Clang and isnan compile error?

[Tor Arne Øigård]

Hi,

 

I have a TMB code which has been developed in a Windows environment and works perfectly well there. I was going to test it under Linux but then it would not compile and it seemed to complain about some usage of isnan(). I have a .R folder containing a Makevars file where it is specified to use clang as a compiler, i.e., CXX=clang++ as (please correct me if I’m wrong) I recall there were some issues when loading the libraries after changes had been made in the cpp-file due to the gcc compiler. However, if I remove the .R folder and compile with the default gcc it compiles fine, but then I guess it still is the issue about the libraries.

 

Any ideas of what could be the problem? I suspect it has something to do with the clang version, as I found in another post someone mentioning a clang version much higher than installed on our system.

 

We are running:

 

Ubuntu 16.04 LTS

R 3.6.2

TMB 1.7.18

Clang 3.8.0-2ubuntu4

g++ (Ubuntu 4.9.3-13ubuntu2) 4.9.3

 

Kind regards,

Tor Arne

[boen...@gmail.com]

What error message are you getting? It sound like https://stackoverflow.com/q/39130040/5861244 as it compiles fine with g++ 4.9.3.

[torarne...@gmail.com]

Hi,

Thanks for the link. When trying to compile with clang it spits out a very long message. Below is some of the "highlights" that appears:

In file included from ../mycoder.cpp:71:
In file included from  /Rlibs/TMB/include/TMB.hpp:53:
In file included from /Rlibs/RcppEigen/include/Eigen/Dense:1:
In file included from /Rlibs/RcppEigen/include/Eigen/Core:535:
/Rlibs/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^

In file included from /Rlibs/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Rlibs/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                 

/Rlibs/TMB/include/TMB.hpp:89:44: error: call to 'isnan' is ambiguous
  bool isnan(const AD<T> &x)CSKIP({ return isnan(Value(x)); })
  

/Rlibs/TMB/include/cppad/local/base_complex.hpp:361:14: note: candidate function
        inline bool isnan(const std::complex<float>& z)
                    ^
../mycode.cpp:157:6: error: call to 'isnan' is ambiguous

make: *** [../mycode.o] Error 1
Error in compile("../mycode.cpp") : Compilation failed

Not sure if this makes any sense. As I said compiling when removing the Makevars file works fine (but might have some issues with loading of libraries).

Best wishes,

Tor Arne

[Kasper Kristensen]

If it works with GCC but your main concern is library unloading I recommend you follow the instructions here:

https://github.com/kaskr/adcomp#issues-with-library-unloading

I.e., modify your Makevars to 'CXX = g++ -fno-gnu-unique'.

You may want to test that library unloading works by running this R script:
https://github.com/kaskr/adcomp/blob/master/tmb_syntax/test_reload.R

On Wednesday, September 23, 2020 at 10:28:47 AM UTC+2 torarne...@gmail.com wrote:

[torarne...@gmail.com]

Hi,

Thanks for this advice! The script works and it seems like the library unloads as it should. Appreciate this.

Best,
Tor Arne