From therneau at mayo.edu  Thu Feb  9 19:56:17 2017
From: therneau at mayo.edu (Therneau, Terry M., Ph.D.)
Date: Thu, 09 Feb 2017 12:56:17 -0600
Subject: [Rd] R CMD check error
In-Reply-To: <1486661008.1872.91.camel@iarc.fr>
References: <f40b15$5q1tpg@ironport10.mayo.edu>
	<1486630455.1872.36.camel@iarc.fr> <f40b15$5q60ma@ironport10.mayo.edu>
	<1486661008.1872.91.camel@iarc.fr>
Message-ID: <f40b15$5q8gau@ironport10.mayo.edu>

Martyn,
   No, that didn't work.
   One other thing in the mix (which I don't think is the issue) is that I call one of the 
C-entry points of expm.  So the DESCRIPTION file imports expm, the NAMESPACE file imports 
expm, and the init.c file is

#include "R.h"
#include "R_ext/Rdynload.h"

/* Interface to expm package. */
typedef enum {Ward_2, Ward_1, Ward_buggy_octave} precond_type;
void (*expm)(double *x, int n, double *z, precond_type precond_kind);
void R_init_hmm(DllInfo *dll)
{
     expm = (void (*)) R_GetCCallable("expm", "expm");
}

I don't expect that this is the problem since I stole the above almost verbatim from the 
msm package.

Terry T.


On 02/09/2017 11:23 AM, Martyn Plummer wrote:
> 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
Therneau, Terry M., Ph.D.