R CMD check error

system("printenv | grep R_LIBS")

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)