[Bioc-devel] package 'msa' not building on veracruz2, but on toluca2 and other Mac OS systems

[Martin Morgan]

On 04/07/2017 11:26 AM, Ulrich Bodenhofer wrote:
> Hi,
>
> The devel version of our package 'msa' currently does not compile on
> veracruz2 (R 3.4.0 alpha under OS X 10.11.6 El Capitan), but it seems to
> work on toluca2 (R-devel on OS X 10.9.5 Mavericks). I also checked on my
> Mac at home (R 3.3.3 under macOS 10.12.3 Sierra using the very latest
> version of Xcode), and it also compiles without any problems.
>
> The error stems from a conflicting definition of the math functions
> 'log2' and 'log10' in the source code of the ClustalOmega library which
> is integrated into 'msa' (the same error appears for the inline
> definition of 'log10'):
>
>    hhalign/util-C.h:53:14: error: 'log2' is missing exception
> specification 'throw()'
>    inline float log2(float x)  {return (x<=0?
> (float)(-100000):1.442695041*log(x));}
>
> Any ideas? 'log2' and 'log10' are defined in the standard math library.
> The definitions work well on Linux along with '#include <cmath>' , while
> Windows requires '#include <math.h>'. So far, '#include <cmath>' also
> worked on Mac OS, but it seems that now, on veracruz2, neither one nor
> the other works. Any thoughts? Is this something I should care about or
> is there something exotic about veracruz2 such that I can simply ignore
> this issue?

I guess the minimal reproducible example is

$ cat log2.cpp
#include <cmath>  // or <math.h>

inline float log2(float x) {return (x<=0? 
(float)(-100000):1.442695041*log(x));}

$ R CMD SHLIB log2.cpp
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG 
-I/usr/local/include -I/opt/X11/include   -fPIC  -Wall -g -O2  -c 
log2.cpp -o log2.o
log2.cpp:3:14: error: 'log2' is missing exception specification 'throw()'
inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*...
              ^
                            throw()
/usr/local/clang+llvm-4.0.0-x86_64-apple-darwin/bin/../include/c++/v1/math.h:1221:46: 
note:
       previous declaration is here
inline _LIBCPP_INLINE_VISIBILITY float       log2(float __lcpp_x) _NOEX...
                                              ^
1 error generated.
make: *** [log2.o] Error 1

It could be that final changes in the compiler used by R to build mac 
binaries could change, but at this point I think it would be prudent to 
implement a work-around; veracruz2 will be our main macOS builder for 
the release, and if the package is not building on it then the package 
will not be available to macOS users.

I am not enough of a C++ programmer to be able to give concrete advice 
on how the problem should be addressed; maybe others on the list have 
insight...?

Martin


> Thanks a lot in advance and best regards,
>
> Ulrich
>
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