From edd at debian.org  Thu Oct 18 17:18:16 2012
From: edd at debian.org (Dirk Eddelbuettel)
Date: Thu, 18 Oct 2012 10:18:16 -0500
Subject: [Rd] Rcmd_environ and R_LIBS_{USER,SITE}
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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



| 
| 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 at debian.org | http://dirk.eddelbuettel.com
| >
| > ______________________________________________
| > R-devel at r-project.org mailing list
| > https://stat.ethz.ch/mailman/listinfo/r-devel

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



[Rd] Rcmd_environ and R_LIBS_{USER,SITE}
Dirk Eddelbuettel