installation error for BiocNeighbors package
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育 • 0
@64c8864a
Last seen 23 hours ago
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I encountered the following errors. I checked some posts about instllation of BiocNeighbors, finally I could not resolve the issue. My machine has gcc-13.2.0, CMake-3.31.0.1, curl-8.10.1 and OpenSSL-1.1.1w in local directory. I will tell you about versions of the other applications installed if it is necessary.


    > BiocManager::install("BiocNeighbors")
    Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)
    Installing package(s) 'BiocNeighbors'
    trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/BiocNeighbors_2.0.0.tar.gz'
    Content type 'application/x-gzip' length 338928 bytes (330 KB)
    ==================================================
    downloaded 330 KB

    * installing *source* package 'BiocNeighbors' ...
    ** package 'BiocNeighbors' successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    using C++ compiler: 'g++ (GCC) 13.2.0'
    using C++17
# (Additional compilation output omitted for brevity)
    ERROR: compilation failed for package 'BiocNeighbors'
    * removing '/home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/BiocNeighbors'

    The downloaded source packages are in
        '/tmp/RtmpKgDWWn/downloaded_packages'
    Updating HTML index of packages in '.Library'
    Making 'packages.html' ... done
    Warning message:
    In install.packages(...) :
      installation of package 'BiocNeighbors' had non-zero exit status

    > sessionInfo()
    R version 4.4.1 (2024-06-14)
    Platform: x86_64-pc-linux-gnu
    Running under: CentOS Linux 7 (Core)

    Matrix products: default
    BLAS:   /home/ikutsu/Tsuchiya_NGS/local/lib64/R/lib/libRblas.so 
    LAPACK: /home/ikutsu/Tsuchiya_NGS/local/lib64/R/lib/libRlapack.so;  LAPACK version 3.12.0

    locale:
     [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
     [3] LC_TIME=ja_JP.UTF-8        LC_COLLATE=en_US.UTF-8    
     [5] LC_MONETARY=ja_JP.UTF-8    LC_MESSAGES=en_US.UTF-8   
     [7] LC_PAPER=ja_JP.UTF-8       LC_NAME=C                 
     [9] LC_ADDRESS=C               LC_TELEPHONE=C            
    [11] LC_MEASUREMENT=ja_JP.UTF-8 LC_IDENTIFICATION=C       

    time zone: Asia/Tokyo
    tzcode source: system (glibc)

    attached base packages:
    [1] stats     graphics  grDevices utils     datasets  methods   base     

    other attached packages:
    [1] BiocManager_1.30.25

    loaded via a namespace (and not attached):
    [1] compiler_4.4.1 tools_4.4.1
BiocNeighbors • 252 views
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omitted error1

    /home/ikutsu/Tsuchiya_NGS/local/bin/g++ -std=gnu++17 -fPIC -std=gnu++17 -I"/home/ikutsu/Tsuchiya_NGS/local/lib64/R/include" -DNDEBUG -I../inst/include -I'/home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/Rcpp/include' -I'/home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/assorthead/include' -I/home/ikutsu/Tsuchiya_NGS/local/include    -fpic  -g -O2   -c RcppExports.cpp -o RcppExports.o
    /home/ikutsu/Tsuchiya_NGS/local/bin/g++ -std=gnu++17 -fPIC -std=gnu++17 -I"/home/ikutsu/Tsuchiya_NGS/local/lib64/R/include" -DNDEBUG -I../inst/include -I'/home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/Rcpp/include' -I'/home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/assorthead/include' -I/home/ikutsu/Tsuchiya_NGS/local/include    -fpic  -g -O2   -c annoy.cpp -o annoy.o
    /home/ikutsu/Tsuchiya_NGS/local/bin/g++ -std=gnu++17 -fPIC -std=gnu++17 -I"/home/ikutsu/Tsuchiya_NGS/local/lib64/R/include" -DNDEBUG -I../inst/include -I'/home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/Rcpp/include' -I'/home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/assorthead/include' -I/home/ikutsu/Tsuchiya_NGS/local/include    -fpic  -g -O2   -c exhaustive.cpp -o exhaustive.o
    /home/ikutsu/Tsuchiya_NGS/local/bin/g++ -std=gnu++17 -fPIC -std=gnu++17 -I"/home/ikutsu/Tsuchiya_NGS/local/lib64/R/include" -DNDEBUG -I../inst/include -I'/home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/Rcpp/include' -I'/home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/assorthead/include' -I/home/ikutsu/Tsuchiya_NGS/local/include    -fpic  -g -O2   -c find_mutual_nns.cpp -o find_mutual_nns.o
    /home/ikutsu/Tsuchiya_NGS/local/bin/g++ -std=gnu++17 -fPIC -std=gnu++17 -I"/home/ikutsu/Tsuchiya_NGS/local/lib64/R/include" -DNDEBUG -I../inst/include -I'/home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/Rcpp/include' -I'/home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/assorthead/include' -I/home/ikutsu/Tsuchiya_NGS/local/include    -fpic  -g -O2   -c generics.cpp -o generics.o
    In file included from /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/c++allocator.h:33,
                     from /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/allocator.h:46,
                     from /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/alloc_traits.h:39,
                     from /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/ext/alloc_traits.h:34,
                     from /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/hashtable_policy.h:39,
                     from /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/hashtable.h:35,
                     from /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/unordered_map.h:33,
                     from /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/unordered_map:41,
                     from /home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                     from /home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/Rcpp/include/Rcpp/r/headers.h:66,
                     from /home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/Rcpp/include/RcppCommon.h:30,
                     from /home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                     from generics.cpp:1:
    /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/new_allocator.h: In instantiation of 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::thread; _Args = {generic_find_knn(SEXP, Rcpp::IntegerVector, bool, Rcpp::Nullable<Rcpp::Vector<13> >, int, bool, bool, bool)::<lambda(int, int)>&, int&, int&}; _Tp = std::thread]':
    /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/alloc_traits.h:537:17:   required from 'static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::thread; _Args = {generic_find_knn(SEXP, Rcpp::IntegerVector, bool, Rcpp::Nullable<Rcpp::Vector<13> >, int, bool, bool, bool)::<lambda(int, int)>&, int&, int&}; _Tp = std::thread; allocator_type = std::allocator<std::thread>]'
    /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/vector.tcc:117:30:   required from 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {generic_find_knn(SEXP, Rcpp::IntegerVector, bool, Rcpp::Nullable<Rcpp::Vector<13> >, int, bool, bool, bool)::<lambda(int, int)>&, int&, int&}; _Tp = std::thread; _Alloc = std::allocator<std::thread>; reference = std::thread&]'
    parallel.h:26:26:   required from 'void generic_parallelize(Index_, int, Function_) [with Index_ = int; Function_ = generic_find_knn(SEXP, Rcpp::IntegerVector, bool, Rcpp::Nullable<Rcpp::Vector<13> >, int, bool, bool, bool)::<lambda(int, int)>]'
    generics.cpp:148:24:   required from here
    /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/new_allocator.h:187:11: error: no matching function for call to 'std::thread::thread(generic_find_knn(SEXP, Rcpp::IntegerVector, bool, Rcpp::Nullable<Rcpp::Vector<13> >, int, bool, bool, bool)::<lambda(int, int)>&, int&, int&)'
      187 |         { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
          |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In file included from /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/thread:45,
                 from /home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/assorthead/include/subpar/range.hpp:9,
                 from /home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/assorthead/include/subpar/subpar.hpp:4,
                 from /home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/assorthead/include/kmeans/parallelize.hpp:10,
                 from /home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/assorthead/include/kmeans/InitializeKmeanspp.hpp:14,
                 from /home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/assorthead/include/kmeans/kmeans.hpp:9,
                 from /home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/assorthead/include/knncolle/Kmknn.hpp:11,
                 from /home/ikutsu/Tsuchiya_NGS/local/lib64/R/library/assorthead/include/knncolle/knncolle.hpp:13,
                 from ../inst/include/BiocNeighbors.h:6,
                 from generics.cpp:2:
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/std_thread.h:178:5: note: candidate: 'std::thread::thread(std::thread&&)'
  178 |     thread(thread&& __t) noexcept
      |     ^~~~~~
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/std_thread.h:178:5: note:   candidate expects 1 argument, 3 provided
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/std_thread.h:132:5: note: candidate: 'std::thread::thread()'
  132 |     thread() noexcept = default;
      |     ^~~~~~
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/std_thread.h:132:5: note:   candidate expects 0 arguments, 3 provided
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/new_allocator.h: In instantiation of 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::thread; _Args = {generic_query_knn(SEXP, Rcpp::NumericMatrix, Rcpp::IntegerVector, bool, int, bool, bool, bool)::<lambda(int, int)>&, int&, int&}; _Tp = std::thread]':
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/alloc_traits.h:537:17:   required from 'static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::thread; _Args = {generic_query_knn(SEXP, Rcpp::NumericMatrix, Rcpp::IntegerVector, bool, int, bool, bool, bool)::<lambda(int, int)>&, int&, int&}; _Tp = std::thread; allocator_type = std::allocator<std::thread>]'
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/vector.tcc:117:30:   required from 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {generic_query_knn(SEXP, Rcpp::NumericMatrix, Rcpp::IntegerVector, bool, int, bool, bool, bool)::<lambda(int, int)>&, int&, int&}; _Tp = std::thread; _Alloc = std::allocator<std::thread>; reference = std::thread&]'
parallel.h:26:26:   required from 'void generic_parallelize(Index_, int, Function_) [with Index_ = int; Function_ = generic_query_knn(SEXP, Rcpp::NumericMatrix, Rcpp::IntegerVector, bool, int, bool, bool, bool)::<lambda(int, int)>]'
generics.cpp:299:24:   required from here
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/new_allocator.h:187:11: error: no matching function for call to 'std::thread::thread(generic_query_knn(SEXP, Rcpp::NumericMatrix, Rcpp::IntegerVector, bool, int, bool, bool, bool)::<lambda(int, int)>&, int&, int&)'
  187 |         { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/std_thread.h:178:5: note: candidate: 'std::thread::thread(std::thread&&)'
  178 |     thread(thread&& __t) noexcept
      |     ^~~~~~
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/std_thread.h:178:5: note:   candidate expects 1 argument, 3 provided
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/std_thread.h:132:5: note: candidate: 'std::thread::thread()'
  132 |     thread() noexcept = default;
      |     ^~~~~~
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/std_thread.h:132:5: note:   candidate expects 0 arguments, 3 provided
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/new_allocator.h: In instantiation of 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::thread; _Args = {generic_find_all(SEXP, Rcpp::Nullable<Rcpp::Vector<13> >, Rcpp::NumericVector, int, bool, bool)::<lambda(int, int)>&, int&, int&}; _Tp = std::thread]':

~~~

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omitted error2

   /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/new_allocator.h: In instantiation of 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::thread; _Args = {generic_find_all(SEXP, Rcpp::Nullable<Rcpp::Vector<13> >, Rcpp::NumericVector, int, bool, bool)::<lambda(int, int)>&, int&, int&}; _Tp = std::thread]':
    /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/alloc_traits.h:537:17:   required from 'static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::thread; _Args = {generic_find_all(SEXP, Rcpp::Nullable<Rcpp::Vector<13> >, Rcpp::NumericVector, int, bool, bool)::<lambda(int, int)>&, int&, int&}; _Tp = std::thread; allocator_type = std::allocator<std::thread>]'
    /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/vector.tcc:117:30:   required from 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {generic_find_all(SEXP, Rcpp::Nullable<Rcpp::Vector<13> >, Rcpp::NumericVector, int, bool, bool)::<lambda(int, int)>&, int&, int&}; _Tp = std::thread; _Alloc = std::allocator<std::thread>; reference = std::thread&]'
    parallel.h:26:26:   required from 'void generic_parallelize(Index_, int, Function_) [with Index_ = int; Function_ = generic_find_all(SEXP, Rcpp::Nullable<Rcpp::Vector<13> >, Rcpp::NumericVector, int, bool, bool)::<lambda(int, int)>]'
    generics.cpp:417:24:   required from here
    /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/new_allocator.h:187:11: error: no matching function for call to 'std::thread::thread(generic_find_all(SEXP, Rcpp::Nullable<Rcpp::Vector<13> >, Rcpp::NumericVector, int, bool, bool)::<lambda(int, int)>&, int&, int&)'
      187 |         { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
          |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/std_thread.h:178:5: note: candidate: 'std::thread::thread(std::thread&&)'
  178 |     thread(thread&& __t) noexcept
      |     ^~~~~~
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/std_thread.h:178:5: note:   candidate expects 1 argument, 3 provided
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/std_thread.h:132:5: note: candidate: 'std::thread::thread()'
  132 |     thread() noexcept = default;
      |     ^~~~~~
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/std_thread.h:132:5: note:   candidate expects 0 arguments, 3 provided
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/new_allocator.h: In instantiation of 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::thread; _Args = {generic_query_all(SEXP, Rcpp::NumericMatrix, Rcpp::NumericVector, int, bool, bool)::<lambda(int, int)>&, int&, int&}; _Tp = std::thread]':
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/alloc_traits.h:537:17:   required from 'static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::thread; _Args = {generic_query_all(SEXP, Rcpp::NumericMatrix, Rcpp::NumericVector, int, bool, bool)::<lambda(int, int)>&, int&, int&}; _Tp = std::thread; allocator_type = std::allocator<std::thread>]'
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/vector.tcc:117:30:   required from 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {generic_query_all(SEXP, Rcpp::NumericMatrix, Rcpp::NumericVector, int, bool, bool)::<lambda(int, int)>&, int&, int&}; _Tp = std::thread; _Alloc = std::allocator<std::thread>; reference = std::thread&]'
parallel.h:26:26:   required from 'void generic_parallelize(Index_, int, Function_) [with Index_ = int; Function_ = generic_query_all(SEXP, Rcpp::NumericMatrix, Rcpp::NumericVector, int, bool, bool)::<lambda(int, int)>]'
generics.cpp:510:24:   required from here
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/new_allocator.h:187:11: error: no matching function for call to 'std::thread::thread(generic_query_all(SEXP, Rcpp::NumericMatrix, Rcpp::NumericVector, int, bool, bool)::<lambda(int, int)>&, int&, int&)'
  187 |         { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/std_thread.h:178:5: note: candidate: 'std::thread::thread(std::thread&&)'
  178 |     thread(thread&& __t) noexcept
      |     ^~~~~~
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/std_thread.h:178:5: note:   candidate expects 1 argument, 3 provided
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/std_thread.h:132:5: note: candidate: 'std::thread::thread()'
  132 |     thread() noexcept = default;
      |     ^~~~~~
/home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/std_thread.h:132:5: note:   candidate expects 0 arguments, 3 provided
make: *** [generics.o] Error 1
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