Remove example packages



In [1]:

    
# Removes package ('fortune') from both container and shared libraries

examplePackages <- list(
    list(name='fortunes', path=Sys.getenv('R_LIBS_SITE_USER')),
    list(name='fortunes', path=Sys.getenv('R_LIBS_USER')))

clearPkg <- function(pkg) {
    state <- 'Not present'
    if(pkg$name %in% rownames(installed.packages(pkg$path))){
         remove.packages(pkg$name, lib=pkg$path)
        state <- 'Removed'
    }
    return(paste0('Package: ', pkg$name, ', Path: ', pkg$path, ', State: ', state))
}

lapply(examplePackages, clearPkg)









    





	'Package: fortunes, Path: /opt/R-libs/user, State: Not present'
	'Package: fortunes, Path: /data/packages/R/x86_64-redhat-linux-gnu/3.4, State: Not present'

Environmental Variables

.libPaths function lists the current paths available within R. In this example a path starting with /data/ will be a shared folder, other paths (eg /usr/ and /opt/) reside within the container. The shared folder is defined by the environmental variable R_LIBS_USER and the variable R_LIBS_SITE_USER gives the user writable site folder.



In [2]:

    
Sys.getenv('R_LIBS_SITE_USER') # Current user writable container R path









    




'/opt/R-libs/user'



In [3]:

    
Sys.getenv('R_LIBS_USER') # Current shared R library folder









    




'/data/packages/R/x86_64-redhat-linux-gnu/3.4'



In [4]:

    
.libPaths() # Should include both paths give above









    





	'/data/packages/R/x86_64-redhat-linux-gnu/3.4'
	'/opt/R-libs/user'
	'/opt/R-libs/site'
	'/usr/lib64/R/library'

Install within the container



In [5]:

    
find.package('fortunes', quiet = TRUE) # Expected to return nothing if package is not installed



In [6]:

    
install.packages('fortunes', lib = Sys.getenv('R_LIBS_SITE_USER'))



In [7]:

    
find.package('fortunes', quiet = TRUE) # Expected to return the install path to the user writable container folder









    




'/opt/R-libs/user/fortunes'



In [8]:

    
remove.packages('fortunes', lib='/opt/R-libs/user')

Install in shared library



In [9]:

    
find.package('fortunes', quiet = TRUE) # Expected to return nothing if package is not installed



In [10]:

    
install.packages('fortunes') # Share location is the default install path









    



Installing package into '/data/packages/R/x86_64-redhat-linux-gnu/3.4'
(as 'lib' is unspecified)



In [11]:

    
find.package('fortunes', quiet = TRUE) # Expected to return the install path to the shared folder









    




'/data/packages/R/x86_64-redhat-linux-gnu/3.4/fortunes'



In [12]:

    
remove.packages('fortunes')









    



Removing package from '/data/packages/R/x86_64-redhat-linux-gnu/3.4'
(as 'lib' is unspecified)



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