* installing *source* package ‘SimBIID’ ...
** package ‘SimBIID’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 18.1.4’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/SimBIID/src'
/usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c RcppExports.cpp -o RcppExports.o
/usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c adaptUpdate.cpp -o adaptUpdate.o
/usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c bootstrapParticleFilter.cpp -o bootstrapParticleFilter.o
In file included from adaptUpdate.cpp:1:
In file included from ./functions.h:6:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29:
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/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages]
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |           ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages]
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |             ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages]
  329 |   #pragma message ("INFO: see the documentation for details")
      |           ^
In file included from bootstrapParticleFilter.cpp:1:
In file included from ./functions.h:6:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29:
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/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages]
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |           ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages]
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |             ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages]
  329 |   #pragma message ("INFO: see the documentation for details")
      |           ^
/usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c bootstrapParticleFilterState.cpp -o bootstrapParticleFilterState.o
3 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c cholArma.cpp -o cholArma.o
3 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c mvrnormArma.cpp -o mvrnormArma.o
In file included from bootstrapParticleFilterState.cpp:1:
In file included from ./functions.h:6:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29:
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/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages]
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |           ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages]
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |             ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages]
  329 |   #pragma message ("INFO: see the documentation for details")
      |           ^
In file included from cholArma.cpp:1:
In file included from ./functions.h:6:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29:
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/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages]
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |           ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages]
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |             ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages]
  329 |   #pragma message ("INFO: see the documentation for details")
      |           ^
In file included from mvrnormArma.cpp:1:
In file included from ./functions.h:6:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29:
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/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages]
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |           ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages]
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |             ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages]
  329 |   #pragma message ("INFO: see the documentation for details")
      |           ^
/usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c pmcmc.cpp -o pmcmc.o
In file included from pmcmc.cpp:1:
In file included from ./functions.h:6:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29:
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/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages]
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |           ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages]
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |             ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages]
  329 |   #pragma message ("INFO: see the documentation for details")
      |           ^
3 warnings generated.
3 warnings generated.
3 warnings generated.
3 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++11 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o SimBIID.so RcppExports.o adaptUpdate.o bootstrapParticleFilter.o bootstrapParticleFilterState.o cholArma.o mvrnormArma.o pmcmc.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortran_main -lFortranRuntime -lFortranDecimal -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/SimBIID/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/SimBIID/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/SimBIID/src'
installing to /data/gannet/ripley/R/packages/tests-clang/SimBIID.Rcheck/00LOCK-SimBIID/00new/SimBIID/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (SimBIID)