[R] libPaths displays truncated path?

[peter dalgaard]

> On 23 Nov 2017, at 17:36 , David Winsemius <dwinsemius at comcast.net> wrote:
> 
>> 
>> 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.

Nope. Chuck B. is almost certainly right: The symlink did it, with the normalizePath, in .libPaths(). (And the OP has cause and effect reversed.)

Not even R functions are smart enough to make a decision like you suggest without actually containing code to do it:

> .libPaths
function (new) 
{
    if (!missing(new)) {
        new <- Sys.glob(path.expand(new))
        paths <- c(new, .Library.site, .Library)
        paths <- paths[dir.exists(paths)]
        .lib.loc <<- unique(normalizePath(paths, "/"))
    }
    else .lib.loc
}
<bytecode: 0x10219a988>
<environment: 0x1021985f0>

-pd

> 
> -- 
> 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
>> 
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> 
> David Winsemius
> Alameda, CA, USA
> 
> 'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com