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nutterb / HydeNet

Hybrid Decision Networks in R
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Do we still depend on Rgraphviz? #71

Closed jarrod-dalton closed 9 years ago

jarrod-dalton commented 9 years ago

Running the vignette on my work PC tells me that the package is required but not installed.

nutterb commented 9 years ago

HydeNet doesn't depend on it directly. HydeNet imports from graph, which suggests Rgraphviz. When a package is installed, all the packages for its dependencies, imports, and suggests are also installed (as well as all of their dependencies). So when you try to install HydeNet it will want to install Rgraphviz.

This won't be an issue when installing from CRAN, as CRAN automatically looks to Bioconductor when it can't find a package on CRAN. When installing from GitHub, we need to tell R to also look at Bioconductor by using 

setRepositories(ind=1:2)

This is included in the Getting Started vignette. We may want to consider adding that to the README file as well.

jarrod-dalton commented 9 years ago

I did that, and it gives me the error message. So I installed using the script provided on the Bioconductor website (i.e., via bioclite). It asked me if I wanted to update a bunch of other packages, so I said 'y'.

So I'm not sure what's going on there.

nutterb commented 9 years ago

I'm going to guess that you are doing the same confusing thing I just did to try and replicate your error.

Try using:

setRepositories(ind=1:2)
devtools::install_github("nutterb/HydeNet", ref = "development")

Without the ref argument, you're installing the old version of HydeNet that lives in the master branch, and that older version does depend on Rgraphviz. Sorry for the confusion.

jarrod-dalton commented 9 years ago

Duh.

nutterb commented 9 years ago

Don't worry. I do it all the time.