can 'install.packages("bspm")' be used if bspm is not installed?
apsteinmetz opened this issue · comments
This may just be a documentation issue. In "step 5" of your setup instructions you say to run
Rscript -e 'install.packages("bspm")'
But bpsm is installed so the user can use install.packages(), right? Catch-22? The script in "Step 5" failed for me but
apt install r-cran-bspm from the console worked fine and install.packages() worked thereafter so no worries.
But
bpsmis installed
Well that depends. What exactly did you start from? An 'empty' initial Ubuntu system? It would not have bspm which is why we suggest it.
In a nutshell, r2y "really" works at the level of system binaries. I.e. ggplot2 is supplied by r-cran-ggplot2. Those who know their way around a Debian/Ubuntu system can get what they want via apt and alike.
But, and that is a big 'but' for most R users it is both easier and more convenient to use install.packages and then "magically" have the packages installed as system binaries. That is what bspm does. It translates and maps the install.packages() call into a system call to apt. (And that is why it has to be installed by the root user.)
Can you talk to me like I am five years old about
a) what Step 5 made you do
b) what error you got
c) and how you overcame it (a manual apt install r-cran-bspm ?)
I have run the scripts a few times by hand, and run the 'manual steps'. But it is always possible that something got out of whack, and if so, I should correct it.
@apsteinmetz -- any follow-up? Else happy to close if all issues are taken care of ...