Install log for 'growfunctions'

* installing *source* package ‘growfunctions’ ...
** this is package ‘growfunctions’ version ‘0.16’
** package ‘growfunctions’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 21.1.1’
using C++ compiler: ‘clang version 21.1.1’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/growfunctions/src'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c dpmix.cpp -o dpmix.o
dpmix.cpp:150:9: warning: 'is_finite<arma::Mat<double>>' is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations]
  150 |     if( is_finite(ksi) ) /* grab number of predictors, R. */
      |         ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:178:3: note: 'is_finite<arma::Mat<double>>' has been explicitly marked deprecated here
  178 | [[deprecated("change arma::is_finite(X) to X.is_finite()")]]
      |   ^
dpmix.cpp:159:9: warning: 'is_finite<arma::Mat<double>>' is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations]
  159 |     if( is_finite(ksi) )
      |         ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:178:3: note: 'is_finite<arma::Mat<double>>' has been explicitly marked deprecated here
  178 | [[deprecated("change arma::is_finite(X) to X.is_finite()")]]
      |   ^
dpmix.cpp:252:14: warning: 'is_finite<arma::Mat<double>>' is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations]
  252 |         if( !is_finite(ksi) ) /* no dependent PPM */
      |              ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:178:3: note: 'is_finite<arma::Mat<double>>' has been explicitly marked deprecated here
  178 | [[deprecated("change arma::is_finite(X) to X.is_finite()")]]
      |   ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c dpmix_count.cpp -o dpmix_count.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c dpmix_moves.cpp -o dpmix_moves.o
3 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c gen_bb.cpp -o gen_bb.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c gp.cpp -o gp.o
dpmix_count.cpp:157:9: warning: 'is_finite<arma::Mat<double>>' is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations]
  157 |     if( is_finite(ksi) ) /* grab number of predictors, R. */
      |         ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:178:3: note: 'is_finite<arma::Mat<double>>' has been explicitly marked deprecated here
  178 | [[deprecated("change arma::is_finite(X) to X.is_finite()")]]
      |   ^
dpmix_count.cpp:166:9: warning: 'is_finite<arma::Mat<double>>' is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations]
  166 |     if( is_finite(ksi) )
      |         ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:178:3: note: 'is_finite<arma::Mat<double>>' has been explicitly marked deprecated here
  178 | [[deprecated("change arma::is_finite(X) to X.is_finite()")]]
      |   ^
dpmix_count.cpp:293:14: warning: 'is_finite<arma::Mat<double>>' is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations]
  293 |         if( !is_finite(ksi) ) /* no dependent PPM */
      |              ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:178:3: note: 'is_finite<arma::Mat<double>>' has been explicitly marked deprecated here
  178 | [[deprecated("change arma::is_finite(X) to X.is_finite()")]]
      |   ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c gpbfix.cpp -o gpbfix.o
3 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c gpdpbmix.cpp -o gpdpbmix.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c gpdpmix.cpp -o gpdpmix.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c gpdpmix_moves.cpp -o gpdpmix_moves.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c gpfix.cpp -o gpfix.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -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    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c growfunctions_init.c -o growfunctions_init.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c lsqcluster_cpp.cpp -o lsqcluster_cpp.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c sppmcarmix_moves.cpp -o sppmcarmix_moves.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c utility.cpp -o utility.o
/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 growfunctions.so dpmix.o dpmix_count.o dpmix_moves.o gen_bb.o gp.o gpbfix.o gpdpbmix.o gpdpmix.o gpdpmix_moves.o gpfix.o growfunctions_init.o lsqcluster_cpp.o sppmcarmix_moves.o utility.o -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/growfunctions/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/growfunctions/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/growfunctions/src'
installing to /data/gannet/ripley/R/packages/tests-clang/growfunctions.Rcheck/00LOCK-growfunctions/00new/growfunctions/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (growfunctions)