cancerit / BRASS

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
GNU Affero General Public License v3.0
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brass (c++): building failed, rearrgroup.cpp issues #35

Closed nvolkova closed 8 years ago

nvolkova commented 8 years ago

When trying to build the last released version, ./setup.sh fails on "brass (c++)" step. When I try to run the commands from setup.sh brass block manually, I constantly get errors:

make -C cansam requires boost/version.hpp in the same folder, so I have copied the boost folder in there make -C c++ reports a variety of mistakes in rearrgroup.cpp and numerous warnings in alignment.h, such as:

c++ -Wall -Wextra -g -I../cansam -O2   -c -o rearrgroup.o rearrgroup.cpp
rearrgroup.cpp:172:7: error: invalid operands to binary expression ('std::ostream' (aka 'basic_ostream<char>') and 'const char *')
  out << aln.rname_c_str() << '\t' << aln.strand_char() << '\t'
  ~~~ ^  ~~~~~~~~~~~~~~~~~
../cansam/cansam/sam/header.h:340:15: note: candidate function not viable: no known conversion from 'const char *' to 'const sam::header' for 2nd argument
std::ostream& operator<< (std::ostream& stream, const header& header);
              ^
../cansam/cansam/sam/header.h:352:15: note: candidate function not viable: no known conversion from 'const char *' to 'const header::tagfield' for 2nd argument
std::ostream& operator<< (std::ostream& stream, const header::tagfield& field);
              ^
../cansam/cansam/sam/header.h:355:15: note: candidate function not viable: no known conversion from 'const char *' to 'header::const_iterator' for 2nd argument
std::ostream& operator<< (std::ostream& stream, header::const_iterator it);
              ^
../cansam/cansam/sam/header.h:611:15: note: candidate function not viable: no known conversion from 'const char *' to 'const sam::collection' for 2nd argument
std::ostream& operator<< (std::ostream& stream, const collection& headers);
              ^
../cansam/cansam/sam/alignment.h:751:15: note: candidate function not viable: no known conversion from 'const char *' to 'const sam::alignment' for 2nd argument
std::ostream& operator<< (std::ostream& stream, const alignment& aln);
              ^
../cansam/cansam/sam/alignment.h:777:15: note: candidate function not viable: no known conversion from 'const char *' to 'const alignment::tagfield' for 2nd argument
std::ostream& operator<< (std::ostream& stream, const alignment::tagfield& aux);
              ^
../cansam/cansam/sam/alignment.h:785:15: note: candidate function not viable: no known conversion from 'const char *' to 'alignment::const_iterator' for 2nd argument
std::ostream& operator<< (std::ostream& stream, alignment::const_iterator it);

Please tell me how can I fix that.