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

[Coffey, David G]

Hello,

My Bioconductor Package ‘LymphoSeq’ received the following build error<http://bioconductor.org/checkResults/3.5/bioc-LATEST/LymphoSeq/veracruz2-buildsrc.html> on veracruz2:

ERROR: dependency ‘msa’ is not available for package ‘LymphoSeq’

Indeed, ‘msa’ is one of my package dependencies.  The package was built under the latest version of MacOS on my computer and I have never see this error before.  I am wondering if this problem is related to this thread.  Will my package not be pushed to the release version because of this error?

Thank you,

David

On Apr 14, 2017, at 12:50 PM, Martin Morgan <martin.morgan at roswellpark.org<mailto:martin.morgan at roswellpark.org>> wrote:

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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