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_SITER_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
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
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