GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
This is what I did - Cloned the GraphMap repository using GIT to my desktop. Then I change dir to GraphMap folder. The I ran the "make modules" command - which completed successfully. Then I ran the "make" command, which ends with an error (‘vasprintf’ was not declared in this scope).
Here is the error that I get:
$ make
Makefile:100: " WARNING g++ minor version <7 "
mkdir -p obj_linux/codebase/seqlib/src/log_system/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/in clude/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seq lib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebas e/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -O3 -fdata-sections -ffunct ion-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werr or=return-type -pthread -o obj_linux/codebase/seqlib/src/log_system/log_system. o codebase/seqlib/src/log_system/log_system.cc
codebase/seqlib/src/log_system/log_system.cc: In member function ‘std::string Lo gSystem::GenerateErrorMessage(uint32_t, const char, ...)’:
codebase/seqlib/src/log_system/log_system.cc:36:16: error: ‘vasprintf’ was not d eclared in this scope
int ret_va = vasprintf(&formatted_c_string, additional_message, args);
^~~~~
codebase/seqlib/src/log_system/log_system.cc:36:16: note: suggested alternative: ‘vsprintf’
int ret_va = vasprintf(&formatted_c_string, additional_message, args);
^~~~~
vsprintf
codebase/seqlib/src/log_system/log_system.cc: In static member function ‘static std::string LogSystem::FormatString(const char, ...)’:
codebase/seqlib/src/log_system/log_system.cc:292:16: error: ‘vasprintf’ was not declared in this scope
int ret_va = vasprintf(&formatted_string, additional_message, args);
^~~~~
codebase/seqlib/src/log_system/log_system.cc:292:16: note: suggested alternative : ‘vsprintf’
int ret_va = vasprintf(&formatted_string, additional_message, args);
^~~~~
vsprintf
make: *** [Makefile:124: obj_linux/codebase/seqlib/src/log_system/log_system.o] Error 1
Hi. I am having trouble compiling GraphMap.
This is what I did - Cloned the GraphMap repository using GIT to my desktop. Then I change dir to GraphMap folder. The I ran the "make modules" command - which completed successfully. Then I ran the "make" command, which ends with an error (‘vasprintf’ was not declared in this scope).
Here is the error that I get:
$ make Makefile:100: " WARNING g++ minor version <7 " mkdir -p obj_linux/codebase/seqlib/src/log_system/ g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/in clude/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seq lib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebas e/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -O3 -fdata-sections -ffunct ion-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werr or=return-type -pthread -o obj_linux/codebase/seqlib/src/log_system/log_system. o codebase/seqlib/src/log_system/log_system.cc codebase/seqlib/src/log_system/log_system.cc: In member function ‘std::string Lo gSystem::GenerateErrorMessage(uint32_t, const char, ...)’: codebase/seqlib/src/log_system/log_system.cc:36:16: error: ‘vasprintf’ was not d eclared in this scope int ret_va = vasprintf(&formatted_c_string, additional_message, args); ^
~~~~ codebase/seqlib/src/log_system/log_system.cc:36:16: note: suggested alternative: ‘vsprintf’ int ret_va = vasprintf(&formatted_c_string, additional_message, args); ^~~~~ vsprintf codebase/seqlib/src/log_system/log_system.cc: In static member function ‘static std::string LogSystem::FormatString(const char, ...)’: codebase/seqlib/src/log_system/log_system.cc:292:16: error: ‘vasprintf’ was not declared in this scope int ret_va = vasprintf(&formatted_string, additional_message, args); ^~~~~ codebase/seqlib/src/log_system/log_system.cc:292:16: note: suggested alternative : ‘vsprintf’ int ret_va = vasprintf(&formatted_string, additional_message, args); ^~~~~ vsprintf make: *** [Makefile:124: obj_linux/codebase/seqlib/src/log_system/log_system.o] Error 1