From plummerm at iarc.fr  Thu Feb  9 18:23:39 2017
From: plummerm at iarc.fr (Martyn Plummer)
Date: Thu, 9 Feb 2017 17:23:39 +0000
Subject: [Rd] R CMD check error
In-Reply-To: <f40b15$5q60ma@ironport10.mayo.edu>
References: <f40b15$5q1tpg@ironport10.mayo.edu>
	<1486630455.1872.36.camel@iarc.fr> <f40b15$5q60ma@ironport10.mayo.edu>
Message-ID: <1486661008.1872.91.camel@iarc.fr>

On Thu, 2017-02-09 at 09:52 -0600, Therneau, Terry M., Ph.D. wrote:
> Martin,
> ? I am aware of --vanilla; I use it myself for some testing.??In this case R_LIBS_USER was?
> set externally (part of my login) and does not involve any of the R scripts.??That means?
> it is inherited by any subprocess.??For example:
> 
> tmt1495% R --vanilla --no-environ
> 
> R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
> Copyright (C) 2016 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
> 
> > 
> > system("printenv | grep R_LIBS")
> R_LIBS_SITE=
> R_LIBS_USER=/people/biostat2/therneau/Rlib
> 
> So, per the manual R CMD check inherits the path.??The question is
> why does it ignore it?

Hmmm. Perhaps it is being overwritten. ?Does this work?

$ export R_CHECK_ENVIRON=
$ R CMD check hmm.gz

Martyn

> Terry T.
> 
> 
> On 02/09/2017 02:54 AM, Martyn Plummer wrote:
> > 
> > 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
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel


[Rd] R CMD check error
Martyn Plummer