Gravy error from R CMD Check

[Namita Gupta]

* checking examples ... ERROR
Running examples in ‘alakazam-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gravy
> ### Title: Calculate GRAVY score
> ### Aliases: gravy
> 
> ### ** Examples
> 
> aa_seq <- "CARDRSTPWRRGIASTTVRTSW"
> gravy(aa_seq)
Warning in data(H, envir = environment()) : data set ‘H’ not found
Error in Peptides::hydrophobicity(aa_seq, scale) : object 'H' not found
Calls: gravy -> <Anonymous>

[Namita Gupta]

Jason mentioned that this may be an issue with the Peptides package, so maybe we should revert back to using in-house functions.

[ssnn]

I will work on this today. I think the code is not yet stable, because I stopped abruptly to work on it and switched to fix shm issues. Sorry.

I think we should have a stable branch and a development branch.

[Jason Vander Heiden]

Usually for a major feature addition - something that'll take more than a couple days - I would make a feature branch, and then merge the branch when the new features work. But... We didn't do that this time, and it's a bit late. Next time for sure. :)

[Jason Vander Heiden]

Namita resolve in 7433a36 by reverting to previous version of gravy()

[Jason Vander Heiden]

I think I know what is going on here now... "H" is the data object (a list) from the Peptides packages and it couldn't find it. Namespace issue of some kind. Probably fixable with proper import directives.