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Description
I am trying to complile the latest famsa in Ubuntu 22, but I keep getting the following error:
~/Downloads/FAMSA (master ✔) make
*** Detecting g++ version 11 ***
*** x86-64 with AVX2 extensions***
make -C libs/libdeflate
make[1]: Entering directory '/home/fer/Downloads/FAMSA/libs/libdeflate'
CC lib/deflate_decompress.o
CC lib/utils.o
CC lib/arm/cpu_features.o
CC lib/x86/cpu_features.o
CC lib/deflate_compress.o
CC lib/adler32.o
CC lib/zlib_decompress.o
CC lib/zlib_compress.o
CC lib/crc32.o
CC lib/gzip_decompress.o
CC lib/gzip_compress.o
AR libdeflate.a
CC lib/deflate_decompress.shlib.o
CC lib/utils.shlib.o
CC lib/arm/cpu_features.shlib.o
CC lib/x86/cpu_features.shlib.o
CC lib/deflate_compress.shlib.o
CC lib/adler32.shlib.o
CC lib/zlib_decompress.shlib.o
CC lib/zlib_compress.shlib.o
CC lib/crc32.shlib.o
CC lib/gzip_decompress.shlib.o
CC lib/gzip_compress.shlib.o
CCLD libdeflate.so.0
LN libdeflate.so
GEN programs/config.h
CC programs/gzip.o
CC programs/prog_util.o
CC programs/tgetopt.o
CCLD gzip
LN gunzip
make[1]: Leaving directory '/home/fer/Downloads/FAMSA/libs/libdeflate'
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/famsa.cpp -o src/famsa.o
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/msa.cpp -o src/msa.o
src/msa.cpp: In member function ‘void CFAMSA::sortAndExtendSequences(std::vector<CSequence>&)’:
src/msa.cpp:255:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CSequence*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
255 | for (int i = 0; i < seq_ptrs.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~~
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/msa_refinement.cpp -o src/msa_refinement.o
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/tree/AbstractTreeGenerator.cpp -o src/tree/AbstractTreeGenerator.o
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/tree/Clustering.cpp -o src/tree/Clustering.o
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/tree/DistanceCalculator.cpp -o src/tree/DistanceCalculator.o
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/tree/FastTree.cpp -o src/tree/FastTree.o
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/tree/GuideTree.cpp -o src/tree/GuideTree.o
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/tree/MSTPrim.cpp -o src/tree/MSTPrim.o
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/tree/NeighborJoining.cpp -o src/tree/NeighborJoining.o
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/tree/NewickParser.cpp -o src/tree/NewickParser.o
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/tree/SingleLinkage.cpp -o src/tree/SingleLinkage.o
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/tree/UPGMA.cpp -o src/tree/UPGMA.o
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/utils/timer.cpp -o src/utils/timer.o
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/utils/log.cpp -o src/utils/log.o
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/core/io_service.cpp -o src/core/io_service.o
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/core/params.cpp -o src/core/params.o
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/core/profile.cpp -o src/core/profile.o
g++ -Wall -Wno-char-subscripts -Wno-attributes -O3 -msse4 -DSIMD=2 -DGIT_COMMIT=7eb7612 -std=c++20 -pthread -I libs -c src/core/profile_par.cpp -o src/core/profile_par.o
In file included from libs/../libs/atomic_wait/barrier:28,
from src/core/profile_par.cpp:39:
libs/../libs/atomic_wait/atomic_wait:355:16: error: redefinition of ‘template<class _Tp> void std::atomic_notify_one(const std::atomic<_ITp>*)’
355 | __ABI void atomic_notify_one(atomic<_Tp> const* a) {
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/stop_token:34,
from /usr/include/c++/11/thread:40,
from src/core/../core/queues.h:12,
from src/core/profile_par.cpp:13:
/usr/include/c++/11/atomic:1424:5: note: ‘template<class _Tp> void std::atomic_notify_one(const std::atomic<_ITp>*)’ previously declared here
1424 | atomic_notify_one(const atomic<_Tp>* __a) noexcept
| ^~~~~~~~~~~~~~~~~
In file included from libs/../libs/atomic_wait/barrier:28,
from src/core/profile_par.cpp:39:
libs/../libs/atomic_wait/atomic_wait:359:16: error: redefinition of ‘template<class _Tp> void std::atomic_notify_all(const std::atomic<_ITp>*)’
359 | __ABI void atomic_notify_all(atomic<_Tp> const* a) {
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/stop_token:34,
from /usr/include/c++/11/thread:40,
from src/core/../core/queues.h:12,
from src/core/profile_par.cpp:13:
/usr/include/c++/11/atomic:1429:5: note: ‘template<class _Tp> void std::atomic_notify_all(const std::atomic<_ITp>*)’ previously declared here
1429 | atomic_notify_all(const atomic<_Tp>* __a) noexcept
| ^~~~~~~~~~~~~~~~~
In file included from src/core/profile_par.cpp:39:
libs/../libs/atomic_wait/barrier: In instantiation of ‘size_t barrier<CompletionF>::__get_id(barrier<CompletionF>::__phase_t, ptrdiff_t) [with CompletionF = EmptyCompletionF; size_t = long unsigned int; barrier<CompletionF>::__phase_t = unsigned char; ptrdiff_t = long int]’:
libs/../libs/atomic_wait/barrier:112:18: required from ‘barrier<CompletionF>::arrival_token barrier<CompletionF>::arrive(ptrdiff_t) [with CompletionF = EmptyCompletionF; barrier<CompletionF>::arrival_token = std::tuple<std::atomic<unsigned char>&, unsigned char>; ptrdiff_t = long int]’
libs/../libs/atomic_wait/barrier:154:14: required from ‘void barrier<CompletionF>::arrive_and_wait() [with CompletionF = EmptyCompletionF]’
src/core/profile_par.cpp:327:24: required from here
libs/../libs/atomic_wait/barrier:71:19: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘ptrdiff_t’ {aka ‘long int’} [-Wsign-compare]
71 | if(id > count)
| ~~~^~~~~~~
make: *** [makefile:227: src/core/profile_par.o] Error 1
Same error replicated in different Ubuntu 22 computers. Any help on how to fix this will be gratly appreciated. I noticed a similiar issue reported elsewhere (#37), but I couldn't get a fix from there.