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
Martin Maechler
2017-Feb-10 16:26 UTC
[Rd] R CMD check error (interfacing to C API of other pkg)
>>>>> Therneau, Terry M , Ph D <therneau at mayo.edu> >>>>> on Thu, 9 Feb 2017 12:56:17 -0600 writes:> 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. Hmm. Yes, I can see that the CRAN package msm does do this, indeed. It is interesting if/why that does not produce any notes or rather even warnings. In principle, if you use the C API of 'expm' you should use 'LinkingTo: expm' see *the* manual, specifically the section https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Linking-to-native-routines-in-other-packages and that section does mention that (unfortunately in my view) you also should use 'Imports:' or 'Depends:' in addition to the 'LinkingTo:' Note howver that 'expm' would not have to mentioned in the NAMESPACE file.... unless your R functions do use some of expm's R level functionality. Martin
Therneau, Terry M., Ph.D.
2017-Feb-10 17:42 UTC
[Rd] R CMD check error (interfacing to C API of other pkg): Solved
Martin, That was it- I forgot the "LinkingTo" line. I had read that section of the manual twice in the last 2 days, yet somehow missed that critical line both times. And even worse, the final sentence of said section references my own coxme package as an example of how to do it correctly! Thank you all for the help. My only remaining defense, but a very weak one, is that the error message could have been better since it led me to believe that R couldn't find the library at all. Terry Therneau On 02/10/2017 10:26 AM, Martin Maechler wrote:>>>>>> Therneau, Terry M , Ph D <therneau at mayo.edu> >>>>>> on Thu, 9 Feb 2017 12:56:17 -0600 writes: > > > 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. > > Hmm. Yes, I can see that the CRAN package msm does do this, indeed. > > It is interesting if/why that does not produce any notes or rather even warnings. > In principle, if you use the C API of 'expm' you should use > 'LinkingTo: expm' > > see *the* manual, specifically the section > > https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Linking-to-native-routines-in-other-packages > > and that section does mention that (unfortunately in my view) > you also should use 'Imports:' or 'Depends:' in addition to the 'LinkingTo:' > > Note howver that 'expm' would not have to mentioned > in the NAMESPACE file.... unless your R functions do use some of > expm's R level functionality. > > > Martin >