Re: [Rd] Rcmd_environ and R_LIBS_{USER,SITE}

From: Dirk Eddelbuettel <edd_at_debian.org>
Date: Fri, 19 Oct 2012 08:21:47 -0500

On 19 October 2012 at 12:39, Gavin Simpson wrote:
| On Thu, 2012-10-18 at 10:18 -0500, Dirk Eddelbuettel wrote:
| > Kasper,
| >
| > On 18 October 2012 at 10:41, Kasper Daniel Hansen wrote:
| > | I set my user libraries in .Rprofile for this very reason. I agree it
| > | is weird that .Renviron is not always read etc.
| >
| > Sorry, no cigar either -- this equivalent to using files in $R_HOME/etc/ and
| > is also ignored by R CMD check, which still fails in my setup as it doesn't
| > find the package -- whereas any normal R session does.
| >
| > Dirk
|
| I have R_LIBS set in my Bash profile (~/.bashrc) for IIRC this very
| reason. Can you do the same on Windows?

Thanks for the suggestion, Gavin, But well, let me count the ways ....

i) As a general principle, I prefer to minimize env variables. So on Linux,

     I prefer (and use) ~/.Rprofile and/or ~/.Renviron, or even the site-wide
     ones

ii)  Similarly, I asked for site-wide config as that can be scripted.
     Your solution, if it worked, would not (as easily) allow that.

iii) The question was specific about the intentional castration of R CMD ...
     I actually get the .libPaths() adjusted on Windows too via the method
     mentioned in i)

iv)  When I do what you helpfully suggest, .libPaths() in R shows the entry
     twice yet the braindead R CMD check .... __still fails the same way__ not
     being able to load the very package tested from the location that is __not
     below__ the $R_HOME/library/ path.

This really is silly beyond words, but seemingly all by design and intentional.

Dirk

|
| G
|
| >
| >
| > |
| > | Kasper
| > |
| > | On Thu, Oct 18, 2012 at 10:12 AM, Dirk Eddelbuettel <edd_at_debian.org> wrote:
| > | >
| > | > Keith,
| > | >
| > | > On 18 October 2012 at 09:14, Keith Jewell wrote:
| > | > | No reply in a number of hours, so here is a suggestion from ignorance :-}
| > | > |
| > | > | ?Startup refers to a number of other "site and user files to process for
| > | >
| > | > Thanks, and I know, and use those on Linux (and on 'doze when I use it). My
| > | > question was specifically about 'R CMD foo' which skips some of these by
| > | > choice, and which Rcmd_environ appears to overcome, albeit imcompletely. I
| > | > still have an issue on Windows where I cannot split my package installations
| > | > between those that come and go with R installations, and the others.
| > | >
| > | > But it is truly bizarre that I can do (on Windows)
| > | >
| > | > R CMD INSTALL foo_1.2-3.tar.gz
| > | >
| > | > and a moment later
| > | >
| > | > R CMD check foo_1.2-3.tar.gz
| > | >
| > | > fails in its tests and examples with "no package called 'foo'"
| > | >
| > | > Doing 'R CMD check --no-examples --no-tests foo_1.2-3.tar.gz' works, but is
| > | > less helpful as we're running the check to run those very tests...
| > | >
| > | > Dirk
| > | >
| > | >
| > | > | setting environment variables" but not to Rcmd_environ. The contents of
| > | > | $R_HOME/etc/Rcmd_environ seem to reflect (some of) the contents of
| > | > | (some) other files.
| > | > |
| > | > | I have similar lines (defining library paths) in
| > | > | $R_HOME/etc/Renviron.site
| > | > |
| > | > | Is it correct to directly edit Rcmd_environ or should it be modified
| > | > | only via other files? (A genuine question).
| > | > |
| > | > | On 17/10/2012 15:59, Dirk Eddelbuettel wrote:
| > | > | >
| > | > | > Is there a fundamental reason why I cannot set either one of
| > | > | >
| > | > | > ## add local library path -- doesn't work either
| > | > | > R_LIBS_USER="c:/opt/R-library"
| > | > | > R_LIBS_SITE="c:/opt/R-library"
| > | > | >
| > | > | > in $R_HOME/etc/Rcmd_environ even though I can seemingly set other things here?
| > | > | >
| > | > | > It breaks "R CMD check" for me as I prefer NOT to install packages in a
| > | > | > versioned path.
| > | > | >
| > | > | > FWIW, defaulting to a versioned path is (to this no-longer-bemused user) as
| > | > | > much a permenent R bug (on Windoze) as the default installation into a path
| > | > | > with spaces.
| > | > | >
| > | > | > Dirk
| > | > | >
| > | > |
| > | > | ______________________________________________
| > | > | R-devel_at_r-project.org mailing list
| > | > | https://stat.ethz.ch/mailman/listinfo/r-devel
| > | >
| > | > --
| > | > Dirk Eddelbuettel | edd@debian.org | http://dirk.eddelbuettel.com
| > | >
| > | > ______________________________________________
| > | > R-devel_at_r-project.org mailing list
| > | > https://stat.ethz.ch/mailman/listinfo/r-devel
| >
|
| --
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| Dr. Gavin Simpson [t] +44 (0)20 7679 0522
| ECRC, UCL Geography, [f] +44 (0)20 7679 0565
| Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
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|

-- 
Dirk Eddelbuettel | edd@debian.org | http://dirk.eddelbuettel.com

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