Installation on Mac Clang Issue?

[samuel-marsh]

Hi,

Trying to install the package and running into issue that at first seemed similar to #3. Following those instructions I ran clang install via conda and added lines to my RMakevars.

# clang: start
CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
CC=/Users/marsh_mbp/opt/anaconda3/envs/basic/bin/clang
CXX=/Users/marsh_mbp/opt/anaconda3/envs/basic/bin/clang-cpp

SHLIB_CXXLDFLAGS+=-Wl,-rpath,${R_HOME}/lib ${R_HOME}/lib/libc++abi.1.dylib
SHLIB_CXX14LDFLAGS+=-Wl,-rpath,${R_HOME}/lib ${R_HOME}/lib/libc++abi.1.dylib
# clang: end

Now I no longer get the error about not having right compiler but I still get non-zero exit status and failed install. Full install warnings and errors and session info below.

Thanks!!
Sam

Build Messages

Running `R CMD build`...
* checking for file ‘/private/var/folders/92/rwb8659d3jl658jf5nmmvw580000gn/T/RtmpTTpNt9/remotes82b74e12e8b9/bnprks-BPCells-2af1b98/DESCRIPTION’ ... OK
* preparing ‘BPCells’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘BPCells_0.1.0.tar.gz’
* installing *source* package ‘BPCells’ ...
** using staged installation
Testing hdf5 by compiling example program...
Found working hdf5
HDF5_CFLAGS=''
HDF5_LIBS='-lhdf5'

Testing architecture flag support support...'-march=native' succeeded
ARCH_FLAG='-march=native'
** libs
using C++ compiler: ‘Apple clang version 13.0.0 (clang-1300.0.27.3)’
using SDK: ‘’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include   -march=native -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas  -fPIC  -falign-functions=64 -Wall -g -O2  -c bitpacking_io.cpp -o bitpacking_io.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include   -march=native -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas  -fPIC  -falign-functions=64 -Wall -g -O2  -c fragment_io.cpp -o fragment_io.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include   -march=native -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas  -fPIC  -falign-functions=64 -Wall -g -O2  -c fragment_utils.cpp -o fragment_utils.o
In file included from fragment_utils.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/Core:367:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_product_op<double> (const double &, const double &)>' is deprecated [-Wdeprecated-declarations]
  typedef typename std::result_of<T>::type type1;
                        ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_product_op<double> (const double &, const double &)>' requested here
  typedef typename result_of<
                   ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1, 1>>, const Eigen::Block<const Eigen::Map<Eigen::Matrix<double, -1, -1, 0>, 0>, 1, -1, false>>>' requested here
template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind>
                                                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1, 1>>, const Eigen::Block<const Eigen::Map<Eigen::Matrix<double, -1, -1, 0>, 0>, 1, -1, false>>>' required here
  : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type
                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1, 1>>, const Eigen::Block<const Eigen::Map<Eigen::Matrix<double, -1, -1, 0>, 0>, 1, -1, false>, Eigen::Dense>' requested here
  public CwiseBinaryOpImpl<
         ^
./matrixIterators/MatrixOps.h:32:63: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1, 1>>, const Eigen::Block<const Eigen::Map<Eigen::Matrix<double, -1, -1, 0>, 0>, 1, -1, false>>' requested here
                res.col(row_data[i]) += ((double)val_data[i]) * B.row(col);
                                                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_product_op<double> (const double &, const double &)>' has been explicitly marked deprecated here
template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of;
                                 ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from fragment_utils.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/Core:367:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_quotient_op<double> (const double &, const double &)>' is deprecated [-Wdeprecated-declarations]
  typedef typename std::result_of<T>::type type1;
                        ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_quotient_op<double> (const double &, const double &)>' requested here
  typedef typename result_of<
                   ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>>>' requested here
template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind>
                                                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>>>' required here
  : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type
                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_quotient_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, Eigen::Dense>' requested here
  public CwiseBinaryOpImpl<
         ^
./matrixIterators/MatrixOps.h:246:43: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>>' requested here
        res.col_stats.row(1) = mean * nnz / n_rows;
                                          ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_quotient_op<double> (const double &, const double &)>' has been explicitly marked deprecated here
template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of;
                                 ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from fragment_utils.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/Core:367:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_square_op<double> (const double &)>' is deprecated [-Wdeprecated-declarations]
  typedef typename std::result_of<T>::type type1;
                        ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:21:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_square_op<double> (const double &)>' requested here
  typedef typename result_of<
                   ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseUnaryOp<Eigen::internal::scalar_square_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>>' requested here
template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind>
                                                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:95:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseUnaryOp<Eigen::internal::scalar_square_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>>' required here
  : public internal::generic_xpr_base<CwiseUnaryOp<UnaryOp, XprType> >::type
                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:55:29: note: in instantiation of template class 'Eigen::CwiseUnaryOpImpl<Eigen::internal::scalar_square_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, Eigen::Dense>' requested here
class CwiseUnaryOp : public CwiseUnaryOpImpl<UnaryOp, XprType, typename internal::traits<XprType>::StorageKind>, internal::no_assignment_operator
                            ^
./matrixIterators/MatrixOps.h:253:24: note: in instantiation of template class 'Eigen::CwiseUnaryOp<Eigen::internal::scalar_square_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>' requested here
            (m2 + mean.square() * nnz * ((double)n_rows - nnz) / n_rows) / (n_rows - 1);
                       ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_square_op<double> (const double &)>' has been explicitly marked deprecated here
template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of;
                                 ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from fragment_utils.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/Core:367:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_difference_op<double> (const double &, const double &)>' is deprecated [-Wdeprecated-declarations]
  typedef typename std::result_of<T>::type type1;
                        ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_difference_op<double> (const double &, const double &)>' requested here
  typedef typename result_of<
                   ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>>' requested here
template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind>
                                                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>>' required here
  : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type
                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, Eigen::Dense>' requested here
  public CwiseBinaryOpImpl<
         ^
./matrixIterators/MatrixOps.h:253:57: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>' requested here
            (m2 + mean.square() * nnz * ((double)n_rows - nnz) / n_rows) / (n_rows - 1);
                                                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_difference_op<double> (const double &, const double &)>' has been explicitly marked deprecated here
template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of;
                                 ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from fragment_utils.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/Core:367:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_sum_op<double> (const double &, const double &)>' is deprecated [-Wdeprecated-declarations]
  typedef typename std::result_of<T>::type type1;
                        ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_sum_op<double> (const double &, const double &)>' requested here
  typedef typename result_of<
                   ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseUnaryOp<Eigen::internal::scalar_square_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>>>>' requested here
template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind>
                                                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseUnaryOp<Eigen::internal::scalar_square_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>>>>' required here
  : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type
                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_sum_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseUnaryOp<Eigen::internal::scalar_square_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>>, Eigen::Dense>' requested here
  public CwiseBinaryOpImpl<
         ^
./matrixIterators/MatrixOps.h:253:17: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseUnaryOp<Eigen::internal::scalar_square_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>>>' requested here
            (m2 + mean.square() * nnz * ((double)n_rows - nnz) / n_rows) / (n_rows - 1);
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_sum_op<double> (const double &, const double &)>' has been explicitly marked deprecated here
template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of;
                                 ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include   -march=native -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas  -fPIC  -falign-functions=64 -Wall -g -O2  -c matrix_io.cpp -o matrix_io.o
In file included from matrix_io.cpp:5:
In file included from ./matrixIterators/ImportMatrixHDF5.h:5:
In file included from ./matrixIterators/StoredMatrix.h:5:
In file included from ./matrixIterators/MatrixIterator.h:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/Core:367:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_product_op<double> (const double &, const double &)>' is deprecated [-Wdeprecated-declarations]
  typedef typename std::result_of<T>::type type1;
                        ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_product_op<double> (const double &, const double &)>' requested here
  typedef typename result_of<
                   ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1, 1>>, const Eigen::Block<const Eigen::Map<Eigen::Matrix<double, -1, -1, 0>, 0>, 1, -1, false>>>' requested here
template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind>
                                                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1, 1>>, const Eigen::Block<const Eigen::Map<Eigen::Matrix<double, -1, -1, 0>, 0>, 1, -1, false>>>' required here
  : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type
                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1, 1>>, const Eigen::Block<const Eigen::Map<Eigen::Matrix<double, -1, -1, 0>, 0>, 1, -1, false>, Eigen::Dense>' requested here
  public CwiseBinaryOpImpl<
         ^
./matrixIterators/MatrixOps.h:32:63: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1, 1>>, const Eigen::Block<const Eigen::Map<Eigen::Matrix<double, -1, -1, 0>, 0>, 1, -1, false>>' requested here
                res.col(row_data[i]) += ((double)val_data[i]) * B.row(col);
                                                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_product_op<double> (const double &, const double &)>' has been explicitly marked deprecated here
template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of;
                                 ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from matrix_io.cpp:5:
In file included from ./matrixIterators/ImportMatrixHDF5.h:5:
In file included from ./matrixIterators/StoredMatrix.h:5:
In file included from ./matrixIterators/MatrixIterator.h:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/Core:367:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_quotient_op<double> (const double &, const double &)>' is deprecated [-Wdeprecated-declarations]
  typedef typename std::result_of<T>::type type1;
                        ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_quotient_op<double> (const double &, const double &)>' requested here
  typedef typename result_of<
                   ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>>>' requested here
template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind>
                                                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>>>' required here
  : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type
                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_quotient_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, Eigen::Dense>' requested here
  public CwiseBinaryOpImpl<
         ^
./matrixIterators/MatrixOps.h:246:43: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>>' requested here
        res.col_stats.row(1) = mean * nnz / n_rows;
                                          ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_quotient_op<double> (const double &, const double &)>' has been explicitly marked deprecated here
template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of;
                                 ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from matrix_io.cpp:5:
In file included from ./matrixIterators/ImportMatrixHDF5.h:5:
In file included from ./matrixIterators/StoredMatrix.h:5:
In file included from ./matrixIterators/MatrixIterator.h:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/Core:367:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_square_op<double> (const double &)>' is deprecated [-Wdeprecated-declarations]
  typedef typename std::result_of<T>::type type1;
                        ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:21:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_square_op<double> (const double &)>' requested here
  typedef typename result_of<
                   ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseUnaryOp<Eigen::internal::scalar_square_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>>' requested here
template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind>
                                                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:95:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseUnaryOp<Eigen::internal::scalar_square_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>>' required here
  : public internal::generic_xpr_base<CwiseUnaryOp<UnaryOp, XprType> >::type
                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:55:29: note: in instantiation of template class 'Eigen::CwiseUnaryOpImpl<Eigen::internal::scalar_square_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, Eigen::Dense>' requested here
class CwiseUnaryOp : public CwiseUnaryOpImpl<UnaryOp, XprType, typename internal::traits<XprType>::StorageKind>, internal::no_assignment_operator
                            ^
./matrixIterators/MatrixOps.h:253:24: note: in instantiation of template class 'Eigen::CwiseUnaryOp<Eigen::internal::scalar_square_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>' requested here
            (m2 + mean.square() * nnz * ((double)n_rows - nnz) / n_rows) / (n_rows - 1);
                       ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_square_op<double> (const double &)>' has been explicitly marked deprecated here
template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of;
                                 ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from matrix_io.cpp:5:
In file included from ./matrixIterators/ImportMatrixHDF5.h:5:
In file included from ./matrixIterators/StoredMatrix.h:5:
In file included from ./matrixIterators/MatrixIterator.h:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/Core:367:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_difference_op<double> (const double &, const double &)>' is deprecated [-Wdeprecated-declarations]
  typedef typename std::result_of<T>::type type1;
                        ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_difference_op<double> (const double &, const double &)>' requested here
  typedef typename result_of<
                   ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>>' requested here
template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind>
                                                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>>' required here
  : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type
                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, Eigen::Dense>' requested here
  public CwiseBinaryOpImpl<
         ^
./matrixIterators/MatrixOps.h:253:57: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>' requested here
            (m2 + mean.square() * nnz * ((double)n_rows - nnz) / n_rows) / (n_rows - 1);
                                                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_difference_op<double> (const double &, const double &)>' has been explicitly marked deprecated here
template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of;
                                 ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from matrix_io.cpp:5:
In file included from ./matrixIterators/ImportMatrixHDF5.h:5:
In file included from ./matrixIterators/StoredMatrix.h:5:
In file included from ./matrixIterators/MatrixIterator.h:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/Core:367:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_sum_op<double> (const double &, const double &)>' is deprecated [-Wdeprecated-declarations]
  typedef typename std::result_of<T>::type type1;
                        ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_sum_op<double> (const double &, const double &)>' requested here
  typedef typename result_of<
                   ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseUnaryOp<Eigen::internal::scalar_square_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>>>>' requested here
template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind>
                                                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseUnaryOp<Eigen::internal::scalar_square_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>>>>' required here
  : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type
                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_sum_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseUnaryOp<Eigen::internal::scalar_square_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>>, Eigen::Dense>' requested here
  public CwiseBinaryOpImpl<
         ^
./matrixIterators/MatrixOps.h:253:17: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double>, const Eigen::CwiseUnaryOp<Eigen::internal::scalar_square_op<double>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>, const Eigen::Block<Eigen::Array<double, -1, -1, 0>, 1, -1, false>>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1>>>>' requested here
            (m2 + mean.square() * nnz * ((double)n_rows - nnz) / n_rows) / (n_rows - 1);
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_sum_op<double> (const double &, const double &)>' has been explicitly marked deprecated here
template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of;
                                 ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from matrix_io.cpp:9:
./matrixIterators/StoredMatrixTransposeWriter.h:39:35: error: no matching function for call to 'min'
            uint32_t copy_count = std::min(row.size() - loaded, available);
                                  ^~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__algorithm/min.h:39:1: note: candidate template ignored: deduced conflicting types for parameter '_Tp' ('unsigned long long' vs. 'unsigned long')
min(const _Tp& __a, const _Tp& __b)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__algorithm/min.h:50:1: note: candidate template ignored: could not match 'initializer_list<type-parameter-0-0>' against 'unsigned long long'
min(initializer_list<_Tp> __t, _Compare __comp)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__algorithm/min.h:59:1: note: candidate function template not viable: requires single argument '__t', but 2 arguments were provided
min(initializer_list<_Tp> __t)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__algorithm/min.h:30:1: note: candidate function template not viable: requires 3 arguments, but 2 were provided
min(const _Tp& __a, const _Tp& __b, _Compare __comp)
^
5 warnings and 1 error generated.
make: *** [matrix_io.o] Error 1
ERROR: compilation failed for package ‘BPCells’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BPCells’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/92/rwb8659d3jl658jf5nmmvw580000gn/T//RtmpTTpNt9/file82b725d082db/BPCells_0.1.0.tar.gz’ had non-zero exit status

sessionInfo() output

> sessionInfo()
R version 4.3.0 Patched (2023-04-27 r84336)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

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

loaded via a namespace (and not attached):
[1] compiler_4.3.0 tools_4.3.0    curl_5.0.0     remotes_2.4.2 

[bnprks]

Hi Sam, I think the issue you're getting is caused by a mistake I had present in the main branch for a couple hours yesterday. I believe it should be fixed now if you try to install again.

Could you let me know if it works for you when you reinstall?

Separately, I've been getting several reports that installing clang via conda is not working for people with older Macs. I've updated the instructions in that original issue here, to a recommendation that I tested successfully on a 2015 iMac. Basically, I installed everything via homebrew and didn't use conda for hdf5 or clang. From your current error messages, I don't think you should need to make changes to your compiler, hopefully it will work with the fix I added last night.

[bnprks]

I'm closing this for inactivity, but please do re-open or comment if you are continuing to have issues.

I've been working on improving the installation process for Mac users, but I don't use a Mac as my daily computer so hearing feedback of what works and doesn't is especially helpful.

[samuel-marsh]

Hi

sounds good! Sorry I have been out of lab for bit so haven’t chance to try solution but will give it a go this week and report back.

Best,
Sam