make error

[yybgood]

when i install cafe ,i got that error icc -std=c++11 -O3 -fopenmp -o bin/cafexp -I. obj/user_data.o obj/simulator.o obj/optimizer.o obj/cafexp.o obj/probability.o obj/gene_family.o obj/gamma.o obj/matrix_cache.o obj/base_model.o obj/error_model.o obj/io.o obj/core.o obj/lambda.o obj/root_equilibrium_distribution.o obj/gamma_core.o obj/clade.o obj/optimizer_scorer.o obj/poisson.o obj/root_distribution.o obj/execute.o obj/gene_family_reconstructor.o obj/main.o -lmkl_sequential -lmkl_core -lmkl_intel_lp64 -lm obj/clade.o: In function parse_newick(std::string, bool)': clade.cpp:(.text+0x7c5): undefined reference to std::regex_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits<char> >::regex_iterator(__gnu_cxx::__normal_iterator<char const*, std::string>, __gnu_cxx::__normal_iterator<char const*, std::string>, std::basic_regex<char, std::regex_traits<char> > const&, std::bitset<11ul>)' clade.cpp:(.text+0x7d2): undefined reference to std::regex_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits >::regex_iterator()' clade.cpp:(.text+0x800): undefined reference to std::regex_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits<char> >::operator!=(std::regex_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits<char> > const&)' clade.cpp:(.text+0x81a): undefined reference to std::regex_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits >::operator->()' clade.cpp:(.text+0x939): undefined reference to std::regex_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits<char> >::operator->()' clade.cpp:(.text+0xa3d): undefined reference to std::regex_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits >::operator->()' clade.cpp:(.text+0xafc): undefined reference to std::regex_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits<char> >::operator->()' clade.cpp:(.text+0xbb6): undefined reference to std::regex_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits >::operator->()' obj/clade.o:clade.cpp:(.text+0xc6c): more undefined references to std::regex_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits<char> >::operator->()' follow obj/clade.o: In function parse_newick(std::string, bool)': clade.cpp:(.text+0xd24): undefined reference to std::regex_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits<char> >::operator++(int)' clade.cpp:(.text+0xd46): undefined reference to std::regex_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits >::operator!=(std::regex_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits > const&)' clade.cpp:(.text+0x10da): undefined reference to std::regex_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits<char> >::operator->()' clade.cpp:(.text+0x11cb): undefined reference to std::regex_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits >::operator->()' make: *** [bin/cafexp] Error 1**The gcc version is **$ gcc -v Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux Thread model: posix gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)` I don't have the root right

[benfulton]

You need at least gcc 4.9.

[yybgood]

thanks

[NINGCHINA]

when I install cafe5 on the Maos ,I encountered an error on the macos platform , bellow is the gcc version (base) ➜ CAFE5 gcc -v Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1 Apple clang version 12.0.5 (clang-1205.0.22.9) Target: x86_64-apple-darwin20.5.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin

(base) ➜ CAFE5 make g++ -std=c++11 -O3 -o bin/cafe5 -I. obj/base_model.o obj/cafexp.o obj/clade.o obj/core.o obj/easylogging++.o obj/error_model.o obj/execute.o obj/gamma.o obj/gamma_core.o obj/gene_family.o obj/gene_family_reconstructor.o obj/io.o obj/lambda.o obj/likelihood_ratio.o obj/matrix_cache.o obj/optimizer.o obj/optimizer_scorer.o obj/poisson.o obj/probability.o obj/root_equilibrium_distribution.o obj/simulator.o obj/user_data.o obj/main.o -lm Undefined symbols for architecture x86_64: "_omp_set_num_threads", referenced from: cafe5(int, char* const*) in cafexp.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [bin/cafe5] Error 1

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This issue is stale because it has been open for 90 days with no activity.

[github-actions[bot]]

This issue was closed because it has been inactive for 14 days since being marked as stale.