[R-sig-dyn-mod] Using dynamically compiled code for use with deSolve in a new package

[Rampal S. Etienne]

Hi Thomas,

Thanks. I got it to work. The solution was to not let roxygen do the
namespace file, as it overwrites the line containing useDynLib.

Cheers, Rampal


On 29-11-2017 23:30, Thomas Petzoldt wrote:
> Hi,
>
> including Fortran and/or C sources in /src is exactly what we (and the
> other CRAN authors) do. It is self-evident, that binary code (like
> dlls) cannot be included in portable packages, that are expected to
> run on different operating systems. Details are found in "Writing R
> Extensions".
>
> I don't see a problem with roxygen2, this is exactly how it was
> implemented in package "growthrates", mentioned earlier. Let's assume
> we have a package called "foo", add the following roxygen-directives
> to a file "R/foo-package.R":
>
> #' @useDynLib foo
> #'
> #' @importFrom deSolve ode
>
> Hope it helps,
>
> Thomas
>
>
> On 29.11.2017 14:44, Rampal S. Etienne wrote:
>> Dear Thomas,
>>
>> Thanks again for this reply. While this may work locally and for some
>> users, it does not work in my case where my namespace file is generated
>> by roxygen2. Also, CRAN does not like dll-file to be in the package
>> (inst folder), so it needs to be built at installation. How do I do
>> this? Simply including the Fortran code in the src directory does not
>> work (gives error 127, whatever that is). Any suggestions?
>>
>> Cheers, Rampal
>>
>>
>> On 11-6-2017 21:15, Thomas Petzoldt wrote:
>>> Hi,
>>>
>>> that's straightforward.
>>>
>>> 1) Put deSolve in Depends of your package DESCRIPTION:
>>>
>>> Depends: deSolve
>>>
>>>
>>> 2) Import the solver function (e.g. ode or lsoda) in the NAMESPACE of
>>> your package and declare your dynamic library (.dll or .so)
>>>
>>> importFrom(deSolve,ode)
>>>
>>> useDynLib(mypackage)
>>>
>>>
>>> 3) and then use this .dll/.so in the call to ode():
>>>
>>> ode(...., dllname = "mypackage", .....)
>>>
>>>
>>> An example can be found in package growthrates:
>>>
>>> https://github.com/tpetzoldt/growthrates/blob/master/pkg/R/grow_twostep.R
>>>
>>>
>>> Hope it helps,
>>>
>>> Thomas
>>>
>>>
>>>
>>> On 11.06.2017 13:20, Rampal Etienne wrote:
>>>> Dear all,
>>>>
>>>> I have written C and FORTRAN functions to use with deSolve and found
>>>> that it works significantly faster than the analogous R functions. So
>>>> far so good! However, now I want to build a package that uses this
>>>> code.
>>>> How do I do this? I can include the DLL in the package (so no more
>>>> compilation by the user of the package, just loading it), but then the
>>>> user needs to be able to find it. Where will this be installed?
>>>> That may
>>>> be different on different systems. Any suggestions?
>>>>
>>>> Cheers, Rampal
>
>