I need to do a local installation of Bioconductor in my home directory on a CentOS 7 system running R 3.4.2. When I use source("https://bioconductor.org/biocLite.R"), I am asked if I want to use a personal library. I have set up a lib in my ../home/R directory, but I don't know how to point to that with the source() function. I read the manual, but it's not clear to me how to edit to function to install Bioconductor locally.
Just as background, I have also tried to install a local copy of R 3.5.0, but that fails because libreadline-dev package is not installed on the server. I could compile it locally, but I'm unsure whether this would create more problems, with some of the dependencies on root and some dependencies installed locally. So I abandoned the plan in favor of just trying to get an older copy of Bioconductor to run. I suspect that when I get source() to work, it's going to tell me to upgrade R. So if someone could give me a workaround for that as well, that would be awesome.
I have spoken with the admins about installing the latest R, but the issue is that I'm under a time crunch for an analysis. I need a normalization package, edgeR, that is a bioconductor package. I've been working on a fix for two days and I'm at my wit's end...I'm about to abandon ship and try using Python.
There are more details about everything I have tried, and all my errors, in my Stack Overflow post here, but I think I have included the germane detail above.
I'd really appreciate some guidance. I'm at sea here.