From edd at debian.org  Sat Oct 20 17:52:36 2012
From: edd at debian.org (Dirk Eddelbuettel)
Date: Sat, 20 Oct 2012 10:52:36 -0500
Subject: [Rd] Rcmd_environ and R_LIBS_{USER,SITE}
In-Reply-To: <5082BBDE.70209@statistik.tu-dortmund.de>
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Message-ID: <20610.51396.940734.395724@max.nulle.part>


Hi Uwe,

On 20 October 2012 at 16:57, Uwe Ligges wrote:
| Dirk,
| 
| if you are checking "foo", then "foo" is found in the examples (on all 
| OSs), even if it is NOT installed at all!

Well the log you asked me to supply very clearly shows otherwise.

All I doing is 

 i)  R itself in  c:\opt\R-current\     (currently 2.15.1)

 ii) packages in c:\opt\R-library\	(incl. the pkg in question)
 
| Can you make the sources available for me?

 a) It contains code from work code I cannot distribute.

 b) I will check next week about using a CRAN package. I suspect that, say,
    my small-ish digest package will fail the same way.

 c) Having authored what must be around two dozen packages of which around
    three quarters are actively maintained and on CRAN, I am reasonably
    confident that I did nothing "wrong" here.

 d) Once I add '--no-tests --no-examples' then R CMD check passes fine. So
    the package seems fine.

 e) No issues whatsoever on Linux. 

More on Monday or Tuesday. 

Thanks,  Dirk
 
| Uwe
| 
| 
| 
| 
| 
| 
| 
| On 19.10.2012 23:58, Dirk Eddelbuettel wrote:
| >
| > Hi Uwe,
| >
| > On 19 October 2012 at 19:25, Uwe Ligges wrote:
| > | 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.
| >
| > That is not what I said, or tried to say. My issue is that the _tests_ and
| > _examples_ fail.
| >
| > | Can we have details?
| >
| > Sure -- See below.  Cut and pasted from an Emacs buffer on Windoze as
| > evidenved by the U:\ directory at mingw id shown. Emacs has no role here, it
| > also fails the same way in a normal DOS prompt.
| >
| >
| > u:\R\src>R CMD check foo_0.2.2.tar.gz
| > R CMD check foo_0.2.2.tar.gz
| > * using log directory 'u:/R/src/foo.Rcheck'
| > * using R version 2.15.1 (2012-06-22)
| > * using platform: x86_64-pc-mingw32 (64-bit)
| > * using session charset: ISO8859-1
| > * checking for file 'foo/DESCRIPTION' ... OK
| > * checking extension type ... Package
| > * this is package 'foo' version '0.2.2'
| > * checking package namespace information ... OK
| > * checking package dependencies ... OK
| > * checking if this is a source package ... OK
| > * checking if there is a namespace ... OK
| > * checking for executable files ... OK
| > * checking whether package 'foo' can be installed ... [34s] OK
| > * checking installed package size ... OK
| > * checking package directory ... OK
| > * checking for portable file names ... OK
| > * checking DESCRIPTION meta-information ... OK
| > * checking top-level files ... OK
| > * checking index information ... OK
| > * checking package subdirectories ... OK
| > * checking R files for non-ASCII characters ... OK
| > * checking R files for syntax errors ... OK
| > * loading checks for arch 'i386'
| > ** checking whether the package can be loaded ... OK
| > ** checking whether the package can be loaded with stated dependencies ... OK
| > ** checking whether the package can be unloaded cleanly ... OK
| > ** checking whether the namespace can be loaded with stated dependencies
| > ... OK
| > ** checking whether the namespace can be unloaded cleanly ... OK
| > * loading checks for arch 'x64'
| > ** checking whether the package can be loaded ... OK
| > ** checking whether the package can be loaded with stated dependencies ... OK
| > ** checking whether the package can be unloaded cleanly ... OK
| > ** checking whether the namespace can be loaded with stated dependencies
| > ... OK
| > ** checking whether the namespace can be unloaded cleanly ... OK
| > * checking for unstated dependencies in R code ... OK
| > * checking S3 generic/method consistency ... OK
| > * checking replacement functions ... OK
| > * checking foreign function calls ... OK
| > * checking R code for possible problems ... OK
| > * checking Rd files ... OK
| > * checking Rd metadata ... OK
| > * checking Rd cross-references ... OK
| > * checking for missing documentation entries ... OK
| > * checking for code/documentation mismatches ... OK
| > * checking Rd \usage sections ... OK
| > * checking Rd contents ... OK
| > * checking for unstated dependencies in examples ... OK
| > * checking contents of 'data' directory ... OK
| > * checking data for non-ASCII characters ... OK
| > * checking data for ASCII and uncompressed saves ... OK
| > * checking line endings in C/C++/Fortran sources/headers ... OK
| > * checking line endings in Makefiles ... OK
| > * checking for portable compilation flags in Makevars ... OK
| > * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
| > * checking compiled code ... OK
| > * checking examples ...
| > ** running examples for arch 'i386' ... ERROR
| > Running examples in 'foo-Ex.R' failed
| > The error occurred in:
| >
| >
| > R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
| > Copyright (C) 2012 The R Foundation for Statistical Computing
| > ISBN 3-900051-07-0
| > Platform: i386-pc-mingw32/i386 (32-bit)
| >
| > R is free software and comes with ABSOLUTELY NO WARRANTY.
| > You are welcome to redistribute it under certain conditions.
| > Type 'license()' or 'licence()' for distribution details.
| >
| >    Natural language support but running in an English locale
| >
| > R is a collaborative project with many contributors.
| > Type 'contributors()' for more information and
| > 'citation()' on how to cite R or R packages in publications.
| >
| > Type 'demo()' for some demos, 'help()' for on-line help, or
| > 'help.start()' for an HTML browser interface to help.
| > Type 'q()' to quit R.
| >
| >> pkgname <- "foo"
| >> source(file.path(R.home("share"), "R", "examples-header.R"))
| >> options(warn = 1)
| >> options(pager = "console")
| >> library('foo')
| > Error in library("foo") : there is no package called 'foo'
| > Execution halted
| > ** running examples for arch 'x64' ... ERROR
| > Running examples in 'foo-Ex.R' failed
| > The error occurred in:
| >
| >
| > R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
| > Copyright (C) 2012 The R Foundation for Statistical Computing
| > ISBN 3-900051-07-0
| > Platform: x86_64-pc-mingw32/x64 (64-bit)
| >
| > R is free software and comes with ABSOLUTELY NO WARRANTY.
| > You are welcome to redistribute it under certain conditions.
| > Type 'license()' or 'licence()' for distribution details.
| >
| >    Natural language support but running in an English locale
| >
| > R is a collaborative project with many contributors.
| > Type 'contributors()' for more information and
| > 'citation()' on how to cite R or R packages in publications.
| >
| > Type 'demo()' for some demos, 'help()' for on-line help, or
| > 'help.start()' for an HTML browser interface to help.
| > Type 'q()' to quit R.
| >
| >> pkgname <- "foo"
| >> source(file.path(R.home("share"), "R", "examples-header.R"))
| >> options(warn = 1)
| >> options(pager = "console")
| >> library('foo')
| > Error in library("foo") : there is no package called 'foo'
| > Execution halted
| >
| > u:\R\src>
| >
| > Needless to say the package __does__ of course exist, is installed and
| > loadable:
| >
| >
| > u:\R\src>R --no-save
| > R --no-save
| >
| > R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
| > Copyright (C) 2012 The R Foundation for Statistical Computing
| > ISBN 3-900051-07-0
| > Platform: x86_64-pc-mingw32/x64 (64-bit)
| >
| > R is free software and comes with ABSOLUTELY NO WARRANTY.
| > You are welcome to redistribute it under certain conditions.
| > Type 'license()' or 'licence()' for distribution details.
| >
| > R is a collaborative project with many contributors.
| > Type 'contributors()' for more information and
| > 'citation()' on how to cite R or R packages in publications.
| >
| > Type 'demo()' for some demos, 'help()' for on-line help, or
| > 'help.start()' for an HTML browser interface to help.
| > Type 'q()' to quit R.
| >
| > R> library(foo)
| > library(foo)
| > Loading required package: Rcpp
| > Loading required package: xts
| > Loading required package: zoo
| >
| > Attaching package: 'zoo'
| >
| > The following object(s) are masked from 'package:base':
| >
| >      as.Date, as.Date.numeric
| >
| > R>
| >
| >
| > [ foo is a placeholder here, the package has a different name which plays no
| > role in the misbehaviour demonstrated above. ]
| >
| > Thanks for looking into this.
| >
| > Dirk
| >
| >
| > | 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
| > | > | %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
| > | > |
| > | > |
| > | >
| >

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



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