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grunwaldlab / poppr

🌶 An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction
https://grunwaldlab.github.io/poppr
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Feature request: separation/removal of sf package requirement #247

Closed alexweisberg closed 3 years ago

alexweisberg commented 3 years ago

Please place an "x" in all the boxes that apply

I would like to request the ability to install poppr without the sf package as a requirement to install. This package is very difficult to install as it requires specific versions of the GDAL library as well as several others. It seems this package is primarily for importing GEO and ArcGIS location data, which is a specific use case. Would it be possible to set up poppr so that this is an optional requirement? Thanks!

zkamvar commented 3 years ago

Hi @alexweisberg, I'm afraid that this is not really possible at the moment because poppr depends on adegenet, which imports spdep for its spatial functions, which imports sf. To quote @hlapp: "adegenet is downloading half of CRAN!"

We might be able to get spdep as a soft dependency of adegenet specifically for the spatial features, but I know a lot of adegenet users do use the spatial analyses, so I'm not sure how well that would go over :(

alexweisberg commented 3 years ago

Hi @zkamvar, thanks for letting me know. I think we'll have to go with setting up a conda environment with everything then. Though that would be nice to have the soft dependency option for adegenet.

zkamvar commented 3 years ago

Hi @alexweisberg, I've updated adegenet to no longer require spdep (not yet on CRAN). It's available on my R-universe if you want:

# Enable this universe
options(repos = c(
    zkamvar = 'https://zkamvar.r-universe.dev',
    CRAN = 'https://cloud.r-project.org'))

# Install some packages
install.packages('adegenet')
alexweisberg commented 3 years ago

Hi Zhian,

Thank you, that worked great! We were able to install adegenet and poppr successfully now.

-Alex On Sep 27, 2021, 8:21 AM -0700, Zhian N. Kamvar @.***>, wrote:

Hi @alexweisberg, I've updated adegenet to no longer require spdep (not yet on CRAN). It's available on my R-universe if you want:

Enable this universe

options(repos = c( zkamvar = 'https://zkamvar.r-universe.dev', CRAN = 'https://cloud.r-project.org'))

Install some packages

install.packages('adegenet') — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

zkamvar commented 3 years ago

That's great! I'll do what I can to get adegenet updated on CRAN in the next month.