Error in Linux setup

[alanocallaghan]

Pretty sure this is libcurl/libxml

ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’
* removing ‘/home/smukherjee/R/x86_64-pc-linux-gnu-library/4.3/rtracklayer’
ERROR: dependency ‘rtracklayer’ is not available for package ‘GenomicFeatures’
* removing ‘/home/smukherjee/R/x86_64-pc-linux-gnu-library/4.3/GenomicFeatures’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘bumphunter’
* removing ‘/home/smukherjee/R/x86_64-pc-linux-gnu-library/4.3/bumphunter’
ERROR: dependency ‘bumphunter’ is not available for package ‘minfi’
* removing ‘/home/smukherjee/R/x86_64-pc-linux-gnu-library/4.3/minfi’

[mallewellyn]

Could link to this page in the setup: https://docs.posit.co/connect/admin/r/dependencies/

This may also fix the igraph issue. I only suggested the current development install because I wanted to avoid installing all the system dependencies. I may be able to identify the essential packages to avoid this. However, there could be an argument for getting people to install all the dependencies in the link above so that their R is able to install packages in the future without too much intervention. I also think linking to that page is probably sensible because it covers a lot of distributions and probably also updates the dependencies. What do you think?

I can test whichever instructions we think are sensible next week when my Linux PC is fixed - currently using Windows in the meantime!!

[alanocallaghan]

Possibly, there is also this: https://r-sysreqs.josiahparry.com/index.html

[alanocallaghan]

Windows should be fine if we ensure people are getting binaries, I think most of the issues were on linux and mac recently

[alanocallaghan]

Happy this'll be resolved with the PR, mostly, hard to predict any and all installation problems across systems tho