Install log for 'shrinkTVP'

* installing *source* package ‘shrinkTVP’ ...
** package ‘shrinkTVP’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 19.1.5’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/shrinkTVP/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c DG_MH_step.cpp -o DG_MH_step.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c DG_log_ratio_value.cpp -o DG_log_ratio_value.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c DG_sampling_functions.cpp -o DG_sampling_functions.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c R_utilities.cpp -o R_utilities.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c TG_MH_step.cpp -o TG_MH_step.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c TG_log_ratio_value.cpp -o TG_log_ratio_value.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c TG_sampling_functions.cpp -o TG_sampling_functions.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c common_sampling_functions.cpp -o common_sampling_functions.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c cpp_utilities.cpp -o cpp_utilities.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c do_rgig1.cpp -o do_rgig1.o
do_rgig1.cpp:20:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
   20 |   int count = 0;
      |       ^
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c dyn_sampling_steps.cpp -o dyn_sampling_steps.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c exports.cpp -o exports.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c rho_p_MH_step.cpp -o rho_p_MH_step.o
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c sample_DG_TVP.cpp -o sample_DG_TVP.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c sample_TG_TVP.cpp -o sample_TG_TVP.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c sample_beta_McCausland.cpp -o sample_beta_McCausland.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c sample_beta_McCausland_dyn.cpp -o sample_beta_McCausland_dyn.o
rho_p_MH_step.cpp:26:10: warning: unused variable 'lone_minus_prop' [-Wunused-variable]
   26 |   double lone_minus_prop = std::log(1 - proposal);
      |          ^~~~~~~~~~~~~~~
rho_p_MH_step.cpp:27:10: warning: unused variable 'lone_minus_old' [-Wunused-variable]
   27 |   double lone_minus_old = std::log(1 - old_val);
      |          ^~~~~~~~~~~~~~
2 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c shrinkDTVP.cpp -o shrinkDTVP.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_WARN_LEVEL=0 -DARMA_NO_DEBUG -DSTRICT_R_HEADERS `/data/gannet/ripley/R/R-clang/bin/Rscript -e "RcppGSL:::CFlags()"` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/GIGrvg/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/stochvol/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c shrinkTVP.cpp -o shrinkTVP.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o shrinkTVP.so DG_MH_step.o DG_log_ratio_value.o DG_sampling_functions.o R_utilities.o TG_MH_step.o TG_log_ratio_value.o TG_sampling_functions.o common_sampling_functions.o cpp_utilities.o do_rgig1.o dyn_sampling_steps.o exports.o rho_p_MH_step.o sample_DG_TVP.o sample_TG_TVP.o sample_beta_McCausland.o sample_beta_McCausland_dyn.o shrinkDTVP.o shrinkTVP.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortranRuntime -lFortranDecimal -lm -lgsl -lgslcblas -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/shrinkTVP/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/shrinkTVP/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/shrinkTVP/src'
installing to /data/gannet/ripley/R/packages/tests-clang/shrinkTVP.Rcheck/00LOCK-shrinkTVP/00new/shrinkTVP/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (shrinkTVP)