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bnprks / BPCells

Scaling Single Cell Analysis to Millions of Cells
https://bnprks.github.io/BPCells
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Installation on Mac Clang Issue? #20

Closed samuel-marsh closed 1 year ago

samuel-marsh commented 1 year ago

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 ```r 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 (const double &, const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::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 (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, const Eigen::CwiseNullaryOp, const Eigen::Matrix>, const Eigen::Block, 0>, 1, -1, false>>>' requested here template::XprKind, typename StorageKind = typename traits::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, const Eigen::CwiseNullaryOp, const Eigen::Matrix>, const Eigen::Block, 0>, 1, -1, false>>>' required here : public internal::generic_xpr_base >::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, const Eigen::CwiseNullaryOp, const Eigen::Matrix>, const Eigen::Block, 0>, 1, -1, false>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ ./matrixIterators/MatrixOps.h:32:63: note: in instantiation of template class 'Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix>, const Eigen::Block, 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 (const double &, const double &)>' has been explicitly marked deprecated here template 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 (const double &, const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::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 (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, const Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::Block, 1, -1, false>>, const Eigen::CwiseNullaryOp, const Eigen::Array>>>' requested here template::XprKind, typename StorageKind = typename traits::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, const Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::Block, 1, -1, false>>, const Eigen::CwiseNullaryOp, const Eigen::Array>>>' required here : public internal::generic_xpr_base >::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, const Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::Block, 1, -1, false>>, const Eigen::CwiseNullaryOp, const Eigen::Array>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ ./matrixIterators/MatrixOps.h:246:43: note: in instantiation of template class 'Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::Block, 1, -1, false>>, const Eigen::CwiseNullaryOp, const Eigen::Array>>' 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 (const double &, const double &)>' has been explicitly marked deprecated here template 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 (const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::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 (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, const Eigen::Block, 1, -1, false>>>' requested here template::XprKind, typename StorageKind = typename traits::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, const Eigen::Block, 1, -1, false>>>' required here : public internal::generic_xpr_base >::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, const Eigen::Block, 1, -1, false>, Eigen::Dense>' requested here class CwiseUnaryOp : public CwiseUnaryOpImpl::StorageKind>, internal::no_assignment_operator ^ ./matrixIterators/MatrixOps.h:253:24: note: in instantiation of template class 'Eigen::CwiseUnaryOp, const Eigen::Block, 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 (const double &)>' has been explicitly marked deprecated here template 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 (const double &, const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::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 (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, const Eigen::CwiseNullaryOp, const Eigen::Array>, const Eigen::Block, 1, -1, false>>>' requested here template::XprKind, typename StorageKind = typename traits::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, const Eigen::CwiseNullaryOp, const Eigen::Array>, const Eigen::Block, 1, -1, false>>>' required here : public internal::generic_xpr_base >::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, const Eigen::CwiseNullaryOp, const Eigen::Array>, const Eigen::Block, 1, -1, false>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ ./matrixIterators/MatrixOps.h:253:57: note: in instantiation of template class 'Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Array>, const Eigen::Block, 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 (const double &, const double &)>' has been explicitly marked deprecated here template 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 (const double &, const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::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 (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, const Eigen::Block, 1, -1, false>, const Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::CwiseUnaryOp, const Eigen::Block, 1, -1, false>>, const Eigen::Block, 1, -1, false>>, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Array>, const Eigen::Block, 1, -1, false>>>, const Eigen::CwiseNullaryOp, const Eigen::Array>>>>' requested here template::XprKind, typename StorageKind = typename traits::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, const Eigen::Block, 1, -1, false>, const Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::CwiseUnaryOp, const Eigen::Block, 1, -1, false>>, const Eigen::Block, 1, -1, false>>, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Array>, const Eigen::Block, 1, -1, false>>>, const Eigen::CwiseNullaryOp, const Eigen::Array>>>>' required here : public internal::generic_xpr_base >::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, const Eigen::Block, 1, -1, false>, const Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::CwiseUnaryOp, const Eigen::Block, 1, -1, false>>, const Eigen::Block, 1, -1, false>>, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Array>, const Eigen::Block, 1, -1, false>>>, const Eigen::CwiseNullaryOp, const Eigen::Array>>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ ./matrixIterators/MatrixOps.h:253:17: note: in instantiation of template class 'Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::CwiseUnaryOp, const Eigen::Block, 1, -1, false>>, const Eigen::Block, 1, -1, false>>, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Array>, const Eigen::Block, 1, -1, false>>>, const Eigen::CwiseNullaryOp, const Eigen::Array>>>' 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 (const double &, const double &)>' has been explicitly marked deprecated here template 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 (const double &, const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::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 (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, const Eigen::CwiseNullaryOp, const Eigen::Matrix>, const Eigen::Block, 0>, 1, -1, false>>>' requested here template::XprKind, typename StorageKind = typename traits::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, const Eigen::CwiseNullaryOp, const Eigen::Matrix>, const Eigen::Block, 0>, 1, -1, false>>>' required here : public internal::generic_xpr_base >::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, const Eigen::CwiseNullaryOp, const Eigen::Matrix>, const Eigen::Block, 0>, 1, -1, false>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ ./matrixIterators/MatrixOps.h:32:63: note: in instantiation of template class 'Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix>, const Eigen::Block, 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 (const double &, const double &)>' has been explicitly marked deprecated here template 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 (const double &, const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::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 (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, const Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::Block, 1, -1, false>>, const Eigen::CwiseNullaryOp, const Eigen::Array>>>' requested here template::XprKind, typename StorageKind = typename traits::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, const Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::Block, 1, -1, false>>, const Eigen::CwiseNullaryOp, const Eigen::Array>>>' required here : public internal::generic_xpr_base >::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, const Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::Block, 1, -1, false>>, const Eigen::CwiseNullaryOp, const Eigen::Array>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ ./matrixIterators/MatrixOps.h:246:43: note: in instantiation of template class 'Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::Block, 1, -1, false>>, const Eigen::CwiseNullaryOp, const Eigen::Array>>' 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 (const double &, const double &)>' has been explicitly marked deprecated here template 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 (const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::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 (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, const Eigen::Block, 1, -1, false>>>' requested here template::XprKind, typename StorageKind = typename traits::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, const Eigen::Block, 1, -1, false>>>' required here : public internal::generic_xpr_base >::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, const Eigen::Block, 1, -1, false>, Eigen::Dense>' requested here class CwiseUnaryOp : public CwiseUnaryOpImpl::StorageKind>, internal::no_assignment_operator ^ ./matrixIterators/MatrixOps.h:253:24: note: in instantiation of template class 'Eigen::CwiseUnaryOp, const Eigen::Block, 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 (const double &)>' has been explicitly marked deprecated here template 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 (const double &, const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::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 (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, const Eigen::CwiseNullaryOp, const Eigen::Array>, const Eigen::Block, 1, -1, false>>>' requested here template::XprKind, typename StorageKind = typename traits::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, const Eigen::CwiseNullaryOp, const Eigen::Array>, const Eigen::Block, 1, -1, false>>>' required here : public internal::generic_xpr_base >::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, const Eigen::CwiseNullaryOp, const Eigen::Array>, const Eigen::Block, 1, -1, false>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ ./matrixIterators/MatrixOps.h:253:57: note: in instantiation of template class 'Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Array>, const Eigen::Block, 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 (const double &, const double &)>' has been explicitly marked deprecated here template 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 (const double &, const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::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 (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, const Eigen::Block, 1, -1, false>, const Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::CwiseUnaryOp, const Eigen::Block, 1, -1, false>>, const Eigen::Block, 1, -1, false>>, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Array>, const Eigen::Block, 1, -1, false>>>, const Eigen::CwiseNullaryOp, const Eigen::Array>>>>' requested here template::XprKind, typename StorageKind = typename traits::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, const Eigen::Block, 1, -1, false>, const Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::CwiseUnaryOp, const Eigen::Block, 1, -1, false>>, const Eigen::Block, 1, -1, false>>, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Array>, const Eigen::Block, 1, -1, false>>>, const Eigen::CwiseNullaryOp, const Eigen::Array>>>>' required here : public internal::generic_xpr_base >::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, const Eigen::Block, 1, -1, false>, const Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::CwiseUnaryOp, const Eigen::Block, 1, -1, false>>, const Eigen::Block, 1, -1, false>>, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Array>, const Eigen::Block, 1, -1, false>>>, const Eigen::CwiseNullaryOp, const Eigen::Array>>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ ./matrixIterators/MatrixOps.h:253:17: note: in instantiation of template class 'Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::CwiseBinaryOp, const Eigen::CwiseUnaryOp, const Eigen::Block, 1, -1, false>>, const Eigen::Block, 1, -1, false>>, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Array>, const Eigen::Block, 1, -1, false>>>, const Eigen::CwiseNullaryOp, const Eigen::Array>>>' 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 (const double &, const double &)>' has been explicitly marked deprecated here template 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' 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 ```r > 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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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