> On 23 Nov 2017, at 17:36 , David Winsemius <dwinsem...@comcast.net> wrote:
>
>>
>> On Nov 23, 2017, at 4:34 AM, Loris Bennett <loris.benn...@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.benn...@fu-berlin.de
>>
>> ______________________________________________
>> R-help@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@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....@cbs.dk Priv: pda...@gmail.com
______________________________________________
R-help@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.
