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traitecoevo / taxonlookup

A versioned and dynamically updating taxonomic lookup table for land plants
http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12517/abstract
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curl / certification problems on Windows #28

Closed rossmounce closed 8 years ago

rossmounce commented 8 years ago

I've been trying to help our plant records officer at the Cambridge University Botanic Garden to install taxonlookup on his Windows 7 work machine (apologies in advance, this won't be a very detailed or reproducible issue report given the difficult circumstances - not my machine!).

We had significant problems getting taxonlookup installed mainly I think due to problems with SSL certificates and/or curl or Rcurl. I ended up installing all the required dependencies from local binary or source packages because of this impediment. I believe I had taxonlookup successfully installed (from local source) but was met with this error message:

lookup_table(c("Pinus ponderosa","Quercus agrifolia"),by_species=TRUE)
Error: key 'traitecoevo/taxonlookup' ('objects') not found, with error: Problem with the SSL CA cert (path? access rights?)

Is there anyway to get around this? Why does the package need SSL CA cert anyway once installed? Isn't the lookup done entirely offline against the .csv data ?

I know this is probably not really an issue with taxonlookup per se but if you had any clue what might be causing it that would be really helpful. Getting the user off Windows is unfortunately not an option.

wcornwell commented 8 years ago

Hi Ross,

Isn't the lookup done entirely offline against the .csv data ?

Yes, but first it has to download the .csv, and that's where the error is, so it's something about R not being able to talk to websites on this computer, probably because curl is not finding the right libraries. basically taxonlookup uses httr which uses curl to talk to github in order to download the data. That only has to happen once on each machine and then everything else is local.

I don't know anything about windows, but my approach would be to try the hello world section of the readme here: https://github.com/jeroenooms/curl and see if that works?

I'll try a few windows machines at work and see if I can reproduce this behavior, but I think this sounds pretty specific.

rossmounce commented 8 years ago

Ahhh... that would explain it.

Can the .csv not just be included in the source of the package? It's not that large. I'll have look to see if I can fix it for him next week. You're right it might be something quite specific, I haven't tested on other Windows boxes.

Thanks

wcornwell commented 8 years ago

The versioning of the data won't work if we include it in the package. @richfitz has strong opinions about this.

I've checked on some windows boxes here and it works fine--I can't replicate the error, so it's got to be something specific about curl and the libraries that it calls on that machine.

It's weird that devtools::install_github would work, but http::GET wouldn't work, but clearly I don't understand this deeply enough...

wcornwell commented 8 years ago

Closing this, as I think it's really a Windows-Curl issue,