Please see my reply below.
On Wed, Jun 29, 2016 at 1:43 PM, Esteban Gabriel Vega Hissi <
egvega.gmail.com> wrote:
> Hi, I get the following error while compiling ambertools16 on a Fedora 24
> OS:
>
> installing ./reduce_src...
> make[3]: Entering directory
> '/usr/local/amber16/AmberTools/src/reduce/reduce_src'
> g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED
> -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX
> -DINCTEMPLATEDEFNS
> -DHET_DICTIONARY='"/usr/local/amber16/dat/reduce_wwPDB_het_dict.txt"'
> -I../libpdb -I../toolclasses -o GraphToHoldScores.o GraphToHoldScores.cpp
> GraphToHoldScores.cpp: In member function ‘int
> DegreeTwoEdge_ths::whichVertex(int) const’:
> GraphToHoldScores.cpp:1152:88: error: no match for ‘operator<<’ (operand
> types are ‘std::basic_ostream<char>’ and ‘std::ostream {aka
> std::basic_ostream<char>}’)
> std::cerr << "CRITICAL ERROR IN whichVertex(" << vertex_index << ")
> called on edge [" <<
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
> std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]"
> << std::endl;
> ~~~
>
> In file included from /usr/include/c++/6.1.1/iostream:39:0,
> from ../toolclasses/Point3d.h:19,
> from AtomDescr.h:10,
> from GraphToHoldScores.h:11,
> from GraphToHoldScores.cpp:1:
> /usr/include/c++/6.1.1/ostream:628:5: note: candidate:
> std::basic_ostream<_CharT, _Traits>&
> std::operator<<(std::basic_ostream<_CharT, _Traits>&&, const _Tp&) [with
> _CharT = char; _Traits = std::char_traits<char>; _Tp =
> std::basic_ostream<char>] <near match>
> operator<<(basic_ostream<_CharT, _Traits>&& __os, const _Tp& __x)
> ^~~~~~~~
> /usr/include/c++/6.1.1/ostream:628:5: note: conversion of argument 1
> would be ill-formed:
> GraphToHoldScores.cpp:1152:64: error: cannot bind
> ‘std::basic_ostream<char>’ lvalue to ‘std::basic_ostream<char>&&’
> std::cerr << "CRITICAL ERROR IN whichVertex(" << vertex_index << ")
> called on edge [" <<
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
> GraphToHoldScores.cpp:1152:88: note: candidate: operator<<(int, int)
> <built-in>
> std::cerr << "CRITICAL ERROR IN whichVertex(" << vertex_index << ")
> called on edge [" <<
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
> std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]"
> << std::endl;
> ~~~
>
> GraphToHoldScores.cpp:1152:88: note: no known conversion for argument 2
> from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘int’
> In file included from /usr/include/c++/6.1.1/iostream:39:0,
> from ../toolclasses/Point3d.h:19,
> from AtomDescr.h:10,
> from GraphToHoldScores.h:11,
> from GraphToHoldScores.cpp:1:
>
> .....
> chunked output
> .....
>
> Makefile:33: recipe for target 'GraphToHoldScores.o' failed
> make[3]: *** [GraphToHoldScores.o] Error 1
> make[3]: Leaving directory
> '/usr/local/amber16/AmberTools/src/reduce/reduce_src'
> Makefile:19: recipe for target 'install' failed
> make[2]: *** [install] Error 2
> make[2]: Leaving directory '/usr/local/amber16/AmberTools/src/reduce'
> Makefile:17: recipe for target 'serial' failed
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory '/usr/local/amber16/AmberTools/src'
> Makefile:7: recipe for target 'install' failed
> make: *** [install] Error 2
>
>
> I found an old post "http://archive.ambermd.org/200903/0267.html"
> suggesting to overcome this error by skipping reduce compiling.
>
> Fedora 24 is updated and GNU tools "gcc*" installed.
>
If I understand correctly, Fedora 24 comes with gcc6.
https://fedoraproject.org/wiki/Changes/GCC6
This compiler is quite new (released 04/2016 ?) and amber developers had
not tested yet.
You can compile Amer16 with gcc5 or 4 (I tested with v5.3, 4.8, 4.9) .
> I'm wondering how to solve any of both issues: compiling with reduce and/or
> skipping compiling it.
>
If you do not use *reduce* yet, you can turn it off for now by comment it
in AmberTools/src/Makefile
Hai
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Received on Wed Jun 29 2016 - 11:00:03 PDT
