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@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel