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soedinglab / CCMpred

Protein Residue-Residue Contacts from Correlated Mutations predicted quickly and accurately.
http://www.ncbi.nlm.nih.gov/pubmed/25064567
GNU Affero General Public License v3.0
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fixed quotes and nvcc directory in CMakeLists.txt #10

Closed grubermar closed 7 years ago

grubermar commented 7 years ago

Should fix issue #9

sseemayer commented 7 years ago

Thanks for the PR Markus! 👍

alsalas commented 7 years ago

Dear CCMpred Team, the CUDA problem is fixed!! Thanks. But, now I have other error, I tried to fix without success. The error is with msgpack, I compile msgpack from GitHub and use gcc-4.7 in centos6 :

CMakeFiles/ccmpred.dir/src/meta.c.o: In function json_string_to_msgpack': /home/alsalas/Phylogeny/CCMpred/src/meta.c:107: undefined reference tomsgpack_pack_str' /home/alsalas/Phylogeny/CCMpred/src/meta.c:107: undefined reference to msgpack_pack_str' /home/alsalas/Phylogeny/CCMpred/src/meta.c:108: undefined reference tomsgpack_pack_str_body' CMakeFiles/ccmpred.dir/src/meta.c.o: In function json_object_to_msgpack': /home/alsalas/Phylogeny/CCMpred/src/meta.c:88: undefined reference tomsgpack_pack_str' /home/alsalas/Phylogeny/CCMpred/src/meta.c:89: undefined reference to msgpack_pack_str_body' CMakeFiles/ccmpred.dir/src/meta.c.o: In functionmeta_write_msgpack': /home/alsalas/Phylogeny/CCMpred/src/meta.c:158: undefined reference to msgpack_pack_str' /home/alsalas/Phylogeny/CCMpred/src/meta.c:159: undefined reference tomsgpack_pack_str_body' CMakeFiles/ccmpred.dir/src/meta.c.o: In function json_string_to_msgpack': /home/alsalas/Phylogeny/CCMpred/src/meta.c:108: undefined reference tomsgpack_pack_str_body' collect2: ld returned 1 exit status make[2]: [bin/ccmpred] Error 1 make[1]: [CMakeFiles/ccmpred.dir/all] Error 2 make: *** [all] Error 2

Thanks,

Alexis

rakeshr10 commented 7 years ago

Hi,

I get this error now when I try to compile.

/usr/lib/gcc/x86_64-redhat-linux/7/include/stddef.h(444): error: identifier "nullptr" is undefined

/usr/lib/gcc/x86_64-redhat-linux/7/include/stddef.h(444): error: expected a ";"

/usr/include/c++/7/x86_64-redhat-linux/bits/c++config.h(2196): error: expected a ";"

/usr/include/c++/7/bits/exception.h(63): error: expected a ";"

/usr/include/c++/7/bits/exception.h(69): error: expected a ";"

/usr/include/c++/7/exception(49): error: expected a ";"

/usr/include/c++/7/exception(57): error: expected a ";"

/usr/include/c++/7/exception(67): error: expected a "{"

/usr/include/c++/7/bits/cxxabi_init_exception.h(63): error: expected a "{"

/usr/include/c++/7/typeinfo(99): error: expected a ";"

/usr/include/c++/7/typeinfo(187): error: not a class or struct name

/usr/include/c++/7/typeinfo(190): error: expected a ";"

/usr/include/c++/7/typeinfo(197): error: expected a ";"

/usr/include/c++/7/typeinfo(204): error: not a class or struct name

/usr/include/c++/7/typeinfo(207): error: expected a ";"

/usr/include/c++/7/typeinfo(214): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(63): error: function "__cxxabiv1::std::current_exception" returns incomplete type "cxxabiv1::std::exception_ptr::exception_ptr"

/usr/include/c++/7/bits/exception_ptr.h(63): error: expected a "{"

/usr/include/c++/7/bits/exception_ptr.h(73): error: namespace "__cxxabiv1::std" has no member "rethrow_exception"

/usr/include/c++/7/bits/exception_ptr.h(83): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(85): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(86): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(88): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(90): error: declaration is incompatible with previous "__cxxabiv1::std::current_exception" (63): here

/usr/include/c++/7/bits/exception_ptr.h(90): error: use of a local type to declare a function

/usr/include/c++/7/bits/exception_ptr.h(90): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(91): error: use of a local type to declare a function

/usr/include/c++/7/bits/exception_ptr.h(93): error: namespace "__cxxabiv1::std" has no member "make_exception_ptr"

/usr/include/c++/7/bits/exception_ptr.h(93): error: a template friend declaration cannot be declared in a local class

/usr/include/c++/7/bits/exception_ptr.h(93): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(96): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(98): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(101): error: incomplete type is not allowed

/usr/include/c++/7/bits/exception_ptr.h(101): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(122): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(132): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(149): error: use of a local type to declare a function

/usr/include/c++/7/bits/exception_ptr.h(150): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(153): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(158): error: use of a local type to declare a function

/usr/include/c++/7/bits/exception_ptr.h(159): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(162): error: use of a local type to declare a function

/usr/include/c++/7/bits/exception_ptr.h(163): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(166): error: use of a local type to declare a function

/usr/include/c++/7/bits/exception_ptr.h(167): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(179): error: expected a ";"

/usr/include/c++/7/bits/exception_ptr.h(214): error: expected a ";"

/usr/include/c++/7/bits/move.h(46): error: identifier "constexpr" is undefined

/usr/include/c++/7/bits/move.h(46): error: "_Tp" is not a function or static data member

/usr/include/c++/7/bits/move.h(51): error: expected a ";"

/usr/include/c++/7/type_traits(71): error: identifier "constexpr" is undefined

/usr/include/c++/7/type_traits(71): error: template parameter "_Tp" may not be redeclared in this scope

/usr/include/c++/7/type_traits(71): error: expected a ";"

/usr/include/c++/7/type_traits(72): error: member "cxxabiv1::std::integral_constant<_Tp, v>::_Tp" is not a type name

/usr/include/c++/7/type_traits(73): error: member "cxxabiv1::std::integral_constant<_Tp, v>::_Tp" is not a type name

/usr/include/c++/7/type_traits(74): error: identifier "constexpr" is undefined

/usr/include/c++/7/type_traits(79): error: identifier "constexpr" is undefined

/usr/include/c++/7/type_traits(79): error: "value_type" has already been declared in the current scope

/usr/include/c++/7/type_traits(79): error: expected a ";"

/usr/include/c++/7/type_traits(84): error: identifier "constexpr" is undefined

/usr/include/c++/7/type_traits(84): error: "_Tp" is not a function or static data member

/usr/include/c++/7/type_traits(93): error: expected a declaration

/usr/include/c++/7/type_traits(93): error: expected a ";"

/usr/include/c++/7/type_traits(126): error: space required between adjacent ">" delimiters of nested template argument lists (">>" is the right shift operator)

/usr/include/c++/7/type_traits(248): error: identifier "char16_t" is undefined

/usr/include/c++/7/type_traits(252): error: identifier "char32_t" is undefined

/usr/include/c++/7/type_traits(252): error: class "cxxabiv1::std::is_integral_helper<>" has already been defined

/usr/include/c++/7/type_traits(350): error: identifier "__float128" is undefined

/usr/include/c++/7/type_traits(365): error: namespace "__cxxabiv1::std" has no member "size_t"

/usr/include/c++/7/type_traits(466): error: expected a ">"

/usr/include/c++/7/type_traits(470): error: expected a ">"

/usr/include/c++/7/type_traits(478): error: expected a ">"

/usr/include/c++/7/type_traits(482): error: expected a ">"

/usr/include/c++/7/type_traits(490): error: expected a ">"

/usr/include/c++/7/type_traits(494): error: expected a ">"

/usr/include/c++/7/type_traits(502): error: expected a ">"

/usr/include/c++/7/type_traits(506): error: expected a ">"

/usr/include/c++/7/type_traits(514): error: expected a ">"

/usr/include/c++/7/type_traits(518): error: expected a ">"

/usr/include/c++/7/type_traits(526): error: expected a ">"

/usr/include/c++/7/type_traits(530): error: expected a ">"

/usr/include/c++/7/type_traits(538): error: expected a ">"

/usr/include/c++/7/type_traits(542): error: expected a ">"

/usr/include/c++/7/type_traits(550): error: expected a ">"

/usr/include/c++/7/type_traits(554): error: expected a ">"

/usr/include/c++/7/type_traits(564): error: namespace "__cxxabiv1::std" has no member "nullptr_t"

/usr/include/c++/7/type_traits(585): error: space required between adjacent ">" delimiters of nested template argument lists (">>" is the right shift operator)

/usr/include/c++/7/type_traits(591): error: space required between adjacent ">" delimiters of nested template argument lists (">>" is the right shift operator)

/usr/include/c++/7/type_traits(598): error: space required between adjacent ">" delimiters of nested template argument lists (">>" is the right shift operator)

/usr/include/c++/7/type_traits(605): error: space required between adjacent ">" delimiters of nested template argument lists (">>" is the right shift operator)

/usr/include/c++/7/type_traits(615): error: space required between adjacent ">" delimiters of nested template argument lists (">>" is the right shift operator)

/usr/include/c++/7/type_traits(641): error: space required between adjacent ">" delimiters of nested template argument lists (">>" is the right shift operator)

/usr/include/c++/7/type_traits(751): error: space required between adjacent ">" delimiters of nested template argument lists (">>" is the right shift operator)

/usr/include/c++/7/type_traits(765): error: expected a ";"

/usr/include/c++/7/type_traits(780): error: space required between adjacent ">" delimiters of nested template argument lists (">>" is the right shift operator)

/usr/include/c++/7/type_traits(790): error: expected a ")"

/usr/include/c++/7/type_traits(801): error: an explicit template argument list is not allowed on this declaration

/usr/include/c++/7/type_traits(801): error: expected a type specifier

/usr/include/c++/7/type_traits(801): error: function returning function is not allowed

/usr/include/c++/7/type_traits(801): error: expected a ";"

Error limit reached. 100 errors detected in the compilation of "/tmp/tmpxft_00007a81_00000000-7_conjugrad_kernels.cpp1.ii". Compilation terminated. CMake Error at conjugrad_generated_conjugrad_kernels.cu.o.cmake:282 (message): Error generating file /home/rakesh/WORK/Softwares/Coevolution_Softwares/CCMpred/lib/libconjugrad/CMakeFiles/conjugrad.dir/src/./conjugrad_generated_conjugrad_kernels.cu.o

make[2]: [lib/libconjugrad/CMakeFiles/conjugrad.dir/build.make:65: lib/libconjugrad/CMakeFiles/conjugrad.dir/src/conjugrad_generated_conjugrad_kernels.cu.o] Error 1 make[1]: [CMakeFiles/Makefile2:157: lib/libconjugrad/CMakeFiles/conjugrad.dir/all] Error 2 make: *** [Makefile:152: all] Error 2