Re: [Rd] R CMD check with non-standard .libPaths

From: Dirk Eddelbuettel <>
Date: Sat, 14 Apr 2012 20:49:05 -0500

On 14 April 2012 at 20:45, Ben Bolker wrote:
| Does anyone have advice on how to instruct R CMD check to use a
| non-standard set of libraries? Here's the situation:

One way around is something like this:

edd_at_max:~$ tail -5 .R/check.Renviron

# edd Apr 2003  Allow local install in /usr/local, also add a directory for
#               Debian packaged CRAN packages, and finally the default dir 
# edd Jul 2007  Now use R_LIBS_SITE, not R_LIBS
R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'} edd_at_max:~$

The file check.Renviron sets up R environment variables just for R CMD check. [ And IIRC there is also build.Renviron ]

| I'm trying to do some automated checking on package dependencies of a
| package I maintain. In order to do that I've written code that takes
| the list of the dependent packages and for each package (1) downloads
| the most recent/available .tar.gz file; (2) installs the "Suggests:" and
| "Depends:" packages for the package that are not already installed; (3)
| runs R CMD check and stores the output.
| I wanted to do this in a way that would not necessarily bloat my base
| installation, so I wanted to do step #2 into a new library. Once I've
| figured out what the missing dependencies are (depMiss), I

So you could have a script setting the check.Renviron up alongside the build-up and later tear-down of you test setup.

Would be good to publish such a set of scripts. I hacked up something much smaller than that and much more ad-hoc too to test the reverse depends of one of my package before uploading it.


| install.packages(depMiss,lib=libdir)
| Then I run R CMD check as follows.
| ss <- suppressWarnings(system(
| paste("export R_LIBS=./library; R CMD check",
| file.path(tarballdir,tn)),
| intern=TRUE))
| However, this only seems to work partially. It does prevent the check
| from failing with an error that the package doesn't exist: *BUT* when
| the examples are actually run, I get results like this (this is from the
| 'agridat' package, which "Suggests:" the hglm package, which has hence
| been installed in the 'libdir' directory).
| [168] "168: Loading required package: hglm"
| [169] "169: Warning in library(package, lib.loc = lib.loc,
| character.only = TRUE, logical.return = TRUE, :"
| [170] "170: there is no package called ‘hglm’"
| Checking installed.packages() shows that hglm is indeed installed in
| the appropriate directory. agridat "Suggests:" hglm. The
| "crowder.germination" example in agridat tries require(hglm) and fails;
| it therefore doesn't fit the relevant HGLM model -- when the example
| tries to reference this model a few lines later, the example fails.
| Admittedly this could be seen as a bug in the example (it shouldn't try
| to access a model it knows it can't fit), but I wonder if there's a way
| I can get the examples run to see the non-standard package location.
| I could (I guess) modify my .Rprofile temporarily ... ? But I'm
| curious if there's a right way to do this ...
| thanks
| Ben Bolker
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