build error narrowing conversion of ‘-9’ from ‘int’ to ‘std::size_t' about gemma

[wanyuac]

I had the same error message as @xiangzhou when I was compiling GEMMA on ubuntu with GCC v5.4.0.

It is a problem of the compiler we have used. As one of my colleagues suspected, I finally got GEMMA compiled successfully using gcc-4.9.3. It seems that the code "SNPINFO sInfo={"-9", rs, -9, -9, minor, major, -9, -9, (long int) -9};" is not compatible with gcc-5+. @xiangzhu @DSLituiev

There is another way to get round of this problem using gcc-5. We can change the class definition:

class SNPINFO { public: ... size_t n_miss; ... };

into

class SNPINFO { public: ... ssize_t n_miss; ... };

However, I would not recommend this method because I am not sure if the substitution of data types would affect results.

[echubaty]

@wanyuac Thank you, your fork of this repo worked for me. The only modification I had to make for my environment was changing CPP to g++-4.9 since I now have multiple versions installed.

[xiangzhu]

@xiangzhou I get the same build error with gcc-5; and I also get the same error using g++ (Ubuntu 6.2.0-3ubuntu11~16.04) 6.2.0 20160901.

Here is the error from gcc-6.

src/io.cpp: In function ‘bool ReadFile_bgen(const string&, const std::set<std::__cxx11::basic_string<char> >&, const gsl_matrix*, std::vector<int>&, std::vector<int>&, std::vector<SNPINFO>&, const double&, const double&, const double&, const double&, std::size_t&)’:
src/io.cpp:2165:73: error: narrowing conversion of ‘-9’ from ‘int’ to ‘std::size_t {aka long unsigned int}’ inside { } [-Wnarrowing]
     SNPINFO sInfo={"-9", rs, -9, -9, minor, major, -9, -9, (long int) -9};
                                                                         ^
Makefile:108: recipe for target 'src/io.o' failed
make: *** [src/io.o] Error 1

[pcarbo]

@wanyuac @xiangzhu @echubaty @DSLituiev Can one of you please check to see if this issue is now resolved? See also Issue #24, which reported the same problem (although using a different C++ compiler).

[pjotrp]

Guix version compiles fine with latest gcc compilers.