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ropensci / phylotaR

An automated pipeline for retrieving orthologous DNA sequences from GenBank in R
https://docs.ropensci.org/phylotaR
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No periods or tildes in file paths #52

Open rvosa opened 3 years ago

rvosa commented 3 years ago

Hi Dom,

when I try to run a dummy analysis I run into the issue that my $HOME directory is /Users/rutger.vos, which the code wants to parse on the period. It tries to instantiate a log file called /Users/rutger.log, which is not allowed.

In trying to circumvent this I tested whether I can use a tilde instead (i.e. for my $HOME, use ~) but it doesn't like that either.

Best,

Rutger

rvosa commented 3 years ago

I think it would be more user friendly if the log had time stamps (to see how long various processes take), as well as functionalities such as reformatting the messages, etc. It might make sense to use log4r.

(Edited: why did I recommend a python package... oops... anyway, I imagine the equivalent exists for R)

rvosa commented 3 years ago

Ah, here we go: https://cran.r-project.org/web/packages/fs/index.html

maelle commented 2 years ago

For info, we're looking for a new maintainer / a new maintainer team for this package, see #57 and feel free to volunteer, we'd be happy to help.