Install log for 'XDNUTS'

* installing *source* package ‘XDNUTS’ ...
** this is package ‘XDNUTS’ version ‘1.6.3’
** package ‘XDNUTS’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 21.1.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/XDNUTS/src'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c dnuts.cpp -o dnuts.o
In file included from dnuts.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c epsilon_adapt.cpp -o epsilon_adapt.o
In file included from epsilon_adapt.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c epsilon_init.cpp -o epsilon_init.o
In file included from epsilon_init.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c globals.cpp -o globals.o
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c globals_functions.cpp -o globals_functions.o
In file included from globals.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
In file included from globals_functions.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c globals_interact.cpp -o globals_interact.o
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c leapfrog.cpp -o leapfrog.o
In file included from globals_interact.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
In file included from leapfrog.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c mcmc.cpp -o mcmc.o
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c recursive_tree.cpp -o recursive_tree.o
In file included from mcmc.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
In file included from recursive_tree.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c single_hmc.cpp -o single_hmc.o
In file included from single_hmc.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c single_nuts.cpp -o single_nuts.o
In file included from single_nuts.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang21/lib/clang/21/lib/x86_64-unknown-linux-gnu -o XDNUTS.so RcppExports.o dnuts.o epsilon_adapt.o epsilon_init.o globals.o globals_functions.o globals_interact.o leapfrog.o mcmc.o recursive_tree.o single_hmc.o single_nuts.o -fopenmp -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lflang_rt.runtime -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/XDNUTS/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/XDNUTS/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/XDNUTS/src'
installing to /data/gannet/ripley/R/packages/tests-clang/XDNUTS.Rcheck/00LOCK-XDNUTS/00new/XDNUTS/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (XDNUTS)