Install error: ‘Alignment’ has not been declared

[shaohaojing]

Hi rvaser,

I try to install the tool and get these errors. Do you know how to fix it? Thanks, Haojing

io2 09:37:11 ~/bin/spoa/build $ make [ 33%] Building CXX object CMakeFiles/spoa.dir/src/alignment_engine.cpp.o In file included from /public/home/shaohaojing/bin/spoa/src/alignment_engine.cpp:3: /public/home/shaohaojing/bin/spoa/include/spoa/alignment_engine.hpp:29: error: expected nested-name-specifier before ‘Alignment’ /public/home/shaohaojing/bin/spoa/include/spoa/alignment_engine.hpp:29: error: ‘Alignment’ has not been declared /public/home/shaohaojing/bin/spoa/include/spoa/alignment_engine.hpp:29: error: expected ‘;’ before ‘=’ token /public/home/shaohaojing/bin/spoa/include/spoa/alignment_engine.hpp:29: error: expected unqualified-id before ‘=’ token /public/home/shaohaojing/bin/spoa/include/spoa/alignment_engine.hpp:61: error: ‘Alignment’ does not name a type /public/home/shaohaojing/bin/spoa/include/spoa/alignment_engine.hpp:66: error: ‘Alignment’ does not name a type In file included from /public/home/shaohaojing/bin/spoa/src/alignment_engine.cpp:10: /public/home/shaohaojing/bin/spoa/src/sisd_alignment_engine.hpp:20: error: ‘spoa::SisdAlignmentEngine::SisdAlignmentEngine(spoa::SisdAlignmentEngine&&)’ cannot be defaulted /public/home/shaohaojing/bin/spoa/src/sisd_alignment_engine.hpp:21: error: ‘spoa::SisdAlignmentEngine& spoa::SisdAlignmentEngine::operator=(spoa::SisdAlignmentEngine&&)’ cannot be defaulted /public/home/shaohaojing/bin/spoa/src/sisd_alignment_engine.hpp:37: error: expected ‘;’ before ‘override’ /public/home/shaohaojing/bin/spoa/src/sisd_alignment_engine.hpp:39: error: ‘Alignment’ does not name a type /public/home/shaohaojing/bin/spoa/src/sisd_alignment_engine.hpp:55: error: ‘Alignment’ does not name a type /public/home/shaohaojing/bin/spoa/src/sisd_alignment_engine.hpp:60: error: ‘Alignment’ does not name a type /public/home/shaohaojing/bin/spoa/src/sisd_alignment_engine.hpp:65: error: ‘Alignment’ does not name a type /public/home/shaohaojing/bin/spoa/src/sisd_alignment_engine.hpp:77: error: expected ‘;’ before ‘noexcept’ In file included from /public/home/shaohaojing/bin/spoa/src/alignment_engine.cpp:11: /public/home/shaohaojing/bin/spoa/src/simd_alignment_engine.hpp:34: error: ‘spoa::SimdAlignmentEngine::SimdAlignmentEngine(spoa::SimdAlignmentEngine&&)’ cannot be defaulted /public/home/shaohaojing/bin/spoa/src/simd_alignment_engine.hpp:51: error: expected ‘;’ before ‘override’ /public/home/shaohaojing/bin/spoa/src/simd_alignment_engine.hpp:53: error: ‘Alignment’ does not name a type /public/home/shaohaojing/bin/spoa/src/simd_alignment_engine.hpp:80: error: expected constructor, destructor, or type conversion before ‘Linear’ /public/home/shaohaojing/bin/spoa/src/simd_alignment_engine.hpp:86: error: expected constructor, destructor, or type conversion before ‘Affine’ /public/home/shaohaojing/bin/spoa/src/simd_alignment_engine.hpp:92: error: expected constructor, destructor, or type conversion before ‘Convex’ /public/home/shaohaojing/bin/spoa/src/simd_alignment_engine.hpp:108: error: expected initializer before ‘noexcept’ /public/home/shaohaojing/bin/spoa/src/alignment_engine.cpp:94: error: ‘Alignment’ does not name a type /public/home/shaohaojing/bin/spoa/src/alignment_engine.cpp: In member function ‘int64_t spoa::AlignmentEngine::WorstCaseAlignmentScore(int64_t, int64_t) const’: /public/home/shaohaojing/bin/spoa/src/alignment_engine.cpp:104: error: expected primary-expression before ‘[’ token /public/home/shaohaojing/bin/spoa/src/alignment_engine.cpp:104: error: expected primary-expression before ‘]’ token /public/home/shaohaojing/bin/spoa/src/alignment_engine.cpp:104: error: expected primary-expression before ‘len’ /public/home/shaohaojing/bin/spoa/src/alignment_engine.cpp:104: error: unable to deduce ‘auto’ from ‘’ /public/home/shaohaojing/bin/spoa/src/alignment_engine.cpp:104: error: expected ‘,’ or ‘;’ before ‘{’ token make[2]: [CMakeFiles/spoa.dir/src/alignment_engine.cpp.o] Error 1 make[1]: [CMakeFiles/spoa.dir/all] Error 2 make: *** [all] Error 2

Hi Haojing, please check your compiler version. If you have a newer one, please check whether it is picked up by cmake by running make VERBOSE=1 (it will print the gcc/g++ path found).

Best regards, Robert

[shaohaojing]

Hi Robert, I fix the old one by updating cmake and gcc version. But I get another one. Do you have some ideas on it? Thanks, Haojing

In file included from /public/home/shaohaojing/bin/spoa/vendor/bioparser/include/bioparser/fasta_parser.hpp:12:0, from /public/home/shaohaojing/bin/spoa/src/main.cpp:5: /public/home/shaohaojing/bin/spoa/vendor/bioparser/include/bioparser/parser.hpp:123:19: error: 'gzFile_s' was not declared in this scope std::unique_ptr<gzFiles, int(*)(gzFile)> file; ^ /public/home/shaohaojing/bin/spoa/vendor/bioparser/include/bioparser/parser.hpp:123:43: error: template argument 1 is invalid std::unique_ptr<gzFiles, int(*)(gzFile)> file; ^

[rvaser]

Hi Haojing, please update zlib.

Best regards, Robert