Install log for 'spCP'

* installing *source* package ‘spCP’ ...
** package ‘spCP’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (GCC) 14.0.1 20240503 (prerelease)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/spCP/src'
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c CovarianceFunctions.cpp -o CovarianceFunctions.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c DIAG_Conversion.cpp -o DIAG_Conversion.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c DIAG_GetLogLik.cpp -o DIAG_GetLogLik.o
DIAG_GetLogLik.cpp: In function 'double GetLogLikMean(Rcpp::List, Rcpp::List)':
DIAG_GetLogLik.cpp:53:10: warning: 'LogLikMean' may be used uninitialized [-Wmaybe-uninitialized]
   53 |   return LogLikMean;
      |          ^~~~~~~~~~
DIAG_GetLogLik.cpp:47:10: note: 'LogLikMean' was declared here
   47 |   double LogLikMean;
      |          ^~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c DIAG_NormalLogLik.cpp -o DIAG_NormalLogLik.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c DIAG_ProbitLogLik.cpp -o DIAG_ProbitLogLik.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c DIAG_SamplePPD.cpp -o DIAG_SamplePPD.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c DIAG_TobitLogLik.cpp -o DIAG_TobitLogLik.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c DistributionFunctions.cpp -o DistributionFunctions.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c MCMC_Conversion.cpp -o MCMC_Conversion.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c MCMC_Samplers.cpp -o MCMC_Samplers.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c MCMC_Utilities.cpp -o MCMC_Utilities.o
MCMC_Samplers.cpp: In function 'std::pair<para, metrobj> SampleEta(datobj, para, metrobj)':
MCMC_Samplers.cpp:611:18: warning: 'ThetaLocProposal' may be used uninitialized [-Wmaybe-uninitialized]
  611 |       Theta(Loc) = ThetaLocProposal;
      |       ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
MCMC_Samplers.cpp:547:42: note: 'ThetaLocProposal' was declared here
  547 |   double TuningSD, LogR, EtaLocProposal, ThetaLocProposal;
      |                                          ^~~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c MCMC_spCP.cpp -o MCMC_spCP.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c PRED_Conversion.cpp -o PRED_Conversion.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c PRED_PredictFuture.cpp -o PRED_PredictFuture.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c Play.cpp -o Play.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c UtilityFunctions.cpp -o UtilityFunctions.o
PRED_PredictFuture.cpp: In function 'arma::cube PredictFuture(Rcpp::List, Rcpp::List, int)':
PRED_PredictFuture.cpp:44:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   44 |   for (arma::uword i = 0; i < NKeep; i++) {
      |                           ~~^~~~~~~
PRED_PredictFuture.cpp:55:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   55 |     for (arma::uword t = 0; t < NNewTimes; t++) {
      |                             ~~^~~~~~~~~~~
PRED_PredictFuture.cpp:56:33: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   56 |       for (arma::uword s = 0; s < M; s++) {
      |                               ~~^~~
PRED_PredictFuture.cpp:63:76: warning: 'Sigma' may be used uninitialized [-Wmaybe-uninitialized]
   63 |         YPred.subcube(i, s, t, i, s, t) = fmax(0, arma::as_scalar(rnormRcpp(1, Mu, Sigma)));
      |                                                                   ~~~~~~~~~^~~~~~~~~~~~~~
PRED_PredictFuture.cpp:41:27: note: 'Sigma' was declared here
   41 |   double NewTime, CP, Mu, Sigma;
      |                           ^~~~~
PRED_PredictFuture.cpp:63:76: warning: 'Mu' may be used uninitialized [-Wmaybe-uninitialized]
   63 |         YPred.subcube(i, s, t, i, s, t) = fmax(0, arma::as_scalar(rnormRcpp(1, Mu, Sigma)));
      |                                                                   ~~~~~~~~~^~~~~~~~~~~~~~
PRED_PredictFuture.cpp:41:23: note: 'Mu' was declared here
   41 |   double NewTime, CP, Mu, Sigma;
      |                       ^~
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o spCP.so CovarianceFunctions.o DIAG_Conversion.o DIAG_GetLogLik.o DIAG_NormalLogLik.o DIAG_ProbitLogLik.o DIAG_SamplePPD.o DIAG_TobitLogLik.o DistributionFunctions.o MCMC_Conversion.o MCMC_Samplers.o MCMC_Utilities.o MCMC_spCP.o PRED_Conversion.o PRED_PredictFuture.o Play.o RcppExports.o UtilityFunctions.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/spCP/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/spCP/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/spCP/src'
installing to /data/gannet/ripley/R/packages/tests-devel/spCP.Rcheck/00LOCK-spCP/00new/spCP/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (spCP)