Erreur de compilation sur macOS

[mgivre]

Erreur lors de la compilation de bpp-seq et bpp-phyl (bppcore ok) Bio++ v3

Environnement :

• OS : MacOS Sequoia 15.6.1
• Architecture : arm64 (Apple M1)
• Compiler : Apple clang version 17.0.0 (clang-1700.0.13.5)
• CMake : version 4.1.2
• Boost : stable 1.89.0 (bottled), HEAD

Commandes :

git clone https://github.com/BioPP/[MODULE_NAME].git
cd [MODULE_NAME]
mkdir build && cd build
cmake -DCMAKE_INSTALL_PREFIX="$HOME/biopp"
-DCMAKE_PREFIX_PATH="$HOME/biopp"
-DCMAKE_OSX_ARCHITECTURES=arm64
..
make -j4

Terminal:

Installation de bpp-seq...
Cloning into 'bpp-seq'...
remote: Enumerating objects: 12040, done.
remote: Counting objects: 100% (358/358), done.
remote: Compressing objects: 100% (70/70), done.
remote: Total 12040 (delta 315), reused 298 (delta 285), pack-reused 11682 (from 4)
Receiving objects: 100% (12040/12040), 3.36 MiB | 23.56 MiB/s, done.
Resolving deltas: 100% (8859/8859), done.
-- The CXX compiler identification is GNU 14.3.0
-- Checking whether CXX compiler has -isysroot
-- Checking whether CXX compiler has -isysroot - yes
-- Checking whether CXX compiler supports OSX deployment target flag
-- Checking whether CXX compiler supports OSX deployment target flag - yes
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /opt/homebrew/bin/g++-14 - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- bpp-core3 1.0.0 found:
-- static lib: not built/installed
-- shared lib: /Users/maya/biopp/lib/libbpp-core3.1.0.0.dylib
-- includes: /Users/maya/biopp/include
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Configuring done (0.8s)
-- Generating done (0.1s)
-- Build files have been written to: /Users/maya/biopp_build/bpp-seq/build
[ 1%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o
[ 2%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o
[ 3%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o
[ 4%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Alphabet/AllelicAlphabet.cpp.o
[ 5%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o
[ 6%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o
[ 7%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o
[ 8%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o
[ 9%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o
[ 10%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o
[ 11%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o
[ 12%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o
[ 13%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o
[ 14%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o
[ 15%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Alphabet/RNA.cpp.o
[ 16%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o
[ 17%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o
[ 18%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o
[ 19%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o
[ 20%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o
[ 21%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o
[ 22%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o
[ 23%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o
[ 24%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o
[ 25%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o
[ 26%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/App/BppSequenceApplication.cpp.o
[ 27%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o
[ 28%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o
[ 29%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o
/Users/maya/biopp_build/bpp-seq/src/Bpp/Seq/App/SequenceApplicationTools.cpp: In static member function 'static std::unique_ptrbpp::Alphabet bpp::SequenceApplicationTools::getAlphabet(const std::map<std::__cxx11::basic_string, std::__cxx11::basic_string >&, const std::string&, bool, bool, bool, int)':
/Users/maya/biopp_build/bpp-seq/src/Bpp/Seq/App/SequenceApplicationTools.cpp:120:5: error: 'uint' was not declared in this scope; did you mean 'rint'?
120 | uint N = TextTools::to(args["N"]);
| ^~~~
| rint
/Users/maya/biopp_build/bpp-seq/src/Bpp/Seq/App/SequenceApplicationTools.cpp:121:42: error: 'N' was not declared in this scope
121 | chars = make_unique(N);
| ^
/Users/maya/biopp_build/bpp-seq/src/Bpp/Seq/App/SequenceApplicationTools.cpp:182:5: error: 'uint' was not declared in this scope; did you mean 'rint'?
182 | uint N = TextTools::to(args["N"]);
| ^~~~
| rint
/Users/maya/biopp_build/bpp-seq/src/Bpp/Seq/App/SequenceApplicationTools.cpp:188:54: error: 'N' was not declared in this scope
188 | chars = make_unique(inAlphabet, N);
| ^
[ 30%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o
[ 31%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/DNAToRNA.cpp.o
[ 32%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o
[ 33%] Building CXX object src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o
make[2]: *** [src/CMakeFiles/bpp-seq3-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [src/CMakeFiles/bpp-seq3-shared.dir/all] Error 2
make: *** [all] Error 2

Merci pour votre aide !

[jydu]

Hi, weird stuff, the code compiles on my Mac. I changed uint to unsigned int. Does that solve the issue?