[R-sig-dyn-mod] Problem with loading compiled code into R

[John Harrold]

Howdy Mathilde,

I have a Mac and I run compiled code in R using deSolve all the time.
If you can send me your C file and an R script to compile, load, and
run it, I can give it a try on my computer.

John

On Fri, Apr 7, 2017 at 10:36 AM, Thomas Petzoldt
<thomas.petzoldt at tu-dresden.de> wrote:
> Hi Mathilde,
>
> a short question: which version of deSolve did you use? The stable version
> 1.14 from CRAN (i.e. the usual case) or a development snapshot from R-Forge
> (currently 1.20)?
>
> Can you test your model on a Windows or Linux system?
>
> Another idea may be a change of the compiler on the Mac. The CRAN tests of
> deSolve (1.14) are ok for the Mac, but I have personally no Mac at hand for
> testing. Is anybody else able to check this, or provide information about
> changes of the C compilers on the Mac?
>
> You may also consider to ask the R-Sig-Mac mailing list:
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> Thomas
>
>
> Am 07.04.2017 um 12:20 schrieb Hagens, M. (Mathilde):
>>
>> Dear all,
>>
>> I’m using compiled code (written in C) in combination with the deSolve
>> package to run a one-dimensional reactive transport model in R. On a server
>> I use running on Linux this works flawlessly, but on a MacBook Pro (macOS
>> 10.12.4) I have problems loading the compiled code into R (version 3.3.3).
>>
>> The output I get when compiling the code in R using
>> system("R CMD SHLIB Model.c”)
>> is:
>> clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
>> -fPIC  -Wall -mtune=core2 -g -O2  -c Model.c -o Model.o
>> clang -dynamiclib -Wl,-headerpad_max_install_names -undefined
>> dynamic_lookup -single_module -multiply_defined suppress
>> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Model.so
>> Model.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>> -Wl,CoreFoundation
>>
>> However, when I try to load the resulting shared object via
>> dyn.load(paste("Model", .Platform$dynlib.ext, sep = ""))
>> I get:
>> Error in dyn.load(paste("Model", .Platform$dynlib.ext, sep = "")) :
>>   unable to load shared object '/Users/mathilde/Model.so':
>>   dlopen(/Users/mathilde/Model.so, 6): Symbol not found: _dH_dt
>>   Referenced from: /Users/mathilde/Model.so
>>   Expected in: flat namespace
>>  in /Users/mathilde/Model.so
>>
>> The shared object created after compiling seems to look fine. Also, I
>> tried compiling directly from the Terminal, but that doesn’t make a
>> difference. Strangely, when I ran this model on a Mac in the past (~1 year
>> ago) it also worked without problems, leaving me wondering whether it may be
>> due to an R / macOS update. However, switching to an older R version
>> (2.15.2) didn’t solve the issue either. Has anyone experienced similar
>> behaviour and/or knows of a possible solution?
>>
>> Best wishes,
>> Mathilde
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
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>> R-sig-dynamic-models at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-dynamic-models
>>
>
>
> --
> Dr. Thomas Petzoldt
> Technische Universitaet Dresden
> Faculty of Environmental Sciences
> Institute of Hydrobiology
> 01062 Dresden, Germany
>
> Tel.: +49 351 463 34954
> Fax:  +49 351 463 37108
> E-Mail: thomas.petzoldt at tu-dresden.de
> http://tu-dresden.de/Members/thomas.petzoldt
>
> -- limnology and ecological modelling --
>
>
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-- 
-------------------------------------
John M. Harrold
john.m.harrold _at_gmail