From plummerm at iarc.fr  Thu Feb  9 09:54:26 2017
From: plummerm at iarc.fr (Martyn Plummer)
Date: Thu, 9 Feb 2017 08:54:26 +0000
Subject: [Rd] R CMD check error
In-Reply-To: <f40b15$5q1tpg@ironport10.mayo.edu>
References: <f40b15$5q1tpg@ironport10.mayo.edu>
Message-ID: <1486630455.1872.36.camel@iarc.fr>

On Wed, 2017-02-08 at 15:51 -0600, Therneau, Terry M., Ph.D. wrote:
> I have a local library which depends on the expm library.??The expm library is loaded into?
> my personal space and I have the environment variable R_LIBS_USER set appropriately.??The?
> command "library(expm)" works just fine from the command line, and in fact the package?
> works if I do the source() and dyn.load() commands by hand.
> 
> The following sequence works:
> 
> tmt% R CMD build --no-build-vignettes hmm
> tmt% R CMD INSTALL hmm*gz
> tmt% R
> ?> library(hmm)
> ?>??run some commands from the hmm library
> 
> But "R CMD check hmm.gz" fails with
> ???ERROR: dependency ?expm? is not available for package ?hmm?
> * removing
> ?/people/biostat2/therneau/consult/alzheimer/hmm.Rcheck/hmm?
> 
> The R CMD build command fails similarly if I let it try to build the
> vignettes.
> 
> What's up?

If you are setting the environment variable R_LIBS_USER in
R_HOME/site/Renviron.site or in .Renviron then this file will not be
read when you run R CMD check or R CMD build, as R is then run with --
vanilla which implies --no-environ.?

You also need to set it in these files:

~/.R/build.Renviron
~/.R/check.Renviron

See R-exts section 1.3 and ?Startup.

Martyn
	
> Terry T
> 
> 
> ?> sessionInfo()
> R version 3.3.1 (2016-06-21)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: CentOS release 6.8 (Final)
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel


[Rd] R CMD check error
Martyn Plummer