[Rd] R CMD check error

[Martyn Plummer]

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