R, RStudio, and release and dev Bioconductor
I have one
Bioconductor package that I am currently responsible for. Each bi-annual release of
Bioconductor requires testing and squashing errors, warnings and bugs in a given package. Doing this means being able to work with multiple versions of
R and multiple versions of
Bioconductor libraries on a single system (assuming that you do production work and development on the same machine, right?).
I really, really like
RStudio as my working
R environment, as some of you have read before. So how do we get
RStudio on our Linux system to respect which version of
R and libraries we want to use?
This assumes that you have your
R installs set somewhere properly, and a normal library for production level packages. You should install whichever
Bioconductor packages you want into the normal library, and then make a copy of that. This copy will be your development library.
cp -R productionLibrary developmentLibrary
I also assume that you are using a local (i.e. sits in your home directory)
.Renviron file to control where
R installs the packages.
RStudio really needs the environment variable
RSTUDIO_WHICH_R set to know where
R is, and
R looks at
R_LIBS in the
.Renviron file. So I simply create two shell scripts that get sourced.
#!/bin/sh export RSTUDIO_WHICH_R=/pathToDevR/bin/R echo "R_LIBS=pathtoDevLibs" > .Renviron
Then I can simply do
source useRDev.sh when I need to use the development
R and library. Note that you will need to start
RStudio from the shell for it to respect this environment variable.
RStudio generally seems to install to
#!/bin/sh export RSTUDIO_WHICH_R=/pathtoReleaseR/bin/R echo "R_LIBS=pathtoReleaseLibs" > .Renviron
This resets my variables by doint
Bioconductor Dev Version
Bioconductor to use the develoment version, simply:
source useRDev.sh rstudio # once in RStudio library(BiocInstaller) useDev() biocLite(ask=F) # this will update all the installed bioconductor packages
I know this is not the most ideal situation, because I am rewriting over files, but it is working for me, and I thought it might help somone else.