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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 error #95

Closed jjenny closed 5 years ago

jjenny commented 5 years ago

Hi,

I'm using GCC v5.1 and cmake v3.13 and running into the following error when I try to install racon:

Scanning dependencies of target edlib_static
[  3%] Building CXX object vendor/edlib/CMakeFiles/edlib_static.dir/edlib/src/edlib.cpp.o
[  6%] Linking CXX static library ../../lib/libedlib_static.a
[  6%] Built target edlib_static
Scanning dependencies of target zlibstatic
[  9%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/adler32.o
[ 12%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/compress.o
[ 16%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/crc32.o
[ 19%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/deflate.o
[ 22%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzclose.o
[ 25%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzlib.o
[ 29%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzread.o
[ 32%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzwrite.o
[ 35%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inflate.o
[ 38%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/infback.o
[ 41%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inftrees.o
[ 45%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inffast.o
[ 48%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/trees.o
[ 51%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/uncompr.o
[ 54%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/zutil.o
[ 58%] Linking C static library ../../lib/libz.a
[ 58%] Built target zlibstatic
Scanning dependencies of target spoa
[ 61%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o
In file included from /projects/Zoo/ddRAD/racon/vendor/spoa/src/sisd_alignment_engine.hpp:15,
                 from /projects/Zoo/ddRAD/racon/vendor/spoa/src/alignment_engine.cpp:11:
/projects/Zoo/ddRAD/racon/vendor/spoa/include/spoa/alignment_engine.hpp:24: error: expected nested-name-specifier before ‘Alignment’
/projects/Zoo/ddRAD/racon/vendor/spoa/include/spoa/alignment_engine.hpp:24: error: ‘Alignment’ has not been declared
/projects/Zoo/ddRAD/racon/vendor/spoa/include/spoa/alignment_engine.hpp:24: error: expected ‘;’ before ‘=’ token
/projects/Zoo/ddRAD/racon/vendor/spoa/include/spoa/alignment_engine.hpp:24: error: expected unqualified-id before ‘=’ token
/projects/Zoo/ddRAD/racon/vendor/spoa/include/spoa/alignment_engine.hpp:36: error: ‘Alignment’ does not name a type
/projects/Zoo/ddRAD/racon/vendor/spoa/include/spoa/alignment_engine.hpp:39: error: ‘Alignment’ does not name a type
In file included from /projects/Zoo/ddRAD/racon/vendor/spoa/src/alignment_engine.cpp:11:
/projects/Zoo/ddRAD/racon/vendor/spoa/src/sisd_alignment_engine.hpp:29: error: expected ‘;’ before ‘override’
/projects/Zoo/ddRAD/racon/vendor/spoa/src/sisd_alignment_engine.hpp:31: error: ‘Alignment’ does not name a type
/projects/Zoo/ddRAD/racon/vendor/spoa/src/sisd_alignment_engine.hpp:42: error: ‘Alignment’ does not name a type
/projects/Zoo/ddRAD/racon/vendor/spoa/src/sisd_alignment_engine.hpp:49: error: expected ‘;’ before ‘noexcept’
In file included from /projects/Zoo/ddRAD/racon/vendor/spoa/src/alignment_engine.cpp:12:
/projects/Zoo/ddRAD/racon/vendor/spoa/src/simd_alignment_engine.hpp:29: error: expected ‘;’ before ‘override’
/projects/Zoo/ddRAD/racon/vendor/spoa/src/simd_alignment_engine.hpp:31: error: ‘Alignment’ does not name a type
/projects/Zoo/ddRAD/racon/vendor/spoa/src/simd_alignment_engine.hpp:43: error: expected constructor, destructor, or type conversion before ‘align’
/projects/Zoo/ddRAD/racon/vendor/spoa/src/simd_alignment_engine.hpp:52: error: expected initializer before ‘noexcept’
/projects/Zoo/ddRAD/racon/vendor/spoa/src/alignment_engine.cpp: In function ‘std::unique_ptr<spoa::AlignmentEngine, std::default_delete<spoa::AlignmentEngine> > spoa::createAlignmentEngine(spoa::AlignmentType, int8_t, int8_t, int8_t)’:
/projects/Zoo/ddRAD/racon/vendor/spoa/src/alignment_engine.cpp:39: error: ‘nullptr’ was not declared in this scope
/projects/Zoo/ddRAD/racon/vendor/spoa/src/alignment_engine.cpp: At global scope:
/projects/Zoo/ddRAD/racon/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 5 years ago

Hi Jenny, please run make VERBOSE=1 and copy the output here (I suspect that CMake has picked up the wrong compiler).

Best regards, Robert

jjenny commented 5 years ago

Ah, found a related answer (https://github.com/isovic/racon/issues/82) which fixed my problem. Thanks!