From therneau at mayo.edu  Thu Feb  9 16:52:29 2017
From: therneau at mayo.edu (Therneau, Terry M., Ph.D.)
Date: Thu, 09 Feb 2017 09:52:29 -0600
Subject: [Rd] R CMD check error
In-Reply-To: <1486630455.1872.36.camel@iarc.fr>
References: <f40b15$5q1tpg@ironport10.mayo.edu>
	<1486630455.1872.36.camel@iarc.fr>
Message-ID: <f40b15$5q60ma@ironport10.mayo.edu>

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?

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



[Rd] R CMD check error
Therneau, Terry M., Ph.D.