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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
271 stars 49 forks source link

make failure #82

Closed weiminlee1 closed 6 years ago

weiminlee1 commented 6 years ago

Dear sir: my gcc version is 4.9.0 and cmake version is 3.11.4. i followed the installation command to install racon, however, when i processed the make step, the error appeared as follows. And i am a fresher in bioinformatics, would you mind telling me the methods to solve this problem. i am look forward to hear from you soon. thank you weimin

c/alignment_engine.cpp:11: /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/include/spoa/alignment_e ngine.hpp:24: error: expected nested-name-specifier before ‘Alignment’ /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/include/spoa/alignment_e ngine.hpp:24: error: ‘Alignment’ has not been declared /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/include/spoa/alignment_e ngine.hpp:24: error: expected ‘;’ before ‘=’ token /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/include/spoa/alignment_e ngine.hpp:24: error: expected unqualified-id before ‘=’ token /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/include/spoa/alignment_e ngine.hpp:36: error: ‘Alignment’ does not name a type /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/include/spoa/alignment_e ngine.hpp:39: error: ‘Alignment’ does not name a type In file included from /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/sr c/alignment_engine.cpp:11: /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/src/sisd_alignment_engin e.hpp:29: error: expected ‘;’ before ‘override’ /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/src/sisd_alignment_engin e.hpp:31: error: ‘Alignment’ does not name a type /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/src/sisd_alignment_engin e.hpp:42: error: ‘Alignment’ does not name a type /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/src/sisd_alignment_engin e.hpp:49: error: expected ‘;’ before ‘noexcept’ In file included from /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/sr c/alignment_engine.cpp:12: /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/src/simd_alignment_engin e.hpp:29: error: expected ‘;’ before ‘override’ /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/src/simd_alignment_engin e.hpp:31: error: ‘Alignment’ does not name a type /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/src/simd_alignment_engin e.hpp:43: error: expected constructor, destructor, or type conversion before ‘align ’ /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/src/simd_alignment_engin e.hpp:52: error: expected initializer before ‘noexcept’ /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/src/alignment_engine.cpp : In function ‘std::unique_ptr<spoa::AlignmentEngine, std::default_delete > spoa::createAlignmentEngine(spoa::AlignmentType, int8_t, int8_t, in t8_t)’: /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/src/alignment_engine.cpp :39: error: ‘nullptr’ was not declared in this scope /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/src/alignment_engine.cpp : At global scope: /public1/home/stu_liuyanhui/tools/racon-v1.3.1/vendor/spoa/src/alignment_engine.cpp :52: error: ‘Alignment’ does not name a type make[2]: [vendor/spoa/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o] Error 1 make[1]: [vendor/spoa/CMakeFiles/spoa.dir/all] Error 2 make: *** [all] Error 2

rvaser commented 6 years ago

Hello Weimin, I think that cmake picked up another compiler which has a lower version. Run which gcc and use the path you get while running cmake cmake -DCMAKE_C_COMPILER=<paste path here> ...

Best regards, Robert

P.S. You might need to add the g++ compiler as well with the following flag -DCMAKE_CXX_COMPILER=<output of 'which g++'>.

weiminlee1 commented 6 years ago

Hello Robert, thank you for your help firstly. I followed your instruction, but new problems still exist. sorry to bother you again.

Weimin

Scanning dependencies of target spoa [ 61%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o [ 64%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/graph.cpp.o /tmp/ccTXjwsu.s: Assembler messages: /tmp/ccTXjwsu.s:743: Error: no such instruction: shlx %rax,%rdx,%rdx' /tmp/ccTXjwsu.s:998: Error: no such instruction:shlx %rax,%rdx,%rdx' make[2]: [vendor/spoa/CMakeFiles/spoa.dir/src/graph.cpp.o] Error 1 make[1]: [vendor/spoa/CMakeFiles/spoa.dir/all] Error 2 make: *** [all] Error 2

rvaser commented 6 years ago

Hi Weimin, it seems that your assembler is out of date. You can either update it or you can try adding -DCMAKE_CXX_FLAGS="-mno-avx2" while running cmake.

Best regards, Robert

weiminlee1 commented 6 years ago

Hello Robert, thank you for your instruction anyway. I tried your recommend, but install unsuccessfully. Finally, I used BIOCONDA to install racon successfully.

Best wishes, Weimin