From ligges at statistik.tu-dortmund.de  Fri Oct 19 19:25:34 2012
From: ligges at statistik.tu-dortmund.de (Uwe Ligges)
Date: Fri, 19 Oct 2012 19:25:34 +0200
Subject: [Rd] Rcmd_environ and R_LIBS_{USER,SITE}
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Message-ID: <50818D0E.8090104@statistik.tu-dortmund.de>

Dirk,

if you ask R to

R CMD check foo_1.2-3.tar.gz


and the output is

"no package called 'foo'"

then something went wrong with your setup or your package.

Can we have details?

Best,
Uwe




On 19.10.2012 15:21, Dirk Eddelbuettel wrote:
>
> 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 at debian.org | http://dirk.eddelbuettel.com
> | > | >
> | > | > ______________________________________________
> | > | > R-devel at r-project.org mailing list
> | > | > https://stat.ethz.ch/mailman/listinfo/r-devel
> | >
> |
> | --
> | %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
> |  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
> |  Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
> |  UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
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> |
> |
>



[Rd] Rcmd_environ and R_LIBS_{USER,SITE}
Uwe Ligges