problems building simd_alignment_engine.cpp.o

[baverhey]

make Scanning dependencies of target edlib_static [ 2%] Building CXX object vendor/edlib/CMakeFiles/edlib_static.dir/edlib/src/edlib.cpp.o [ 5%] Linking CXX static library ../../lib/libedlib_static.a [ 5%] Built target edlib_static Scanning dependencies of target zlibstatic [ 8%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/adler32.o [ 11%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/compress.o [ 14%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/crc32.o [ 17%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/deflate.o [ 20%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzclose.o [ 22%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzlib.o [ 25%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzread.o [ 28%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzwrite.o [ 31%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inflate.o [ 34%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/infback.o [ 37%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inftrees.o [ 40%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inffast.o [ 42%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/trees.o [ 45%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/uncompr.o [ 48%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/zutil.o [ 51%] Linking C static library ../../lib/libz.a [ 51%] Built target zlibstatic Scanning dependencies of target spoa [ 54%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o [ 57%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/graph.cpp.o [ 60%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/simd_alignment_engine.cpp.o /usr/local/bioinf/racon/vendor/spoa/src/simd_alignment_engine.cpp:313:30: warning: ignoring attributes on template argument ‘spoa::mxxxi [] {aka vector(2) long long int []}’ [-Wignored-attributes] std::unique_ptr<mxxxi[]> sequence_profile_storage; ^ /usr/local/bioinf/racon/vendor/spoa/src/simd_alignment_engine.cpp:318:30: warning: ignoring attributes on template argument ‘spoa::mxxxi [] {aka vector(2) long long int []}’ [-Wignored-attributes] std::unique_ptr<__mxxxi[]> M_storage; ^ /usr/local/bioinf/racon/vendor/spoa/src/simd_alignment_engine.cpp:322:30: warning: ignoring attributes on template argument ‘spoa::mxxxi [] {aka vector(2) long long int []}’ [-Wignored-attributes] std::unique_ptr<__mxxxi[]> masks_storage; ^ /usr/local/bioinf/racon/vendor/spoa/src/simd_alignment_engine.cpp:326:30: warning: ignoring attributes on template argument ‘spoa::mxxxi [] {aka vector(2) long long int []}’ [-Wignored-attributes] std::unique_ptr<mxxxi[]> penalties_storage; ^ /usr/local/bioinf/racon/vendor/spoa/src/simd_alignment_engine.cpp: In member function ‘void spoa::SimdAlignmentEngine::realloc(uint32_t, uint32_t, uint32_t)’: /usr/local/bioinf/racon/vendor/spoa/src/simd_alignment_engine.cpp:386:69: warning: ignoring attributes on template argument ‘spoa::mxxxi [] {aka vector(2) long long int []}’ [-Wignored-attributes] pimpl_->sequence_profile_storage = std::unique_ptr<mxxxi[]>(storage); ^ /usr/local/bioinf/racon/vendor/spoa/src/simd_alignmentengine.cpp:397:54: warning: ignoring attributes on template argument ‘spoa::mxxxi [] {aka vector(2) long long int []}’ [-Wignored-attributes] pimpl->M_storage = std::unique_ptr<mxxxi[]>(storage); ^ /usr/local/bioinf/racon/vendor/spoa/src/simd_alignmentengine.cpp:405:58: warning: ignoring attributes on template argument ‘spoa::mxxxi [] {aka vector(2) long long int []}’ [-Wignored-attributes] pimpl->masks_storage = std::unique_ptr<mxxxi[]>(storage); ^ /usr/local/bioinf/racon/vendor/spoa/src/simd_alignment_engine.cpp:413:62: warning: ignoring attributes on template argument ‘spoa::mxxxi [] {aka _vector(2) long long int []}’ [-Wignored-attributes] pimpl->penalties_storage = std::unique_ptr<__mxxxi[]>(storage); ^ [ 62%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o [ 65%] Linking CXX static library lib/libspoa.a [ 65%] Built target spoa Scanning dependencies of target thread_pool [ 68%] Building CXX object vendor/thread_pool/CMakeFiles/thread_pool.dir/src/thread_pool.cpp.o [ 71%] Linking CXX static library lib/libthread_pool.a [ 71%] Built target thread_pool Scanning dependencies of target racon [ 74%] Building CXX object CMakeFiles/racon.dir/src/main.cpp.o [ 77%] Building CXX object CMakeFiles/racon.dir/src/polisher.cpp.o [ 80%] Building CXX object CMakeFiles/racon.dir/src/overlap.cpp.o [ 82%] Building CXX object CMakeFiles/racon.dir/src/sequence.cpp.o [ 85%] Building CXX object CMakeFiles/racon.dir/src/window.cpp.o [ 88%] Linking CXX executable bin/racon [ 88%] Built target racon Scanning dependencies of target rampler [ 91%] Building CXX object vendor/rampler/CMakeFiles/rampler.dir/src/main.cpp.o [ 94%] Building CXX object vendor/rampler/CMakeFiles/rampler.dir/src/sequence.cpp.o [ 97%] Building CXX object vendor/rampler/CMakeFiles/rampler.dir/src/sampler.cpp.o [100%] Linking CXX executable bin/rampler [100%] Built target rampler

[rvaser]

Hello, you can ignore those warning as the build process has finished.

Best regards, Robert

[baverhey]

Ohh Fast response! Good news but we have problems running unicyler

'Error: Racon was found but does not produce output' Also does not respond to the --version but racon -h works as expected

We tried with racon_wrapper and withoud

Met vriendelijke groeten, Bart Verheyde Leopard Solutions Webdesign and IT- Consulting

[rvaser]

Hmmm, not sure why that would happen. Did you try raising an issue at Unicycler repository? You can also try building and running racon_test to see if racon works properly on your machine.