ERROR: compilation failed for package ‘Rphylopars’

[jailynai]

I can't upload the package

I don't know what happened

the code following behind:

require(devtools) library(bitops) library(RCurl) library(httr) set_config( config( ssl_verifypeer = 0L ) ) install_github("ericgoolsby/Rphylopars",dependencies = TRUE) Downloading GitHub repo ericgoolsby/Rphylopars@master Your system is ready to build packages! ✔ checking for file ‘/private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmpCCU1Wv/remotes638d4c5086c6/ericgoolsby-Rphylopars-9378482/DESCRIPTION’ ... ─ preparing ‘Rphylopars’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:103: unknown macro '\item' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:105: unknown macro '\item' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:109: unexpected section header '\value' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:111: unknown macro '\item' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:112: unknown macro '\item' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:113: unknown macro '\item' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:114: unknown macro '\item' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:115: unknown macro '\item' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:116: unknown macro '\item' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:117: unknown macro '\item' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:118: unknown macro '\item' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:119: unknown macro '\item' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:120: unknown macro '\item' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:121: unknown macro '\item' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:123: unexpected section header '\references' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:133: unexpected section header '\author' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:137: unexpected section header '\examples' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.Rd:164: unexpected END_OF_INPUT ' ' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.lm.Rd:110: unknown macro '\item' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.lm.Rd:114: unexpected section header '\value' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.lm.Rd:117: unexpected section header '\examples' Warning: /private/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T/RtmprpwSmq/Rbuild657138654f11/Rphylopars/man/phylopars.lm.Rd:123: unexpected END_OF_INPUT ' ' ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘Rphylopars_0.2.10.tar.gz’

• installing source package ‘Rphylopars’ ... using staged installation libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c phylopars_rcpp.cpp -o phylopars_rcpp.o phylopars_rcpp.cpp:125:11: warning: 'set_stream_err2' is deprecated [-Wdeprecated-declarations] arma::set_stream_err2(nullstream); ^ /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include/armadillo_bits/debug.hpp:99:1: note: 'set_stream_err2' has been explicitly marked deprecated here arma_deprecated ^ /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:303:44: note: expanded from macro 'arma_deprecated'

  define arma_deprecated attribute((deprecated))

                                     ^

  phylopars_rcpp.cpp:128:12: warning: 'inv<arma::Mat >' is deprecated [-Wdeprecated-declarations] Minv = inv(M,"std");
  ^ /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include/armadillo_bits/fn_inv.hpp:60:1: note: 'inv<arma::Mat >' has been explicitly marked deprecated here arma_deprecated ^ /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:303:44: note: expanded from macro 'arma_deprecated'

  define arma_deprecated attribute((deprecated))

                                     ^

  phylopars_rcpp.cpp:144:11: warning: 'set_stream_err2' is deprecated [-Wdeprecated-declarations] arma::set_stream_err2(nullstream); ^ /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include/armadillo_bits/debug.hpp:99:1: note: 'set_stream_err2' has been explicitly marked deprecated here arma_deprecated ^ /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:303:44: note: expanded from macro 'arma_deprecated'

  define arma_deprecated attribute((deprecated))

                                     ^

  phylopars_rcpp.cpp:146:14: warning: 'solve<arma::Mat, arma::Mat >' is deprecated [-Wdeprecated-declarations] Msolve = solve(M,V,"std"); ^ /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include/armadillo_bits/fn_solve.hpp:67:1: note: 'solve<arma::Mat, arma::Mat >' has been explicitly marked deprecated here arma_deprecated ^ /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:303:44: note: expanded from macro 'arma_deprecated'

  define arma_deprecated attribute((deprecated))

                                     ^

  phylopars_rcpp.cpp:179:11: warning: 'set_stream_err2' is deprecated [-Wdeprecated-declarations] arma::set_stream_err2(nullstream); ^ /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include/armadillo_bits/debug.hpp:99:1: note: 'set_stream_err2' has been explicitly marked deprecated here arma_deprecated ^ /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:303:44: note: expanded from macro 'arma_deprecated'

  define arma_deprecated attribute((deprecated))

                                     ^

  5 warnings generated. clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rphylopars.so RcppExports.o phylopars_rcpp.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' ld: warning: directory not found for option '-L/usr/local/gfortran/lib' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [Rphylopars.so] Error 1 ERROR: compilation failed for package ‘Rphylopars’

• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rphylopars’ Error: Failed to install 'Rphylopars' from GitHub: (converted from warning) installation of package ‘/var/folders/v2/pjk2jy6530q27qj22dyhkzgc0000gn/T//RtmpCCU1Wv/file638d29e58704/Rphylopars_0.2.10.tar.gz’ had non-zero exit status

[r03ert0]

maybe you need to install gfortran first?

[ntraut]

If you are under a new version of macOS, maybe you have to reconfigure the R toolchain for compilation. See: https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/