* installing *source* package ‘momentuHMM’ ...
** this is package ‘momentuHMM’ version ‘1.5.6’
** package ‘momentuHMM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 21.1.2’
using C++ compiler: ‘clang version 21.1.2’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/momentuHMM/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 RcppExports.cpp -o RcppExports.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 XBloop.cpp -o XBloop.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 getDM.cpp -o getDM.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 momentuHMM_init.c -o momentuHMM_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 nLogLike.cpp -o nLogLike.o
In file included from nLogLike.cpp:1:
./densities.h:58:15: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
   58 |     if(!arma::is_finite(x(i)))
      |               ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
  164 | [[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
      |   ^
In file included from nLogLike.cpp:1:
./densities.h:83:15: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
   83 |     if(!arma::is_finite(x(i)))
      |               ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
  164 | [[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
      |   ^
In file included from nLogLike.cpp:1:
./densities.h:108:15: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  108 |     if(!arma::is_finite(x(i)))
      |               ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
  164 | [[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
      |   ^
In file included from nLogLike.cpp:1:
./densities.h:133:15: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  133 |     if(!arma::is_finite(x(i)))
      |               ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
  164 | [[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
      |   ^
In file included from nLogLike.cpp:1:
./densities.h:160:15: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  160 |     if(!arma::is_finite(x(i)))
      |               ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
  164 | [[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
      |   ^
In file included from nLogLike.cpp:1:
./densities.h:215:15: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  215 |     if(!arma::is_finite(x(i)))
      |               ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
  164 | [[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
      |   ^
In file included from nLogLike.cpp:1:
./densities.h:240:15: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  240 |     if(!arma::is_finite(x(i)))
      |               ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
  164 | [[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
      |   ^
In file included from nLogLike.cpp:1:
./densities.h:265:15: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  265 |     if(!arma::is_finite(x(i)))
      |               ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
  164 | [[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
      |   ^
In file included from nLogLike.cpp:1:
./densities.h:462:15: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  462 |     if(!arma::is_finite(x(i)))
      |               ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
  164 | [[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
      |   ^
In file included from nLogLike.cpp:1:
./densities.h:487:15: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  487 |     if(!arma::is_finite(x(i)))
      |               ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
  164 | [[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
      |   ^
In file included from nLogLike.cpp:1:
./densities.h:512:15: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  512 |     if(!arma::is_finite(x(i)))
      |               ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
  164 | [[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
      |   ^
nLogLike.cpp:242:19: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  242 |         if(!arma::is_finite(tmpL(i))) {
      |                   ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
  164 | [[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
      |   ^
/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 trMatrix.cpp -o trMatrix.o
12 warnings 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 momentuHMM.so RcppExports.o XBloop.o getDM.o momentuHMM_init.o nLogLike.o trMatrix.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/momentuHMM/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/momentuHMM/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/momentuHMM/src'
installing to /data/gannet/ripley/R/packages/tests-clang/momentuHMM.Rcheck/00LOCK-momentuHMM/00new/momentuHMM/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 (momentuHMM)