* installing *source* package ‘BayesianLasso’ ...
** this is package ‘BayesianLasso’ version ‘0.3.5’
** package ‘BayesianLasso’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/BayesianLasso/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/RcppNumerical/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/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 Modified_Hans_Gibbs.cpp -o Modified_Hans_Gibbs.o
Modified_Hans_Gibbs.cpp: In function ‘Rcpp::List Modified_Hans_Gibbs(arma::mat, arma::vec, double, double, double, double, int, arma::vec, double, double, int)’:
Modified_Hans_Gibbs.cpp:85:12: warning: variable ‘denom’ set but not used [-Wunused-but-set-variable]
   85 |     double denom;
      |            ^~~~~
Modified_Hans_Gibbs.cpp:72:10: warning: unused variable ‘b_til’ [-Wunused-variable]
   72 |   double b_til = b1;
      |          ^~~~~
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/RcppNumerical/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/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 Modified_PC_Gibbs.cpp -o Modified_PC_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/RcppNumerical/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/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
Modified_PC_Gibbs.cpp: In function ‘arma::mat crossprod_cpp(arma::mat, arma::vec, arma::mat, double)’:
Modified_PC_Gibbs.cpp:153:7: warning: unused variable ‘n’ [-Wunused-variable]
  153 |   int n = mX.n_rows;
      |       ^
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/RcppNumerical/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/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
lasso_distribution.cpp: In function ‘int check_abc(double, double, double)’:
lasso_distribution.cpp:221:33: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  221 |   bool a_inf = (!arma::is_finite(a)),
      |                  ~~~~~~~~~~~~~~~^~~
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:518,
                 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 lasso_distribution.cpp:3:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
lasso_distribution.cpp:222:30: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  222 |     b_inf = (!arma::is_finite(b)),
      |               ~~~~~~~~~~~~~~~^~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
lasso_distribution.cpp:223:30: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  223 |     c_inf = (!arma::is_finite(c));
      |               ~~~~~~~~~~~~~~~^~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
lasso_distribution.cpp: In function ‘double zcalc_7sf(double, double, double, int)’:
lasso_distribution.cpp:265:7: warning: unused variable ‘error_type’ [-Wunused-variable]
  265 |   int error_type = check_abc( a,  b,  c);
      |       ^~~~~~~~~~
lasso_distribution.cpp: In function ‘Rcpp::List calculate_lasso_dist_stats_c_v2(double, double, double)’:
lasso_distribution.cpp:420:38: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  420 |   bool m_plus_inf = (!arma::is_finite(m_plus));
      |                       ~~~~~~~~~~~~~~~^~~~~~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
lasso_distribution.cpp:421:39: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  421 |   bool m_minus_inf = (!arma::is_finite(m_plus));
      |                        ~~~~~~~~~~~~~~~^~~~~~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
lasso_distribution.cpp:348:7: warning: unused variable ‘error_type’ [-Wunused-variable]
  348 |   int error_type = check_abc( a, b, c);
      |       ^~~~~~~~~~
lasso_distribution.cpp: In function ‘double zlasso(double, double, double, bool)’:
lasso_distribution.cpp:491:23: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  491 |   if (!arma::is_finite(z)) {
      |        ~~~~~~~~~~~~~~~^~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
lasso_distribution.cpp: In function ‘arma::vec dlasso_internal(arma::vec, double, double, double, bool)’:
lasso_distribution.cpp:528:23: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  528 |   if (!arma::is_finite(z)) {
      |        ~~~~~~~~~~~~~~~^~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
lasso_distribution.cpp: In function ‘arma::vec plasso_internal(arma::vec, double, double, double)’:
lasso_distribution.cpp:586:10: warning: unused variable ‘m_plus’ [-Wunused-variable]
  586 |   double m_plus = res["m_plus"];
      |          ^~~~~~
lasso_distribution.cpp:587:10: warning: unused variable ‘m_minus’ [-Wunused-variable]
  587 |   double m_minus = res["m_minus"];
      |          ^~~~~~~
lasso_distribution.cpp: In function ‘arma::vec qlasso_internal(arma::vec, double, double, double)’:
lasso_distribution.cpp:768:25: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  768 |     if (!arma::is_finite(x[i])) {
      |          ~~~~~~~~~~~~~~~^~~~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
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/RcppNumerical/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/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
rinvgaussian.cpp: In function ‘double rinvgaussian_slice(double, double, double, double)’:
rinvgaussian.cpp:116:10: warning: unused variable ‘sigma’ [-Wunused-variable]
  116 |   double sigma  = sqrt(sigma2);
      |          ^~~~~
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/RcppNumerical/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/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_sampler.cpp -o slice_sampler.o
slice_sampler.cpp: In function ‘double slice_sampler_precision_c(double, double, double, double)’:
slice_sampler.cpp:51:10: warning: unused variable ‘p_star’ [-Wunused-variable]
   51 |   double p_star = exp(f_star);
      |          ^~~~~~
slice_sampler.cpp:56:10: warning: unused variable ‘sigma’ [-Wunused-variable]
   56 |   double sigma  = sqrt(sigma2);
      |          ^~~~~
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/RcppNumerical/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/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
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o BayesianLasso.so Modified_Hans_Gibbs.o Modified_PC_Gibbs.o RcppExports.o lasso_distribution.o rinvgaussian.o slice_sampler.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/BayesianLasso/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/BayesianLasso/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/BayesianLasso/src'
installing to /data/gannet/ripley/R/packages/tests-devel/BayesianLasso.Rcheck/00LOCK-BayesianLasso/00new/BayesianLasso/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** 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 (BayesianLasso)