[R] libPaths displays truncated path?

[David Winsemius]

> On Nov 23, 2017, at 4:34 AM, Loris Bennett <loris.bennett at fu-berlin.de> wrote:
> 
> Hi,
> 
> TL;DR
> -----
> 
>  I define the path
> 
>    /cm/shared/apps/R/site-library/3.4.2
> 
>  and add it to libPath.  Why does libPath then display it as
> 
>    /cm/shared/apps/R/site-library/3.4

Generally one only has a different library for each major version of R. Major versions are consider just the first two numbers in the dot-separated versions system. Apparently libPaths is "smart" enough to make an effort to adhere to that convention.  It appears your definition of "major" differs from the usual convention.

-- 
David
> 
>  ?
> 
> Long version
> ------------
> 
> I run a cluster of diskless nodes for which the OS is loaded
> directly into RAM and other software is provided by an NFS server.
> However, in the case of R, we use the R version provided by the OS and
> just install additional packages on the NFS server.
> 
> So that R can find these additional packages, I have the following in
> the site-wide Rprofile
> 
>  v <- R.Version()
>  base_path = "/cm/shared/apps/R/site-library/"
>  major_minor_version = paste(v["major"],v["minor"],sep=".")
>  cm_shared_lib_path = paste0(base_path,major_minor_version)
>  full_cm_shared_lib_path <- c(file.path(chartr("\\", "/", R.home()), "site-library"), cm_shared_lib_path)
>  .libPaths( c( .libPaths(), full_cm_shared_lib_path ) )
> 
> Thus, when I start R I get this:
> 
>> full_cm_shared_lib_path
>  [1] "/usr/lib64/R/site-library"           
>  [2] "/cm/shared/apps/R/site-library/3.4.2"
> 
> but also this
> 
>> .libPaths()
>  [1] "/home/loris/R/x86_64-redhat-linux-gnu-library/3.4"
>  [2] "/usr/lib64/R/library"                             
>  [3] "/usr/share/R/library"                             
>  [4] "/usr/lib64/R/site-library"                        
>  [5] "/cm/shared/apps/R/site-library/3.4"       
> 
> However, in order to get R to find the packages, I have to add a
> symbolic link, thus:
> 
>  [/cm/shared/apps/R/site-library] $ ls -l 3.4.2
>  lrwxrwxrwx 1 root root 3 Nov 23 09:21 3.4.2 -> 3.4
> 
> So, my mistake was to think that "minor" would return "4", whereas it in
> fact returns "4.2".  So I actually set the path to ".../3.4.2" and
> that's where R looks for packages.
> 
> But why does libPaths display the the path I *thought* I had set, but in
> fact looks at the path I *really did* set?
> 
> Cheers,
> 
> Loris
> 
> -- 
> Dr. Loris Bennett (Mr.)
> ZEDAT, Freie Universität Berlin         Email loris.bennett at fu-berlin.de
> 
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David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law