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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
261 stars 48 forks source link

Racon cmake build error #186

Closed MrDotOne closed 3 years ago

MrDotOne commented 3 years ago

I am trying to build racon on our HPC and get the following error:

[root@cc-dclrilog51 build]# cmake -DCMAKE_INSTALL_PREFIX=/cm/shared/apps/racon/1.4.3 -DCMAKE_BUILD_TYPE=Release .. -- The C compiler identification is GNU 4.4.7 -- The CXX compiler identification is GNU 4.4.7 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done CMakeOutput.log

-- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Error at CMakeLists.txt:51 (add_subdirectory): The source directory

/root/temp/racon-master/vendor/bioparser

does not contain a CMakeLists.txt file.

CMake Error at CMakeLists.txt:54 (add_subdirectory): The source directory

/root/temp/racon-master/vendor/spoa

does not contain a CMakeLists.txt file.

CMake Error at CMakeLists.txt:57 (add_subdirectory): The source directory

/root/temp/racon-master/vendor/thread_pool

does not contain a CMakeLists.txt file.

CMake Error at CMakeLists.txt:60 (add_subdirectory): The source directory

/root/temp/racon-master/vendor/edlib

does not contain a CMakeLists.txt file.

-- Configuring incomplete, errors occurred! See also "/root/temp/racon-master/build/CMakeFiles/CMakeOutput.log".

I have the following environment modules loaded:

[root@cc-dclrilog51 build]# module list Currently Loaded Modulefiles: 1) shared 3) cmsh 5) cluster-tools/7.0 7) cmake/3.9.1 9) python/3.6.2 2) cmgui/7.0 4) cmd 6) slurm/14.03.0 8) gcc/8.3.0 10) minimap2/2.17

Any thoughts?

rvaser commented 3 years ago

Hello, either run git submodule update --init --recursive or download the complete source code from https://github.com/lbcb-sci/racon/releases/download/1.4.20/racon-v1.4.20.tar.gz

Best regards, Robert

MrDotOne commented 3 years ago

Thank you, i will give that a try. OK, that got me through the config phase but it fails to compile with the following:

Scanning dependencies of target spoa [ 59%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o In file included from /root/temp/racon/vendor/spoa/src/sisd_alignment_engine.hpp:14, from /root/temp/racon/vendor/spoa/src/alignment_engine.cpp:12: /root/temp/racon/vendor/spoa/include/spoa/alignment_engine.hpp:30: error: expected nested-name-specifier before ‘Alignment’ /root/temp/racon/vendor/spoa/include/spoa/alignment_engine.hpp:30: error: ‘Alignment’ has not been declared /root/temp/racon/vendor/spoa/include/spoa/alignment_engine.hpp:30: error: expected ‘;’ before ‘=’ token /root/temp/racon/vendor/spoa/include/spoa/alignment_engine.hpp:30: error: expected unqualified-id before ‘=’ token /root/temp/racon/vendor/spoa/include/spoa/alignment_engine.hpp:50: error: ‘Alignment’ does not name a type /root/temp/racon/vendor/spoa/include/spoa/alignment_engine.hpp:53: error: ‘Alignment’ does not name a type In file included from /root/temp/racon/vendor/spoa/src/alignment_engine.cpp:12: /root/temp/racon/vendor/spoa/src/sisd_alignment_engine.hpp:30: error: expected ‘;’ before ‘override’ /root/temp/racon/vendor/spoa/src/sisd_alignment_engine.hpp:32: error: ‘Alignment’ does not name a type /root/temp/racon/vendor/spoa/src/sisd_alignment_engine.hpp:47: error: ‘Alignment’ does not name a type /root/temp/racon/vendor/spoa/src/sisd_alignment_engine.hpp:50: error: ‘Alignment’ does not name a type /root/temp/racon/vendor/spoa/src/sisd_alignment_engine.hpp:53: error: ‘Alignment’ does not name a type /root/temp/racon/vendor/spoa/src/sisd_alignment_engine.hpp:60: error: expected ‘;’ before ‘noexcept’ In file included from /root/temp/racon/vendor/spoa/src/alignment_engine.cpp:13: /root/temp/racon/vendor/spoa/src/simd_alignment_engine.hpp:30: error: expected ‘;’ before ‘override’ /root/temp/racon/vendor/spoa/src/simd_alignment_engine.hpp:32: error: ‘Alignment’ does not name a type /root/temp/racon/vendor/spoa/src/simd_alignment_engine.hpp:48: error: expected constructor, destructor, or type conversion before ‘linear’ /root/temp/racon/vendor/spoa/src/simd_alignment_engine.hpp:52: error: expected constructor, destructor, or type conversion before ‘affine’ /root/temp/racon/vendor/spoa/src/simd_alignment_engine.hpp:56: error: expected constructor, destructor, or type conversion before ‘convex’ /root/temp/racon/vendor/spoa/src/simd_alignment_engine.hpp:65: error: expected initializer before ‘noexcept’ /root/temp/racon/vendor/spoa/src/alignment_engine.cpp: In function ‘std::unique_ptr<spoa::AlignmentEngine, std::default_delete > spoa::createAlignmentEngine(spoa::AlignmentType, int8_t, int8_t, int8_t, int8_t, int8_t, int8_t)’: /root/temp/racon/vendor/spoa/src/alignment_engine.cpp:64: error: ‘nullptr’ was not declared in this scope /root/temp/racon/vendor/spoa/src/alignment_engine.cpp: At global scope: /root/temp/racon/vendor/spoa/src/alignment_engine.cpp:77: 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

zzzqiii commented 3 years ago

Thank you, i will give that a try. OK, that got me through the config phase but it fails to compile with the following:

Scanning dependencies of target spoa [ 59%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o In file included from /root/temp/racon/vendor/spoa/src/sisd_alignment_engine.hpp:14, from /root/temp/racon/vendor/spoa/src/alignment_engine.cpp:12: /root/temp/racon/vendor/spoa/include/spoa/alignment_engine.hpp:30: error: expected nested-name-specifier before ‘Alignment’ /root/temp/racon/vendor/spoa/include/spoa/alignment_engine.hpp:30: error: ‘Alignment’ has not been declared /root/temp/racon/vendor/spoa/include/spoa/alignment_engine.hpp:30: error: expected ‘;’ before ‘=’ token /root/temp/racon/vendor/spoa/include/spoa/alignment_engine.hpp:30: error: expected unqualified-id before ‘=’ token /root/temp/racon/vendor/spoa/include/spoa/alignment_engine.hpp:50: error: ‘Alignment’ does not name a type /root/temp/racon/vendor/spoa/include/spoa/alignment_engine.hpp:53: error: ‘Alignment’ does not name a type In file included from /root/temp/racon/vendor/spoa/src/alignment_engine.cpp:12: /root/temp/racon/vendor/spoa/src/sisd_alignment_engine.hpp:30: error: expected ‘;’ before ‘override’ /root/temp/racon/vendor/spoa/src/sisd_alignment_engine.hpp:32: error: ‘Alignment’ does not name a type /root/temp/racon/vendor/spoa/src/sisd_alignment_engine.hpp:47: error: ‘Alignment’ does not name a type /root/temp/racon/vendor/spoa/src/sisd_alignment_engine.hpp:50: error: ‘Alignment’ does not name a type /root/temp/racon/vendor/spoa/src/sisd_alignment_engine.hpp:53: error: ‘Alignment’ does not name a type /root/temp/racon/vendor/spoa/src/sisd_alignment_engine.hpp:60: error: expected ‘;’ before ‘noexcept’ In file included from /root/temp/racon/vendor/spoa/src/alignment_engine.cpp:13: /root/temp/racon/vendor/spoa/src/simd_alignment_engine.hpp:30: error: expected ‘;’ before ‘override’ /root/temp/racon/vendor/spoa/src/simd_alignment_engine.hpp:32: error: ‘Alignment’ does not name a type /root/temp/racon/vendor/spoa/src/simd_alignment_engine.hpp:48: error: expected constructor, destructor, or type conversion before ‘linear’ /root/temp/racon/vendor/spoa/src/simd_alignment_engine.hpp:52: error: expected constructor, destructor, or type conversion before ‘affine’ /root/temp/racon/vendor/spoa/src/simd_alignment_engine.hpp:56: error: expected constructor, destructor, or type conversion before ‘convex’ /root/temp/racon/vendor/spoa/src/simd_alignment_engine.hpp:65: error: expected initializer before ‘noexcept’ /root/temp/racon/vendor/spoa/src/alignment_engine.cpp: In function ‘std::unique_ptr<spoa::AlignmentEngine, std::default_deletespoa::AlignmentEngine > spoa::createAlignmentEngine(spoa::AlignmentType, int8_t, int8_t, int8_t, int8_t, int8_t, int8_t)’: /root/temp/racon/vendor/spoa/src/alignment_engine.cpp:64: error: ‘nullptr’ was not declared in this scope /root/temp/racon/vendor/spoa/src/alignment_engine.cpp: At global scope: /root/temp/racon/vendor/spoa/src/alignment_engine.cpp:77: 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

Hi, I got the the same error when I tried to make. Have you solved it?

rvaser commented 3 years ago

@MrDotOne, I am sorry but I did not get a notification for your edited question. The error you have means that your compiler does not meet the minimum required version.

@zzzqiii, the same error. I will answer your question in #190.