Install log for 'LassoHiDFastGibbs'

* installing *source* package ‘LassoHiDFastGibbs’ ...
** this is package ‘LassoHiDFastGibbs’ version ‘0.1.4’
** package ‘LassoHiDFastGibbs’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/LassoHiDFastGibbs/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppNumerical/include' -I'/data/gannet/ripley/R/test-dev/RcppClock/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c LassoHiDFastGibbs-package.cpp -o LassoHiDFastGibbs-package.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppNumerical/include' -I'/data/gannet/ripley/R/test-dev/RcppClock/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c LassoHiDFastGibbs.cpp -o LassoHiDFastGibbs.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppNumerical/include' -I'/data/gannet/ripley/R/test-dev/RcppClock/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppNumerical/include' -I'/data/gannet/ripley/R/test-dev/RcppClock/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c blasso_2bg.cpp -o blasso_2bg.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppNumerical/include' -I'/data/gannet/ripley/R/test-dev/RcppClock/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c blasso_gibbs_hans.cpp -o blasso_gibbs_hans.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppNumerical/include' -I'/data/gannet/ripley/R/test-dev/RcppClock/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c lasso_distribution.cpp -o lasso_distribution.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppNumerical/include' -I'/data/gannet/ripley/R/test-dev/RcppClock/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c lm_penalized_gibbs.cpp -o lm_penalized_gibbs.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppNumerical/include' -I'/data/gannet/ripley/R/test-dev/RcppClock/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c lm_penalized_nested_gibbs.cpp -o lm_penalized_nested_gibbs.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppNumerical/include' -I'/data/gannet/ripley/R/test-dev/RcppClock/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c lm_penalized_pcg.cpp -o lm_penalized_pcg.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppNumerical/include' -I'/data/gannet/ripley/R/test-dev/RcppClock/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c rao_blackwell_densities.cpp -o rao_blackwell_densities.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppNumerical/include' -I'/data/gannet/ripley/R/test-dev/RcppClock/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c rinvgaussian.cpp -o rinvgaussian.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppNumerical/include' -I'/data/gannet/ripley/R/test-dev/RcppClock/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c slice_samplers.cpp -o slice_samplers.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppNumerical/include' -I'/data/gannet/ripley/R/test-dev/RcppClock/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c zeta.cpp -o zeta.o
slice_samplers.cpp: In function ‘double slice_orthogonal(double, arma::vec, arma::vec, double, double, double, double, double, double, double)’:
slice_samplers.cpp:204:35: warning: ‘x_star’ may be used uninitialized [-Wmaybe-uninitialized]
  204 |   double f_star = f_fun_orthogonal(x_star, vs2, vc2, a_til, b, u_til, v, yTy); num_fun_evals ++;
      |                   ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
slice_samplers.cpp:179:10: note: ‘x_star’ was declared here
  179 |   double x_star;
      |          ^~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:435,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32,
                 from slice_samplers.cpp:3:
In function ‘void arma::arma_check(bool, const T1&) [with T1 = char [66]]’,
    inlined from ‘arma::vec arma::randu(uword, const distr_param&)’ at /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_randu.hpp:122:23,
    inlined from ‘double slice_orthogonal(double, arma::vec, arma::vec, double, double, double, double, double, double, double)’ at slice_samplers.cpp:289:34:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/debug.hpp:434:3: warning: ‘xL’ may be used uninitialized [-Wmaybe-uninitialized]
  434 |   if(state)  { arma_stop_logic_error(arma_str::str_wrapper(x)); }
      |   ^~
slice_samplers.cpp: In function ‘double slice_orthogonal(double, arma::vec, arma::vec, double, double, double, double, double, double, double)’:
slice_samplers.cpp:230:10: note: ‘xL’ was declared here
  230 |   double xL;
      |          ^~
In function ‘void arma::arma_check(bool, const T1&) [with T1 = char [66]]’,
    inlined from ‘arma::vec arma::randu(uword, const distr_param&)’ at /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_randu.hpp:122:23,
    inlined from ‘double slice_orthogonal(double, arma::vec, arma::vec, double, double, double, double, double, double, double)’ at slice_samplers.cpp:289:34:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/debug.hpp:434:3: warning: ‘xR’ may be used uninitialized [-Wmaybe-uninitialized]
  434 |   if(state)  { arma_stop_logic_error(arma_str::str_wrapper(x)); }
      |   ^~
slice_samplers.cpp: In function ‘double slice_orthogonal(double, arma::vec, arma::vec, double, double, double, double, double, double, double)’:
slice_samplers.cpp:231:10: note: ‘xR’ was declared here
  231 |   double xR;
      |          ^~
lm_penalized_nested_gibbs.cpp: In function ‘Rcpp::List lm_penalized_nested_gibbs(const arma::vec&, const arma::mat&, Rcpp::String, const double&, const double&, const double&, const double&, const int&, const double&, const arma::vec&, const int&, const double&, const double&, int, int)’:
lm_penalized_nested_gibbs.cpp:202:57: warning: ‘sigma2’ may be used uninitialized [-Wmaybe-uninitialized]
  202 |         vu = sqrt(sigma2/lambda2)*(va_invsqrt % randn(p)); // O(p)
      |                                                         ^
lm_penalized_nested_gibbs.cpp:103:10: note: ‘sigma2’ was declared here
  103 |   double sigma2;
      |          ^~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:667,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32,
                 from lm_penalized_nested_gibbs.cpp:10:
In constructor ‘arma::eOp<T1, eop_type>::eOp(const T1&, typename T1::elem_type) [with T1 = arma::Col<double>; eop_type = arma::eop_scalar_times]’,
    inlined from ‘typename arma::enable_if2<arma::is_arma_type<T1>::value, const arma::eOp<T1, arma::eop_scalar_times> >::result arma::operator*(typename T1::elem_type, const T1&) [with T1 = Col<double>]’ at /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/operator_times.hpp:47:39,
    inlined from ‘Rcpp::List lm_penalized_nested_gibbs(const arma::vec&, const arma::mat&, Rcpp::String, const double&, const double&, const double&, const double&, const int&, const double&, const arma::vec&, const int&, const double&, const double&, int, int)’ at lm_penalized_nested_gibbs.cpp:195:55:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/eOp_meat.hpp:38:5: warning: ‘sigma’ may be used uninitialized [-Wmaybe-uninitialized]
   38 |   , aux(in_aux)
      |     ^~~~~~~~~~~
lm_penalized_nested_gibbs.cpp: In function ‘Rcpp::List lm_penalized_nested_gibbs(const arma::vec&, const arma::mat&, Rcpp::String, const double&, const double&, const double&, const double&, const int&, const double&, const arma::vec&, const int&, const double&, const double&, int, int)’:
lm_penalized_nested_gibbs.cpp:104:10: note: ‘sigma’ was declared here
  104 |   double sigma;
      |          ^~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o LassoHiDFastGibbs.so LassoHiDFastGibbs-package.o LassoHiDFastGibbs.o RcppExports.o blasso_2bg.o blasso_gibbs_hans.o lasso_distribution.o lm_penalized_gibbs.o lm_penalized_nested_gibbs.o lm_penalized_pcg.o rao_blackwell_densities.o rinvgaussian.o slice_samplers.o zeta.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/LassoHiDFastGibbs/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/LassoHiDFastGibbs/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/LassoHiDFastGibbs/src'
installing to /data/gannet/ripley/R/packages/tests-devel/LassoHiDFastGibbs.Rcheck/00LOCK-LassoHiDFastGibbs/00new/LassoHiDFastGibbs/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (LassoHiDFastGibbs)