How to solve this error in the "read.gb" R function?

Question

[João]

So I am trying to read a file with the extension "gb", that a downloaded directly from the website. I am using the "read.gb" function:

library(read.gb)

df<-read.gb("sequence.gb",Type = "full", Source = "File")

I thought it would be straightfoward, and it seems to read the first 5 "samples", but them it returns this error (I inspected the file and it looked ok):

Sample 1 in 759 done
Sample 2 in 759 done
Sample 3 in 759 done
Sample 4 in 759 done
Sample 5 in 759 done
Sample 6 in 759 done
Error in apply(D_loop, 2, function(x) { : 
  dim(X) must have a positive length

Anyone has any idea what might be happening?

Thank you in advance!

[zx8754]

The codes are on GitHub, hard to guess why it breaks, have a look and test:

• https://github.com/Largon-Denayah/read.gb-2.0.1/blob/392615f000ac8d11109da729896d3c55f6b5a2d4/R/D_loop.F.R#L28

Answer 1

[Laise]

I experienced a similar issue with the apply(F_UTR and apply(T_UTR functions. To address this problem, I made some modifications to original code. I have uploaded the updated version to my GitHub repository at https://github.com/lpmor22/read.gb.