Installation issue due to graph package not on CRAN

[lepennec]

Hi, I would like to report that I had an issue updating CodeDepends on Linux: it requires graph which is not available on CRAN. I was able to update CodeDepends by installing the graph package from BioConductor:

source("https://bioconductor.org/biocLite.R")
biocLite("graph")

Not sure it is the best way.

I assume this is related to https://github.com/duncantl/CodeDepends/issues/30.

Thnk your for your work,

Erwan

[wlandau]

By extension, this also affects the installation of drake (ref: https://github.com/ropensci/drake#installation, https://ropenscilabs.github.io/drake-manual/index.html#installation).

[gmbecker]

Erwin,

graph is a Bioconductor package, which is why it isn't installable the normal way from CRAN. That said, CRAN does allow Bioconductor packages as dependencies, and Bioc packages just recently got easier to install in a CRAN centric way.

The way to install graph (or any other Bioc package) is to

1. Install the BiocManager package from CRAN
2. load BiocManager normally, via library,
3. install the packages via the install function in BiocManager

So you can do:

install.packages("BiocManager")
library(BiocManager)
BiocManager::install("graph")

And this should work. You can also use install to install CodeDepends (or even drake) and it will manage getting all of the necessary dependencies from both CRAN and Bioc:

library(BiocManager)
BiocManager::install("drake")

I hope that helps and allows yo uto use the packages without further difficulty.

Best, ~G

[lepennec]

Thank you for the very clear explanation. I wasn't aware of the BiocManager package.

On Mon, Jun 25, 2018 at 5:59 PM, Gabe Becker [email protected] wrote:

Erwin,

graph is a Bioconductor package, which is why it isn't installable the normal way from CRAN. That said, CRAN does allow Bioconductor packages as dependencies, and Bioc packages just recently got easier to install in a CRAN centric way.

The way to install graph (or any other Bioc package) is to

1. Install the BiocManager package from CRAN
2. load BiocManager normally, via library,
3. install the packages via the install function in BiocManager

So you can do:

install.packages("BiocManager") library(BiocManager) BiocManager::install("graph")

And this should work. You can also use install to install CodeDepends (or even drake) and it will manage getting all of the necessary dependencies from both CRAN and Bioc:

library(BiocManager) BiocManager::install("drake")

I hope that helps and allows yo uto use the packages without further difficulty.

Best, ~G

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/duncantl/CodeDepends/issues/34#issuecomment-400004052, or mute the thread https://github.com/notifications/unsubscribe-auth/AHgR6cg2eGqYn97f0MqlLURk8I4AjowSks5uAQjggaJpZM4U1SC2 .