* installing *source* package ‘hdtg’ ...
** this is package ‘hdtg’ version ‘0.2.1’
** package ‘hdtg’ successfully unpacked and MD5 sums checked
** using staged installation
SIMD optimizations DISABLED for Debian/CRAN.
** libs
using C++ compiler: ‘clang version 21.1.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/hdtg/src'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -I. -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppHarmonic.cpp -o RcppHarmonic.o
In file included from RcppHarmonic.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from RcppHarmonic.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from RcppHarmonic.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from RcppHarmonic.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
5 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -I. -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppZigZag.cpp -o RcppZigZag.o
In file included from RcppZigZag.cpp:10:
In file included from ./ZigZag.h:32:
In file included from ./MemoryManagement.h:7:
./aligned_allocator.h:34:45: warning: 'pointer' is deprecated [-Wdeprecated-declarations]
34 | typedef typename std::allocator<T>::pointer pointer;
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/allocator_traits.h:229:59: note: in instantiation of template class 'util::aligned_allocator<double, 16>' requested here
229 | using value_type = typename allocator_type::value_type;
| ^
/usr/local/clang21/bin/../include/c++/v1/__vector/vector.h:99:51: note: in instantiation of template class 'std::allocator_traits<util::aligned_allocator<double, 16>>' requested here
99 | using size_type = typename __alloc_traits::size_type;
| ^
./MemoryManagement.h:41:7: note: in instantiation of template class 'std::vector<double, util::aligned_allocator<double, 16>>' requested here
41 | mm::MemoryManager<double>::iterator destination, Buffer&) {
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/allocator.h:126:3: note: 'pointer' has been explicitly marked deprecated here
126 | _LIBCPP_DEPRECATED_IN_CXX17 typedef _Tp* pointer;
| ^
/usr/local/clang21/bin/../include/c++/v1/__config:740:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
740 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/usr/local/clang21/bin/../include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED'
713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
In file included from RcppZigZag.cpp:10:
In file included from ./ZigZag.h:32:
In file included from ./MemoryManagement.h:7:
./aligned_allocator.h:35:45: warning: 'const_pointer' is deprecated [-Wdeprecated-declarations]
35 | typedef typename std::allocator<T>::const_pointer const_pointer;
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/allocator.h:127:3: note: 'const_pointer' has been explicitly marked deprecated here
127 | _LIBCPP_DEPRECATED_IN_CXX17 typedef const _Tp* const_pointer;
| ^
/usr/local/clang21/bin/../include/c++/v1/__config:740:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
740 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/usr/local/clang21/bin/../include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED'
713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
In file included from RcppZigZag.cpp:10:
In file included from ./ZigZag.h:32:
In file included from ./MemoryManagement.h:7:
./aligned_allocator.h:34:45: warning: 'pointer' is deprecated [-Wdeprecated-declarations]
34 | typedef typename std::allocator<T>::pointer pointer;
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/allocator_traits.h:229:59: note: in instantiation of template class 'util::aligned_allocator<float, 16>' requested here
229 | using value_type = typename allocator_type::value_type;
| ^
/usr/local/clang21/bin/../include/c++/v1/__vector/vector.h:99:51: note: in instantiation of template class 'std::allocator_traits<util::aligned_allocator<float, 16>>' requested here
99 | using size_type = typename __alloc_traits::size_type;
| ^
./MemoryManagement.h:47:7: note: in instantiation of template class 'std::vector<float, util::aligned_allocator<float, 16>>' requested here
47 | mm::MemoryManager<float>::iterator destination, Buffer& buffer) {
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/allocator.h:126:3: note: 'pointer' has been explicitly marked deprecated here
126 | _LIBCPP_DEPRECATED_IN_CXX17 typedef _Tp* pointer;
| ^
/usr/local/clang21/bin/../include/c++/v1/__config:740:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
740 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/usr/local/clang21/bin/../include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED'
713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
In file included from RcppZigZag.cpp:10:
In file included from ./ZigZag.h:32:
In file included from ./MemoryManagement.h:7:
./aligned_allocator.h:35:45: warning: 'const_pointer' is deprecated [-Wdeprecated-declarations]
35 | typedef typename std::allocator<T>::const_pointer const_pointer;
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/allocator.h:127:3: note: 'const_pointer' has been explicitly marked deprecated here
127 | _LIBCPP_DEPRECATED_IN_CXX17 typedef const _Tp* const_pointer;
| ^
/usr/local/clang21/bin/../include/c++/v1/__config:740:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
740 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/usr/local/clang21/bin/../include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED'
713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
In file included from RcppZigZag.cpp:10:
In file included from ./ZigZag.h:33:
In file included from ./Simd.h:8:
In file included from /data/gannet/ripley/R/test-clang/RcppXsimd/include/xsimd/xsimd.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/RcppXsimd/include/xsimd/memory/xsimd_alignment.hpp:13:
/data/gannet/ripley/R/test-clang/RcppXsimd/include/xsimd/memory/xsimd_aligned_allocator.hpp:72:70: warning: 'const_pointer' is deprecated [-Wdeprecated-declarations]
72 | pointer allocate(size_type n, typename std::allocator<void>::const_pointer hint = 0);
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/allocator.h:44:3: note: 'const_pointer' has been explicitly marked deprecated here
44 | _LIBCPP_DEPRECATED_IN_CXX17 typedef const void* const_pointer;
| ^
/usr/local/clang21/bin/../include/c++/v1/__config:740:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
740 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/usr/local/clang21/bin/../include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED'
713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
In file included from RcppZigZag.cpp:10:
In file included from ./ZigZag.h:33:
In file included from ./Simd.h:8:
In file included from /data/gannet/ripley/R/test-clang/RcppXsimd/include/xsimd/xsimd.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/RcppXsimd/include/xsimd/memory/xsimd_alignment.hpp:13:
/data/gannet/ripley/R/test-clang/RcppXsimd/include/xsimd/memory/xsimd_aligned_allocator.hpp:173:44: warning: 'const_pointer' is deprecated [-Wdeprecated-declarations]
173 | typename std::allocator<void>::const_pointer) -> pointer
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/allocator.h:44:3: note: 'const_pointer' has been explicitly marked deprecated here
44 | _LIBCPP_DEPRECATED_IN_CXX17 typedef const void* const_pointer;
| ^
/usr/local/clang21/bin/../include/c++/v1/__config:740:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
740 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/usr/local/clang21/bin/../include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED'
713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
6 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -I. -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
5 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang21/lib/clang/21/lib/x86_64-unknown-linux-gnu -o hdtg.so RcppHarmonic.o RcppZigZag.o RcppExports.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/hdtg/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/hdtg/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/hdtg/src'
installing to /data/gannet/ripley/R/packages/tests-clang/hdtg.Rcheck/00LOCK-hdtg/00new/hdtg/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (hdtg)