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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 make error #190

Closed zzzqiii closed 3 years ago

zzzqiii commented 3 years ago

On trying to make racon-v1.4.21 on Red Hat 6.6, I got the following error: [ 0%] Building CXX object vendor/edlib/CMakeFiles/edlib_static.dir/edlib/src/edlib.cpp.o [ 0%] Linking CXX static library ../../lib/libedlib_static.a [ 0%] Built target edlib_static [ 0%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o In file included from /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/alignment_engine.cpp:3: /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/include/spoa/alignment_engine.hpp:29: error: expected nested-name-specifier before 'Alignment' /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/include/spoa/alignment_engine.hpp:29: error: 'Alignment' has not been declared /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/include/spoa/alignment_engine.hpp:29: error: expected ';' before '=' token /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/include/spoa/alignment_engine.hpp:29: error: expected unqualified-id before '=' token /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/include/spoa/alignment_engine.hpp:61: error: 'Alignment' does not name a type /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/include/spoa/alignment_engine.hpp:66: error: 'Alignment' does not name a type In file included from /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/alignment_engine.cpp:10: /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/sisd_alignment_engine.hpp:20: error: 'spoa::SisdAlignmentEngine::SisdAlignmentEngine(spoa::SisdAlignmentEngine&&)' cannot be defaulted /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/sisd_alignment_engine.hpp:21: error: 'spoa::SisdAlignmentEngine& spoa::SisdAlignmentEngine::operator=(spoa::SisdAlignmentEngine&&)' cannot be defaulted /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/sisd_alignment_engine.hpp:37: error: expected ';' before 'override' /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/sisd_alignment_engine.hpp:39: error: 'Alignment' does not name a type /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/sisd_alignment_engine.hpp:55: error: 'Alignment' does not name a type /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/sisd_alignment_engine.hpp:60: error: 'Alignment' does not name a type /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/sisd_alignment_engine.hpp:65: error: 'Alignment' does not name a type /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/sisd_alignment_engine.hpp:77: error: expected ';' before 'noexcept' In file included from /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/alignment_engine.cpp:11: /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/simd_alignment_engine.hpp:34: error: 'spoa::SimdAlignmentEngine::SimdAlignmentEngine(spoa::SimdAlignmentEngine&&)' cannot be defaulted /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/simd_alignment_engine.hpp:51: error: expected ';' before 'override' /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/simd_alignment_engine.hpp:53: error: 'Alignment' does not name a type /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/simd_alignment_engine.hpp:80: error: expected constructor, destructor, or type conversion before 'Linear' /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/simd_alignment_engine.hpp:86: error: expected constructor, destructor, or type conversion before 'Affine' /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/simd_alignment_engine.hpp:92: error: expected constructor, destructor, or type conversion before 'Convex' /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/simd_alignment_engine.hpp:108: error: expected initializer before 'noexcept' /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/alignment_engine.cpp:94: error: 'Alignment' does not name a type /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/alignment_engine.cpp: In member function 'int64_t spoa::AlignmentEngine::WorstCaseAlignmentScore(int64_t, int64_t) const': /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/alignment_engine.cpp:104: error: expected primary-expression before '[' token /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/alignment_engine.cpp:104: error: expected primary-expression before ']' token /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/alignment_engine.cpp:104: error: expected primary-expression before 'len' /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/alignment_engine.cpp:104: error: unable to deduce 'auto' from '' /public/home/zuozhangqi/software/racon-v1.4.21/vendor/spoa/src/alignment_engine.cpp:104: error: expected ',' or ';' before '{' token 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

When building racon by cmake -DCMAKE_BUILD_TYPE=Release .., it seemed no error with following output: -- The C compiler identification is GNU 4.4.7 -- The CXX compiler identification is GNU 4.4.7 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found ZLIB: /usr/local/lib/libz.so (found version "1.2.8")
CMake Deprecation Warning at vendor/spoa/vendor/cereal/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Warning (dev) at vendor/spoa/vendor/cereal/CMakeLists.txt:2 (project): Policy CMP0048 is not set: project() command manages VERSION variables. Run "cmake --help-policy CMP0048" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The following variable(s) would be set to empty: PROJECT_VERSION PROJECT_VERSION_MAJOR PROJECT_VERSION_MINOR PROJECT_VERSION_PATCH This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/local/lib/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: serialization
-- boost_variant.cpp -- Found Doxygen: /usr/bin/doxygen (found version "1.6.1") found components: doxygen dot
-- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Check if compiler accepts -pthread -- Check if compiler accepts -pthread - yes -- Found Threads: TRUE
Setting warning flags -- Configuring done -- Generating done -- Build files have been written to: /public/home/zuozhangqi/software/racon-v1.4.21/build

The gcc version is 6.4.0, and cmake version is 3.20.0-rc5. I found the issue is same as issue #186, but there is no reply to this error in issue #186, so I open a new issue. Do you have any suggestions on this issue?

rvaser commented 3 years ago

Hello, CMake picks up the older compiler on your system (you can check with make VERBOSE=1 and see the path of gcc/g++ used). To manually set the newer compiler run: cmake -DCMAKE_C_COMPILER=<path to gcc> -DCMAKE_CXX_COMPILER=<path to g++> -DCMAKE_BUILD_TYPE=Release ..

Best regards, Robert

zzzqiii commented 3 years ago

Hello Robert, Thank you very much for quick reply! I solved it successfully.

Best regards!