Error running make all

[Thomas O'Reilly-Pol]

Mac OSX 10.11.6, g++ 6.3.0_1, I get this error running make all

In file included from /Users/johnsonlab/delly/src/modular-boost/boost/config.hpp:61:0,
                 from /Users/johnsonlab/delly/src/modular-boost/boost/graph/adjacency_list.hpp:15,
                 from src/delly.h:31,
                 from src/delly.cpp:40:
/Users/johnsonlab/delly/src/modular-boost/boost/multiprecision/cpp_int.hpp:181:4: error: right operand of shift expression '(1u << 63u)' is >= than the precision of the left operand [-fpermissive]
    BOOST_STATIC_CONSTANT(limb_type, sign_bit_mask = 1u << (limb_bits - 1));
    ^
/Users/johnsonlab/delly/src/modular-boost/boost/multiprecision/cpp_int.hpp:401:4: error: right operand of shift expression '(1u << 63u)' is >= than the precision of the left operand [-fpermissive]
    BOOST_STATIC_CONSTANT(limb_type, sign_bit_mask = 1u << (limb_bits - 1));
    ^
/Users/johnsonlab/delly/src/modular-boost/boost/multiprecision/cpp_int.hpp:548:4: error: right operand of shift expression '(1u << 63u)' is >= than the precision of the left operand [-fpermissive]
    BOOST_STATIC_CONSTANT(limb_type, sign_bit_mask = 1u << (limb_bits - 1));
    ^
make: *** [src/delly] Error 1

[Tobias Rausch]

Hi,

Delly is regularly tested using gcc4, gcc5 and gcc6. The default for gcc6 is still 6.2.0 for travis ( https://travis-ci.org/dellytools/delly ) and that seems to work fine. Could you use gcc 6.2 instead? This seems to be a problem with boost and gcc 6.3 so I may not have an immediate solution for that.

Best, Tobias

[Thomas O'Reilly-Pol]

(Figured out how to and) downgraded to gcc 6.2.0, I get hundreds of lines of like

/var/folders/ck/mxcjlvgd6yz1tpthnhj23yth0000gn/T//cc4Yq4mC.s:6009:11: warning: section "__textcoal_nt" is deprecated
        .section __TEXT,__textcoal_nt,coalesced,pure_instructions
                 ^      ~~~~~~~~~~~~~
/var/folders/ck/mxcjlvgd6yz1tpthnhj23yth0000gn/T//cc4Yq4mC.s:6009:11: note: change section name to "__text"
        .section __TEXT,__textcoal_nt,coalesced,pure_instructions

and ends with