\Rcpp.dll: Permission denied

Dhihram commented 1 month ago

I want to inform you, I have successfully installed the treedater 0.5.3