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installation of package ‘/home/data/vip55/software/xtail_1.1.5-source.tar.gz’ had non-zero exit status

when i install xtail: it shows:

inferring 'repos = NULL' from 'pkgs'
* installing *source* package ‘xtail’ ...
** using staged installation
** libs
x86_64-conda-linux-gnu-c++ -std=gnu++11 -I"/home/data/vip55/miniconda3/lib/R/include" -DNDEBUG  -I'/home/data/vip55/miniconda3/lib/R/library/Rcpp/include' -I'/home/data/vip55/miniconda3/lib/R/library/RcppArmadillo/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/data/vip55/miniconda3/include -I/home/data/vip55/miniconda3/include -Wl,-rpath-link,/home/data/vip55/miniconda3/lib   -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/data/vip55/miniconda3/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1621013729234/work=/usr/local/src/conda/r-base-4.0.5 -fdebug-prefix-map=/home/data/vip55/miniconda3=/usr/local/src/conda-prefix  -c RcppExports.cpp -o RcppExports.o
x86_64-conda-linux-gnu-c++ -std=gnu++11 -I"/home/data/vip55/miniconda3/lib/R/include" -DNDEBUG  -I'/home/data/vip55/miniconda3/lib/R/library/Rcpp/include' -I'/home/data/vip55/miniconda3/lib/R/library/RcppArmadillo/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/data/vip55/miniconda3/include -I/home/data/vip55/miniconda3/include -Wl,-rpath-link,/home/data/vip55/miniconda3/lib   -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/data/vip55/miniconda3/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1621013729234/work=/usr/local/src/conda/r-base-4.0.5 -fdebug-prefix-map=/home/data/vip55/miniconda3=/usr/local/src/conda-prefix  -c fitBeta2.cpp -o fitBeta2.o
fitBeta2.cpp: In function 'Rcpp::List fitBeta2(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
fitBeta2.cpp:155:62: error: no matching function for call to 'arma::eGlue<arma::Glue<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::eglue_plus>::i(bool) const'
  155 |     hat_matrix = sqrt(w) * x * (x.t() * w * x + ridge).i(true) * x.t() * sqrt(w);
      |                                                              ^
In file included from /home/data/vip55/miniconda3/lib/R/library/RcppArmadillo/include/armadillo:586,
                 from /home/data/vip55/miniconda3/lib/R/library/RcppArmadillo/include/RcppArmadilloForward.h:49,
                 from /home/data/vip55/miniconda3/lib/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from fitBeta2.cpp:4:
/home/data/vip55/miniconda3/lib/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:846:1: note: candidate: 'const arma::Op<T2, arma::op_inv> arma::Base_extra_yes<elem_type, derived>::i() const [with elem_type = double; derived = arma::eGlue<arma::Glue<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::eglue_plus>]'
  846 | Base_extra_yes<elem_type, derived>::i() const
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/data/vip55/miniconda3/lib/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:846:1: note:   candidate expects 0 arguments, 1 provided
fitBeta2.cpp:158:43: error: no matching function for call to 'arma::eGlue<arma::Glue<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::eglue_plus>::i(bool) const'
  158 |     sigma = (x.t() * w * x + ridge).i(true) * x.t() * w * x * (x.t() * w * x + ridge).i(true);
      |                                           ^
In file included from /home/data/vip55/miniconda3/lib/R/library/RcppArmadillo/include/armadillo:586,
                 from /home/data/vip55/miniconda3/lib/R/library/RcppArmadillo/include/RcppArmadilloForward.h:49,
                 from /home/data/vip55/miniconda3/lib/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from fitBeta2.cpp:4:
/home/data/vip55/miniconda3/lib/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:846:1: note: candidate: 'const arma::Op<T2, arma::op_inv> arma::Base_extra_yes<elem_type, derived>::i() const [with elem_type = double; derived = arma::eGlue<arma::Glue<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::eglue_plus>]'
  846 | Base_extra_yes<elem_type, derived>::i() const
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/data/vip55/miniconda3/lib/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:846:1: note:   candidate expects 0 arguments, 1 provided
fitBeta2.cpp:158:93: error: no matching function for call to 'arma::eGlue<arma::Glue<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::eglue_plus>::i(bool) const'
  158 |     sigma = (x.t() * w * x + ridge).i(true) * x.t() * w * x * (x.t() * w * x + ridge).i(true);
      |                                                                                             ^
In file included from /home/data/vip55/miniconda3/lib/R/library/RcppArmadillo/include/armadillo:586,
                 from /home/data/vip55/miniconda3/lib/R/library/RcppArmadillo/include/RcppArmadilloForward.h:49,
                 from /home/data/vip55/miniconda3/lib/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from fitBeta2.cpp:4:
/home/data/vip55/miniconda3/lib/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:846:1: note: candidate: 'const arma::Op<T2, arma::op_inv> arma::Base_extra_yes<elem_type, derived>::i() const [with elem_type = double; derived = arma::eGlue<arma::Glue<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::eglue_plus>]'
  846 | Base_extra_yes<elem_type, derived>::i() const
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/data/vip55/miniconda3/lib/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:846:1: note:   candidate expects 0 arguments, 1 provided
make: *** [/home/data/vip55/miniconda3/lib/R/etc/Makeconf:181: fitBeta2.o] Error 1
ERROR: compilation failed for package ‘xtail’
* removing ‘/home/data/vip55/miniconda3/lib/R/library/xtail’
Warning message:
In install.packages("/home/data/vip55/software/xtail_1.1.5-source.tar.gz") :
  installation of package ‘/home/data/vip55/software/xtail_1.1.5-source.tar.gz’ had non-zero exit status

it's why? and how to solve?

ribo-seq xtail r install
• 1,067 views • link
updated by Michael Dondrup Michael Dondrup • written by 17318598206 • 17318598206

Please contact the maintainer or authors of this software directly, e.g. via github repo https://github.com/xryanglab/xtail and provide all details from systemInfo() in R. These kind of compilation errors are cases in which the authors of the software can help you best with. You can also try to find the R-package in conda and install it like that. Without system and version information there is nothing they or we could do though.

• 0 views • link
written by Michael Dondrup Michael Dondrup

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