Issues installing package #3
Description
Hi @dickoa ,
I'm having trouble installing the package after recently updating some system libraries (see below for session info). Specifically, running this code remotes::install_github('dickoa/prepr', force=T) produces the following log/error:
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo dickoa/prepr@HEAD
── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/tmp/RtmpyY5VGN/remotes22372521911d2/dickoa-prepr-5eae64f/DESCRIPTION’
─ preparing ‘prepr’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ running ‘cleanup’
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories (395ms)
─ building ‘prepr_0.1.9000.tar.gz’
Installing package into ‘/home/jeff/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
* installing *source* package ‘prepr’ ...
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++17
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.6.4
checking GDAL version >= 2.0.1... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for __gmpz_init in -lgmp... yes
checking for mpfr_init in -lmpfr... yes
configure: Package CXX flags: -I/usr/include/gdal -O3 -DNDEBUG -frounding-math -DCGAL_USE_GMPXX=1
configure: Package LIBS: -L/usr/lib/x86_64-linux-gnu -lgdal -lgmpxx -lgmp -lmpfr -lpthread
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++17
g++ -std=gnu++17 -I"/opt/R/R-4.3.2/lib/R/include" -DNDEBUG -I'/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include' -I'/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include' -I'/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/sf/include' -I'/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include' -I/usr/local/include -O3 -march=native -mtune=native -Wno-ignored-attributes -I/usr/include/gdal -O3 -DNDEBUG -frounding-math -DCGAL_USE_GMPXX=1 -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/opt/R/R-4.3.2/lib/R/include" -DNDEBUG -I'/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include' -I'/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include' -I'/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/sf/include' -I'/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include' -I/usr/local/include -O3 -march=native -mtune=native -Wno-ignored-attributes -I/usr/include/gdal -O3 -DNDEBUG -frounding-math -DCGAL_USE_GMPXX=1 -fpic -g -O2 -c prepr.cpp -o prepr.o
In file included from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Intersections_3/Plane_3_Triangle_3.h:25,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/intersection_3.h:59,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Kernel/function_objects.h:29,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Cartesian/function_objects.h:20,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Cartesian/Cartesian_base.h:62,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Simple_cartesian.h:20,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Exact_predicates_inexact_constructions_kernel.h:20,
from Polygon_repair.h:25,
from prepr.cpp:10:
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Intersections_3/internal/Plane_3_Triangle_3_intersection.h: In function ‘typename CGAL::Intersection_traits<K, typename K::Plane_3, typename K::Triangle_3>::result_type CGAL::Intersections::internal::intersection(const typename K::Plane_3&, const typename K::Triangle_3&, const K&)’:
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Intersections_3/internal/Plane_3_Triangle_3_intersection.h:144:65: error: ‘prior’ is not a member of ‘boost’; did you mean ‘boost::mpl::prior’?
144 | k.construct_segment_3_object()(*pts.begin(), *boost::prior(pts.end())));
| ^~~~~
In file included from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/mpl/next.hpp:17,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/mpl/bind.hpp:25,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/mpl/lambda.hpp:18,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/mpl/apply.hpp:25,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/iterator/iterator_facade.hpp:36,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/iterator/iterator_adaptor.hpp:15,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/iterator/transform_iterator.hpp:13,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/boost/iterator/transform_iterator.hpp:27,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Coercion_traits.h:27,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/number_type_basic.h:35,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/basic.h:28,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Cartesian/Cartesian_base.h:20,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Simple_cartesian.h:20,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Exact_predicates_inexact_constructions_kernel.h:20,
from Polygon_repair.h:25,
from prepr.cpp:10:
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/mpl/next_prior.hpp:38:8: note: ‘boost::mpl::prior’ declared here
38 | struct prior
| ^~~~~
In file included from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/property_map/property_map.hpp:598,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/property_map.h:18,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Spatial_sort_traits_adapter_2.h:19,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Triangulation_2.h:37,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Constrained_triangulation_2.h:26,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Constrained_Delaunay_triangulation_2.h:20,
from Polygon_repair.h:26,
from prepr.cpp:10:
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp: At global scope:
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/RcppCommon.h:53,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/Rcpp.h:27,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/sf/include/sf_RcppExports.h:7,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/sf/include/sf.h:7,
from prepr.cpp:4:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/property_map/property_map.hpp:598,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/property_map.h:18,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Spatial_sort_traits_adapter_2.h:19,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Triangulation_2.h:37,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Constrained_triangulation_2.h:26,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Constrained_Delaunay_triangulation_2.h:20,
from Polygon_repair.h:26,
from prepr.cpp:10:
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/RcppCommon.h:53,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/Rcpp.h:27,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/sf/include/sf_RcppExports.h:7,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/sf/include/sf.h:7,
from prepr.cpp:4:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/property_map/property_map.hpp:598,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/property_map.h:18,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Spatial_sort_traits_adapter_2.h:19,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Triangulation_2.h:37,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Constrained_triangulation_2.h:26,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Constrained_Delaunay_triangulation_2.h:20,
from Polygon_repair.h:26,
from prepr.cpp:10:
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/RcppCommon.h:53,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/Rcpp.h:27,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/sf/include/sf_RcppExports.h:7,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/sf/include/sf.h:7,
from prepr.cpp:4:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/property_map/property_map.hpp:598,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/property_map.h:18,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Spatial_sort_traits_adapter_2.h:19,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Triangulation_2.h:37,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Constrained_triangulation_2.h:26,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Constrained_Delaunay_triangulation_2.h:20,
from Polygon_repair.h:26,
from prepr.cpp:10:
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/RcppCommon.h:53,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/Rcpp.h:27,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/sf/include/sf_RcppExports.h:7,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/sf/include/sf.h:7,
from prepr.cpp:4:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/property_map/property_map.hpp:598,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/property_map.h:18,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Spatial_sort_traits_adapter_2.h:19,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Triangulation_2.h:37,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Constrained_triangulation_2.h:26,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Constrained_Delaunay_triangulation_2.h:20,
from Polygon_repair.h:26,
from prepr.cpp:10:
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/RcppCommon.h:53,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/Rcpp.h:27,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/sf/include/sf_RcppExports.h:7,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/sf/include/sf.h:7,
from prepr.cpp:4:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/property_map/property_map.hpp:598,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/property_map.h:18,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Spatial_sort_traits_adapter_2.h:19,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Triangulation_2.h:37,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Constrained_triangulation_2.h:26,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Constrained_Delaunay_triangulation_2.h:20,
from Polygon_repair.h:26,
from prepr.cpp:10:
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/RcppCommon.h:53,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/Rcpp.h:27,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/sf/include/sf_RcppExports.h:7,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/sf/include/sf.h:7,
from prepr.cpp:4:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/property_map/property_map.hpp:598,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/property_map.h:18,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Spatial_sort_traits_adapter_2.h:19,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Triangulation_2.h:37,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Constrained_triangulation_2.h:26,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Constrained_Delaunay_triangulation_2.h:20,
from Polygon_repair.h:26,
from prepr.cpp:10:
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/RcppCommon.h:53,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/Rcpp.h:27,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/sf/include/sf_RcppExports.h:7,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/sf/include/sf.h:7,
from prepr.cpp:4:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/linear_least_squares_fitting_3.h:27,
from Polygon_repair.h:29,
from prepr.cpp:10:
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Default_diagonalize_traits.h: In instantiation of ‘static bool CGAL::Default_diagonalize_traits<FT, dim>::diagonalize_selfadjoint_covariance_matrix(const Covariance_matrix&, CGAL::Default_diagonalize_traits<FT, dim>::Vector&, CGAL::Default_diagonalize_traits<FT, dim>::Matrix&) [with FT = double; unsigned int dim = 3; CGAL::Default_diagonalize_traits<FT, dim>::Covariance_matrix = std::array<double, 6>; CGAL::Default_diagonalize_traits<FT, dim>::Vector = std::array<double, 3>; CGAL::Default_diagonalize_traits<FT, dim>::Matrix = std::array<double, 9>]’:
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/PCA_util.h:709:5: required from ‘typename K::FT CGAL::internal::fitting_plane_3(typename DiagonalizeTraits::Covariance_matrix&, const typename K::Point_3&, typename K::Plane_3&, const K&, const DiagonalizeTraits&) [with K = CGAL::Epick; DiagonalizeTraits = CGAL::Default_diagonalize_traits<double, 3>; typename K::FT = double; typename DiagonalizeTraits::Covariance_matrix = std::array<double, 6>; typename K::Point_3 = CGAL::Point_3<CGAL::Epick>; typename K::Plane_3 = CGAL::Plane_3<CGAL::Epick>]’
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/linear_least_squares_fitting_points_3.h:57:25: required from ‘typename K::FT CGAL::internal::linear_least_squares_fitting_3(InputIterator, InputIterator, typename K::Plane_3&, typename K::Point_3&, const typename K::Point_3*, const K&, const CGAL::Dimension_tag<0>&, const DiagonalizeTraits&) [with InputIterator = std::_List_iterator<CGAL::Point_3<CGAL::Epick> >; K = CGAL::Epick; DiagonalizeTraits = CGAL::Default_diagonalize_traits<double, 3>; typename K::FT = double; typename K::Plane_3 = CGAL::Plane_3<CGAL::Epick>; typename K::Point_3 = CGAL::Point_3<CGAL::Epick>]’
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/linear_least_squares_fitting_3.h:53:50: required from ‘typename Kernel::FT CGAL::linear_least_squares_fitting_3(InputIterator, InputIterator, Object&, typename Kernel::Point_3&, const Tag&, const Kernel&, const DiagonalizeTraits&) [with InputIterator = std::_List_iterator<CGAL::Point_3<CGAL::Epick> >; Object = CGAL::Plane_3<CGAL::Epick>; Kernel = CGAL::Epick; Tag = CGAL::Dimension_tag<0>; DiagonalizeTraits = CGAL::Default_diagonalize_traits<double, 3>; typename Kernel::FT = double; typename Kernel::Point_3 = CGAL::Point_3<CGAL::Epick>]’
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/linear_least_squares_fitting_3.h:94:46: required from ‘typename CGAL::Kernel_traits<T1>::Kernel::FT CGAL::linear_least_squares_fitting_3(InputIterator, InputIterator, Object&, const Tag&) [with InputIterator = std::_List_iterator<CGAL::Point_3<CGAL::Epick> >; Object = CGAL::Plane_3<CGAL::Epick>; Tag = CGAL::Dimension_tag<0>; typename CGAL::Kernel_traits<T1>::Kernel::FT = double; typename CGAL::Kernel_traits<T1>::Kernel = CGAL::Epick]’
Polygon_repair.h:98:35: required from here
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Default_diagonalize_traits.h:65:59: warning: ‘static bool CGAL::Diagonalize_traits<FT, dim>::diagonalize_selfadjoint_covariance_matrix(const Covariance_matrix&, CGAL::Diagonalize_traits<FT, dim>::Vector&, CGAL::Diagonalize_traits<FT, dim>::Matrix&) [with FT = double; unsigned int dim = 3; CGAL::Diagonalize_traits<FT, dim>::Covariance_matrix = std::array<double, 6>; CGAL::Diagonalize_traits<FT, dim>::Vector = std::array<double, 3>; CGAL::Diagonalize_traits<FT, dim>::Matrix = std::array<double, 9>]’ is deprecated: CGAL::Diagonalize_traits is a deprecated class that can lead to precision issues, please use CGAL::Eigen_diagonalize_traits [-Wdeprecated-declarations]
65 | return Base::diagonalize_selfadjoint_covariance_matrix(cov, eigenvalues, eigenvectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Default_diagonalize_traits.h:17,
from /home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/linear_least_squares_fitting_3.h:27,
from Polygon_repair.h:29,
from prepr.cpp:10:
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Diagonalize_traits.h:88:15: note: declared here
88 | static bool diagonalize_selfadjoint_covariance_matrix(const Covariance_matrix& mat,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make: *** [/opt/R/R-4.3.2/lib/R/etc/Makeconf:200: prepr.o] Error 1
ERROR: compilation failed for package ‘prepr’
* removing ‘/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/prepr’
* restoring previous ‘/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/prepr’
Warning message:
In i.p(...) :
installation of package ‘/tmp/RtmpyY5VGN/file22372226617dd/prepr_0.1.9000.tar.gz’ had non-zero exit status
My guess is that I have recently updated the version of boost on my computer, and this in turn, is causing incompaitiblities with the version of CGAL in the version of the cgal4h R package installed my computer. I'm guessing this based on this error message, but I could be wrong?
/home/jeff/R/x86_64-pc-linux-gnu-library/4.3/cgalh/include/CGAL/Intersections_3/internal/Plane_3_Triangle_3_intersection.h:144:65: error: ‘prior’ is not a member of ‘boost’; did you mean ‘boost::mpl::prior’?
Do you have any ideas on what I could do to resolve this?
Session information
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS: /opt/R/R-4.3.2/lib/R/lib/libRblas.so
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Pacific/Auckland
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] testthat_3.2.1 devtools_2.4.5 usethis_2.2.2
loaded via a namespace (and not attached):
[1] vctrs_0.6.5 cli_3.6.2 rlang_1.1.3 stringi_1.8.3
[5] purrr_1.0.2 pkgload_1.3.4 promises_1.2.1 shiny_1.8.0
[9] xtable_1.8-4 glue_1.7.0 htmltools_0.5.7 httpuv_1.6.13
[13] pkgbuild_1.4.3 brio_1.1.4 ellipsis_0.3.2 fastmap_1.1.1
[17] lifecycle_1.0.4 memoise_2.0.1 stringr_1.5.1 compiler_4.3.2
[21] miniUI_0.1.1.1 sessioninfo_1.2.2 fs_1.6.3 htmlwidgets_1.6.4
[25] Rcpp_1.0.12 urlchecker_1.0.1 later_1.3.2 digest_0.6.35
[29] R6_2.5.1 magrittr_2.0.3 tools_4.3.2 mime_0.12
[33] profvis_0.3.8 remotes_2.4.2.1 cachem_1.0.8