[Debian-med-packaging] Bug#853656: Help needed with gcc-7 error

[Andreas Tille]

Hi,

when trying to build sga it results in an error:

...
g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp  -I/usr//include -I/usr//include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -std=c++98 -O3 -c -o libutil_a-VariantIndex.o `test -f 'VariantIndex.cpp' || echo './'`VariantIndex.cpp
VariantIndex.cpp: In member function 'VariantRecordVector VariantIndex::getNearVariants(const string&, int, int) const':
VariantIndex.cpp:89:46: error: call of overloaded 'abs(long unsigned int)' is ambiguous
             if(abs(record.position - position) < distance)
                                              ^
In file included from /usr/include/c++/7/cstdlib:75:0,
                 from /usr/include/c++/7/bits/stl_algo.h:59,
                 from /usr/include/c++/7/algorithm:62,
                 from VariantIndex.cpp:11:
/usr/include/stdlib.h:735:12: note: candidate: int abs(int)
 extern int abs (int __x) __THROW __attribute__ ((__const__)) __wur;
            ^~~
In file included from /usr/include/c++/7/cstdlib:77:0,
                 from /usr/include/c++/7/bits/stl_algo.h:59,
                 from /usr/include/c++/7/algorithm:62,
                 from VariantIndex.cpp:11:
/usr/include/c++/7/bits/std_abs.h:56:3: note: candidate: long int std::abs(long int)
   abs(long __i) { return __builtin_labs(__i); }
   ^~~
...


I have no idea in how far abs() is overloaded and how to fix this.

Kind regards

       Andreas.

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