fail to install skyspline

[ghost]

I try to install the package "skyspline" using command install_github("emvolz-phylodynamics/skyspline") many times in window system. I fail to install it, could you please tell me how to deal with it, thanks.

[emvolz]

Hi Lixing. Can you you post the error message?

You may also want to try `skygrowth' which may be easier to use. https://github.com/mrc-ide/skygrowth

[ghost]

install_github("emvolz-phylodynamics/skyspline") Downloading GitHub repo emvolz-phylodynamics/skyspline@master from URL https://api.github.com/repos/emvolz-phylodynamics/skyspline/zipball/master Installing skyspline Installing 1 package: ggplot2 Installing package into ‘C:/Users/xingguang/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/windows/contrib/3.5/ggplot2_3.0.0.zip' Content type 'application/zip' length 3579961 bytes (3.4 MB) downloaded 3.4 MB

package ‘ggplot2’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\xingguang\AppData\Local\Temp\RtmpaEfR2x\downloaded_packages Installing 1 package: RcppArmadillo Installing package into ‘C:/Users/xingguang/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/windows/contrib/3.5/RcppArmadillo_0.8.600.0.0.zip' Content type 'application/zip' length 2262528 bytes (2.2 MB) downloaded 2.2 MB

package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\xingguang\AppData\Local\Temp\RtmpaEfR2x\downloaded_packages "C:/PROGRA~1/R/R-35~1.0/bin/x64/R" --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ "C:/Users/xingguang/AppData/Local/Temp/RtmpaEfR2x/devtoolsf4069ad4808/emvolz-phylodynamics-skyspline-46512fe" \ --library="C:/Users/xingguang/Documents/R/win-library/3.5" --install-tests

• installing source package 'skyspline' ... * libs c:/Rtools/mingw_64/bin/g++ -I"C:/PROGRA~1/R/R-35~1.0/include" -DNDEBUG -I"C:/Users/xingguang/Documents/R/win-library/3.5/Rcpp/include" -I"C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include" -I"C:/Users/xingguang/Documents/R/win-library/3.5/BH/include" -O2 -Wall -mtune=generic -c Mmodel0.cpp -o Mmodel0.o Mmodel0.cpp: In function 'Rcpp::List update_lambda_gx_node(double, double, arma::vec, double)': Mmodel0.cpp:22:6: warning: unused variable 'i' [-Wunused-variable] int i,j,k; ^ Mmodel0.cpp:22:8: warning: unused variable 'j' [-Wunused-variable] int i,j,k; ^ Mmodel0.cpp: In function 'Rcpp::List update_lambda_gx_node2(double, double, arma::vec, double)': Mmodel0.cpp:57:6: warning: unused variable 'i' [-Wunused-variable] int i,j,k; ^ Mmodel0.cpp:57:8: warning: unused variable 'j' [-Wunused-variable] int i,j,k; ^ Mmodel0.cpp:71:9: warning: unused variable 'sumwk' [-Wunused-variable] double sumwk = 0.; ^ Mmodel0.cpp: In function 'Rcpp::List eventTimes2extant(arma::vec, arma::vec, arma::vec)': Mmodel0.cpp:99:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i =0 ; i < eventTimes.size(); i++){ ^ Mmodel0.cpp:105:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int u = 0 ; u < nodeheights.size(); u++){ ^ c:/Rtools/mingw_64/bin/g++ -I"C:/PROGRA~1/R/R-35~1.0/include" -DNDEBUG -I"C:/Users/xingguang/Documents/R/win-library/3.5/Rcpp/include" -I"C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include" -I"C:/Users/xingguang/Documents/R/win-library/3.5/BH/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o c:/Rtools/mingw_64/bin/g++ -I"C:/PROGRA~1/R/R-35~1.0/include" -DNDEBUG -I"C:/Users/xingguang/Documents/R/win-library/3.5/Rcpp/include" -I"C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include" -I"C:/Users/xingguang/Documents/R/win-library/3.5/BH/include" -O2 -Wall -mtune=generic -c dgdt0.cpp -o dgdt0.o dgdt0.cpp:42:26: error: reference to 'state_type' is ambiguous void operator() ( const state_type &x , state_type &dxdt , double t)//, const double / t / ) ^ dgdt0.cpp:22:29: note: candidates are: typedef class std::vector<double, std::allocator > state_type typedef std::vector state_type; ^ In file included from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo:103:0, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadilloForward.h:46, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadillo.h:31, from dgdt0.cpp:14: C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo_bits/arma_forward.hpp:235:8: note: struct arma::state_type struct state_type ^ dgdt0.cpp:42:26: error: 'state_type' does not name a type void operator() ( const state_type &x , state_type &dxdt , double t)//, const double / t / ) ^ dgdt0.cpp:42:42: error: reference to 'state_type' is ambiguous void operator() ( const state_type &x , state_type &dxdt , double t)//, const double / t / ) ^ dgdt0.cpp:22:29: note: candidates are: typedef class std::vector<double, std::allocator > state_type typedef std::vector state_type; ^ In file included from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo:103:0, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadilloForward.h:46, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadillo.h:31, from dgdt0.cpp:14: C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo_bits/arma_forward.hpp:235:8: note: struct arma::state_type struct state_type ^ dgdt0.cpp:42:42: error: 'state_type' has not been declared void operator() ( const state_type &x , state_type &dxdt , double t)//, const double / t / ) ^ dgdt0.cpp:97:2: error: reference to 'state_type' is ambiguous state_type get_statevec0(){ ^ dgdt0.cpp:22:29: note: candidates are: typedef class std::vector<double, std::allocator > state_type typedef std::vector state_type; ^ In file included from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo:103:0, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadilloForward.h:46, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadillo.h:31, from dgdt0.cpp:14: C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo_bits/arma_forward.hpp:235:8: note: struct arma::state_type struct state_type ^ dgdt0.cpp:97:2: error: 'state_type' does not name a type state_type get_statevec0(){ ^ dgdt0.cpp:105:20: error: reference to 'state_type' is ambiguous double get_Lambda(state_type x){ ^ dgdt0.cpp:22:29: note: candidates are: typedef class std::vector<double, std::allocator > state_type typedef std::vector state_type; ^ In file included from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo:103:0, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadilloForward.h:46, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadillo.h:31, from dgdt0.cpp:14: C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo_bits/arma_forward.hpp:235:8: note: struct arma::state_type struct state_type ^ dgdt0.cpp:105:20: error: 'state_type' has not been declared double get_Lambda(state_type x){ ^ dgdt0.cpp:108:12: error: reference to 'state_type' is ambiguous vec get_g(state_type x){ ^ dgdt0.cpp:22:29: note: candidates are: typedef class std::vector<double, std::allocator > state_type typedef std::vector state_type; ^ In file included from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo:103:0, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadilloForward.h:46, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadillo.h:31, from dgdt0.cpp:14: C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo_bits/arma_forward.hpp:235:8: note: struct arma::state_type struct state_type ^ dgdt0.cpp:108:12: error: 'state_type' has not been declared vec get_g(state_type x){ ^ dgdt0.cpp: In member function 'void ODE_dgdt0::operator()(const int&, int&, double)': dgdt0.cpp:56:23: error: request for member 'at' in 'x', which is of non-class type 'const int' g(k-1) = max(0., x.at(k-1)); ^ dgdt0.cpp:57:24: error: request for member 'at' in 'x', which is of non-class type 'const int' ug(k-1) = max(0., x.at(k-1)); ^ dgdt0.cpp:80:10: error: request for member 'at' in 'x', which is of non-class type 'const int' if (x.at(k-1) < 0){ ^ dgdt0.cpp:81:10: error: request for member 'at' in 'dxdt', which is of non-class type 'int' dxdt.at(k - 1)= max(0., (g2(k-1) - g(k-1)) tr); // ^ dgdt0.cpp:83:10: error: request for member 'at' in 'dxdt', which is of non-class type 'int' dxdt.at(k - 1)= (g2(k-1) - g(k-1)) tr; // ^ dgdt0.cpp:95:8: error: request for member 'at' in 'dxdt', which is of non-class type 'int' dxdt.at( i_Lambda() ) = dLdt; ^ dgdt0.cpp: In member function 'double ODE_dgdt0::get_Lambda(int)': dgdt0.cpp:106:12: error: request for member 'at' in 'x', which is of non-class type 'int' return x.at(i_Lambda()); ^ dgdt0.cpp: In member function 'arma::vec ODE_dgdt0::get_g(int)': dgdt0.cpp:111:13: error: request for member 'at' in 'x', which is of non-class type 'int' g(i) = x.at(i); ^ dgdt0.cpp: In function 'Rcpp::List solve_dgdt0(arma::vec, arma::vec, arma::vec, arma::vec, double, double, double, double, double, double)': dgdt0.cpp:142:2: error: reference to 'state_type' is ambiguous state_type x = dgdt0.get_statevec0(); ^ dgdt0.cpp:22:29: note: candidates are: typedef class std::vector<double, std::allocator > state_type typedef std::vector state_type; ^ In file included from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo:103:0, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadilloForward.h:46, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadillo.h:31, from dgdt0.cpp:14: C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo_bits/arma_forward.hpp:235:8: note: struct arma::state_type struct state_type ^ dgdt0.cpp:143:61: error: 'x' was not declared in this scope size_t steps = boost::numeric::odeint::integrate( dgdt0 , x, h0 , h1 , (h1-h0)/100. );
  ^ dgdt0.cpp:143:9: warning: unused variable 'steps' [-Wunused-variable] size_t steps = boost::numeric::odeint::integrate( dgdt0 , x, h0 , h1 , (h1-h0)/100. );
  ^ dgdt0.cpp: At global scope: dgdt0.cpp:166:26: error: reference to 'state_type' is ambiguous void operator() ( const state_type &x , state_type &dxdt , double t)//, const double / t / ) ^ dgdt0.cpp:22:29: note: candidates are: typedef class std::vector<double, std::allocator > state_type typedef std::vector state_type; ^ In file included from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo:103:0, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadilloForward.h:46, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadillo.h:31, from dgdt0.cpp:14: C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo_bits/arma_forward.hpp:235:8: note: struct arma::state_type struct state_type ^ dgdt0.cpp:166:26: error: 'state_type' does not name a type void operator() ( const state_type &x , state_type &dxdt , double t)//, const double / t / ) ^ dgdt0.cpp:166:42: error: reference to 'state_type' is ambiguous void operator() ( const state_type &x , state_type &dxdt , double t)//, const double / t / ) ^ dgdt0.cpp:22:29: note: candidates are: typedef class std::vector<double, std::allocator > state_type typedef std::vector state_type; ^ In file included from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo:103:0, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadilloForward.h:46, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadillo.h:31, from dgdt0.cpp:14: C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo_bits/arma_forward.hpp:235:8: note: struct arma::state_type struct state_type ^ dgdt0.cpp:166:42: error: 'state_type' has not been declared void operator() ( const state_type &x , state_type &dxdt , double t)//, const double / t / ) ^ dgdt0.cpp:175:2: error: reference to 'state_type' is ambiguous state_type get_statevec0(){ ^ dgdt0.cpp:22:29: note: candidates are: typedef class std::vector<double, std::allocator > state_type typedef std::vector state_type; ^ In file included from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo:103:0, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadilloForward.h:46, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadillo.h:31, from dgdt0.cpp:14: C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo_bits/arma_forward.hpp:235:8: note: struct arma::state_type struct state_type ^ dgdt0.cpp:175:2: error: 'state_type' does not name a type state_type get_statevec0(){ ^ dgdt0.cpp:180:20: error: reference to 'state_type' is ambiguous double get_Lambda(state_type x){ ^ dgdt0.cpp:22:29: note: candidates are: typedef class std::vector<double, std::allocator > state_type typedef std::vector state_type; ^ In file included from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo:103:0, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadilloForward.h:46, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadillo.h:31, from dgdt0.cpp:14: C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo_bits/arma_forward.hpp:235:8: note: struct arma::state_type struct state_type ^ dgdt0.cpp:180:20: error: 'state_type' has not been declared double get_Lambda(state_type x){ ^ dgdt0.cpp: In member function 'void ODE_CoM12L::operator()(const int&, int&, double)': dgdt0.cpp:173:8: error: request for member 'at' in 'dxdt', which is of non-class type 'int' dxdt.at(0) = (g_A (g_A-1.)/2.) 2. f / std::max(1., ( y * y- y )); ^ dgdt0.cpp: In member function 'double ODE_CoM12L::get_Lambda(int)': dgdt0.cpp:181:12: error: request for member 'at' in 'x', which is of non-class type 'int' return x.at(0); ^ dgdt0.cpp: In function 'double solve_CoM12L(arma::vec, arma::vec, arma::vec, double, double, double, double)': dgdt0.cpp:199:2: error: reference to 'state_type' is ambiguous state_type x = com12L.get_statevec0(); ^ dgdt0.cpp:22:29: note: candidates are: typedef class std::vector<double, std::allocator > state_type typedef std::vector state_type; ^ In file included from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo:103:0, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadilloForward.h:46, from C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/RcppArmadillo.h:31, from dgdt0.cpp:14: C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include/armadillo_bits/arma_forward.hpp:235:8: note: struct arma::state_type struct state_type ^ dgdt0.cpp:200:62: error: 'x' was not declared in this scope size_t steps = boost::numeric::odeint::integrate( com12L , x, h0 , h1 , (h1-h0)/100. );
  ^ dgdt0.cpp:200:9: warning: unused variable 'steps' [-Wunused-variable] size_t steps = boost::numeric::odeint::integrate( com12L , x, h0 , h1 , (h1-h0)/100. );
  ^ dgdt0.cpp:203:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ make: *** [dgdt0.o] Error 1 ERROR: compilation failed for package 'skyspline'
• removing 'C:/Users/xingguang/Documents/R/win-library/3.5/skyspline' In R CMD INSTALL Installation failed: Command failed (1)

[ghost]

I tried many times, but failed to install it, could you please figure it out, thanks.

[emvolz]

The package hasn't been tested on windows. If you have access to linux or mac, can you try installing on that?

Can you post the output of

sessionInfo()

It's possible this would work with a more recent version of R.

I also suggest updating to most recent possible version of Rtools.

[ghost]

sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 [2] LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 [4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936

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

other attached packages: [1] Matrix_1.2-14

loaded via a namespace (and not attached): [1] compiler_3.5.0 tools_3.5.0 yaml_2.1.19 grid_3.5.0
[5] lattice_0.20-35

[emvolz]

I cleaned up the code in latest version (fc98171b937a9a390856b92defe724c75687075c) This was suggested by @richfitz. Can you checkout the latest and let me know if it compiles?

[ghost]

@emvolz ，thanks, I will checkout it now.

[ghost]

install_github("emvolz-phylodynamics/skyspline") Downloading GitHub repo emvolz-phylodynamics/skyspline@master from URL https://api.github.com/repos/emvolz-phylodynamics/skyspline/zipball/master Installing skyspline "C:/PROGRA~1/R/R-35~1.0/bin/x64/R" --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ "C:/Users/xingguang/AppData/Local/Temp/RtmpisFPfL/devtools3ac87a901282/emvolz-phylodynamics-skyspline-3b4957a" \ --library="C:/Users/xingguang/Documents/R/win-library/3.5" --install-tests

• installing source package 'skyspline' ... ** libs c:/Rtools/mingw_64/bin/g++ -I"C:/PROGRA~1/R/R-35~1.0/include" -DNDEBUG -I"C:/Users/xingguang/Documents/R/win-library/3.5/Rcpp/include" -I"C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include" -I"C:/Users/xingguang/Documents/R/win-library/3.5/BH/include" -O2 -Wall -mtune=generic -c Mmodel0.cpp -o Mmodel0.o Mmodel0.cpp: In function 'Rcpp::List update_lambda_gx_node(double, double, arma::vec, double)': Mmodel0.cpp:22:6: warning: unused variable 'i' [-Wunused-variable] int i,j,k; ^ Mmodel0.cpp:22:8: warning: unused variable 'j' [-Wunused-variable] int i,j,k; ^ Mmodel0.cpp: In function 'Rcpp::List update_lambda_gx_node2(double, double, arma::vec, double)': Mmodel0.cpp:57:6: warning: unused variable 'i' [-Wunused-variable] int i,j,k; ^ Mmodel0.cpp:57:8: warning: unused variable 'j' [-Wunused-variable] int i,j,k; ^ Mmodel0.cpp:71:9: warning: unused variable 'sumwk' [-Wunused-variable] double sumwk = 0.; ^ Mmodel0.cpp: In function 'Rcpp::List eventTimes2extant(arma::vec, arma::vec, arma::vec)': Mmodel0.cpp:99:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i =0 ; i < eventTimes.size(); i++){ ^ Mmodel0.cpp:105:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int u = 0 ; u < nodeheights.size(); u++){ ^ c:/Rtools/mingw_64/bin/g++ -I"C:/PROGRA~1/R/R-35~1.0/include" -DNDEBUG -I"C:/Users/xingguang/Documents/R/win-library/3.5/Rcpp/include" -I"C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include" -I"C:/Users/xingguang/Documents/R/win-library/3.5/BH/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o c:/Rtools/mingw_64/bin/g++ -I"C:/PROGRA~1/R/R-35~1.0/include" -DNDEBUG -I"C:/Users/xingguang/Documents/R/win-library/3.5/Rcpp/include" -I"C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include" -I"C:/Users/xingguang/Documents/R/win-library/3.5/BH/include" -O2 -Wall -mtune=generic -c dgdt0.cpp -o dgdt0.o dgdt0.cpp: In function 'Rcpp::List solve_dgdt0(arma::vec, arma::vec, arma::vec, arma::vec, double, double, double, double, double, double)': dgdt0.cpp:143:9: warning: unused variable 'steps' [-Wunused-variable] size_t steps = boost::numeric::odeint::integrate( dgdt0 , x, h0 , h1 , (h1-h0)/100. );
  ^ dgdt0.cpp: In function 'double solve_CoM12L(arma::vec, arma::vec, arma::vec, double, double, double, double)': dgdt0.cpp:200:9: warning: unused variable 'steps' [-Wunused-variable] size_t steps = boost::numeric::odeint::integrate( com12L , x, h0 , h1 , (h1-h0)/100. );
  ^ c:/Rtools/mingw_64/bin/g++ -I"C:/PROGRA~1/R/R-35~1.0/include" -DNDEBUG -I"C:/Users/xingguang/Documents/R/win-library/3.5/Rcpp/include" -I"C:/Users/xingguang/Documents/R/win-library/3.5/RcppArmadillo/include" -I"C:/Users/xingguang/Documents/R/win-library/3.5/BH/include" -O2 -Wall -mtune=generic -c semiparDemoProcessModel0.cpp -o semiparDemoProcessModel0.o semiparDemoProcessModel0.cpp: In constructor 'ODE_sp0::ODE_sp0(double, double, int)': semiparDemoProcessModel0.cpp:27:9: warning: 'ODE_sp0::t0' will be initialized after [-Wreorder] double t0; ^ semiparDemoProcessModel0.cpp:26:9: warning: 'double ODE_sp0::t1' [-Wreorder] double t1; ^ semiparDemoProcessModel0.cpp:31:2: warning: when initialized here [-Wreorder] ODEsp0(double t0, double t1, int res) : t0(t0),t1(t1),res(res_) { ^ semiparDemoProcessModel0.cpp: In function 'arma::vec solve_semiPar0(double, double, int, double, arma::vec, double, double, double)': semiparDemoProcessModel0.cpp:74:9: warning: unused variable 'steps' [-Wunused-variable] size_t steps = integrate_const( make_controlled( eps_abs , eps_rel , runge_kutta_fehlberg78() ) ^ c:/Rtools/mingw64/bin/g++ -shared -s -static-libgcc -o skyspline.dll tmp.def Mmodel0.o RcppExports.o dgdt0.o semiparDemoProcessModel0.o -LC:/PROGRA~1/R/R-35~1.0/bin/x64 -lR dgdt0.o:dgdt0.cpp:(.text+0x113f): undefined reference to `dasum' dgdt0.o:dgdt0.cpp:(.text$_ZN9ODE_dgdt0clERKSt6vectorIdSaIdEERS2_d[_ZN9ODE_dgdt0clERKSt6vectorIdSaIdEERS2d]+0x7aa): undefined reference to `dasum' collect2.exe: error: ld returned 1 exit status no DLL was created ERROR: compilation failed for package 'skyspline'
• removing 'C:/Users/xingguang/Documents/R/win-library/3.5/skyspline' In R CMD INSTALL Installation failed: Command failed (1)

[ghost]

@emvolz, error was the same as @sdwfrost

[richfitz]

This is I think a reference to a fortran library on linking. See https://github.com/RcppCore/RcppArmadillo/blob/34cafa7aaba76afe132e14627ee2cc171131b822/man/RcppArmadillo-package.Rd#L56-L59 - this will likely need adding to Makevars and Makevars.win

[ghost]

@richfitz can you solve this problem, thanks.