Hi, I'm trying to install a package from CRAN, URL: https://CRAN.R-project.org/package=imputeLCMD. But there is something wrong with my commands in my dockerfile because it's not installing, or at least when I submit my code to the express lane I get an error that "there is no package called "imputeLCMD"" (submission ID: 9646520). Here are the docker commands I'm using: RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile RUN Rscript -e "install.packages('imputeLCMD')"

Created by Jacob Hartman-Kenzler jakehk
Hi Jacob, Is it possible you're missing some bioconductor packages? "imputeLCMD" appears to require "pcaMethods" and "impute". I got your original example to work by changing the Rscript call to: Rscript -e ' source("https://bioconductor.org/biocLite.R"); biocLite("pcaMethods"); biocLite("impute"); install.packages("imputeLCMD"); ' After that I can launch a new R session and run library(imputeLCMD) with no errors.
Hi, I tried a few different attempts at this, and my latest error messages (submission ID: 9649135) are kind of confusing and includes the text: Warning: unable to access index for repository http://cran.us.r-project.org/src/contrib: cannot open URL 'http://cran.us.r-project.org/src/contrib/PACKAGES' I feel like I'm struggling with the easiest parts of this (i.e. package installation), and I'm probably missing something obvious. I tried making a second script in R to install everything but I had an error in docker that it couldn't find the file specified... Thanks so much for your help. Jacob
Dear Jacob, Another easier way to do this is to actually have a Rscript that just installs everything so in your Rscript: ``` install.packages("imputeLCMD") ``` Then you copy this script into your docker file lets say into /install.R. You can then have this line in your Dockerfile. ``` RUN Rscript /install.R ``` Best, Tom

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