* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* 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: ‘gcc-14 (Debian 14.3.0-8) 14.3.0’
using C++ compiler: ‘g++-14 (Debian 14.3.0-8) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpHsHrs8/R.INSTALL248f63772e1a5d/momentuHMM/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c XBloop.cpp -o XBloop.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c getDM.cpp -o getDM.o
gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c momentuHMM_init.c -o momentuHMM_init.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c nLogLike.cpp -o nLogLike.o
In file included from nLogLike.cpp:1:
densities.h: In function ‘arma::colvec dweibull_rcpp(Rcpp::NumericVector, arma::mat, arma::mat)’:
densities.h:58:24: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
58 | if(!arma::is_finite(x(i)))
| ~~~~~~~~~~~~~~~^~~~~~
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:518,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32,
from densities.h:4:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
densities.h: In function ‘arma::colvec dnorm_rcpp(Rcpp::NumericVector, arma::mat, arma::mat)’:
densities.h:83:24: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
83 | if(!arma::is_finite(x(i)))
| ~~~~~~~~~~~~~~~^~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
densities.h: In function ‘arma::colvec dlnorm_rcpp(Rcpp::NumericVector, arma::mat, arma::mat)’:
densities.h:108:24: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
108 | if(!arma::is_finite(x(i)))
| ~~~~~~~~~~~~~~~^~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
densities.h: In function ‘arma::colvec dexp_rcpp(Rcpp::NumericVector, arma::mat, arma::mat)’:
densities.h:133:24: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
133 | if(!arma::is_finite(x(i)))
| ~~~~~~~~~~~~~~~^~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
densities.h: In function ‘arma::colvec dvm_rcpp(Rcpp::NumericVector, arma::mat, arma::mat)’:
densities.h:160:24: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
160 | if(!arma::is_finite(x(i)))
| ~~~~~~~~~~~~~~~^~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
densities.h: In function ‘arma::colvec dbeta_rcpp(Rcpp::NumericVector, arma::mat, arma::mat)’:
densities.h:215:24: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
215 | if(!arma::is_finite(x(i)))
| ~~~~~~~~~~~~~~~^~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
densities.h: In function ‘arma::colvec dpois_rcpp(Rcpp::NumericVector, arma::mat, arma::mat)’:
densities.h:240:24: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
240 | if(!arma::is_finite(x(i)))
| ~~~~~~~~~~~~~~~^~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
densities.h: In function ‘arma::colvec dbern_rcpp(Rcpp::NumericVector, arma::mat, arma::mat)’:
densities.h:265:24: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
265 | if(!arma::is_finite(x(i)))
| ~~~~~~~~~~~~~~~^~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
densities.h: In function ‘arma::colvec dnbinom_rcpp(Rcpp::NumericVector, arma::mat, arma::mat)’:
densities.h:462:24: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
462 | if(!arma::is_finite(x(i)))
| ~~~~~~~~~~~~~~~^~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
densities.h: In function ‘arma::colvec dlogis_rcpp(Rcpp::NumericVector, arma::mat, arma::mat)’:
densities.h:487:24: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
487 | if(!arma::is_finite(x(i)))
| ~~~~~~~~~~~~~~~^~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
densities.h: In function ‘arma::colvec dt_rcpp(Rcpp::NumericVector, arma::mat, arma::mat)’:
densities.h:512:24: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
512 | if(!arma::is_finite(x(i)))
| ~~~~~~~~~~~~~~~^~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
nLogLike.cpp: In function ‘double nLogLike_rcpp(int, arma::mat, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::List, Rcpp::List, Rcpp::IntegerVector, Rcpp::List, Rcpp::List, bool, Rcpp::IntegerVector, Rcpp::IntegerVector, int)’:
nLogLike.cpp:242:28: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
242 | if(!arma::is_finite(tmpL(i))) {
| ~~~~~~~~~~~~~~~^~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c trMatrix.cpp -o trMatrix.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o momentuHMM.so RcppExports.o XBloop.o getDM.o momentuHMM_init.o nLogLike.o trMatrix.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpHsHrs8/R.INSTALL248f63772e1a5d/momentuHMM/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpHsHrs8/R.INSTALL248f63772e1a5d/momentuHMM/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpHsHrs8/R.INSTALL248f63772e1a5d/momentuHMM/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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
converting help for package ‘momentuHMM’
finding HTML links ... done
AIC.momentuHMM html
AICweights html
CIbeta html
CIreal html
HMMfits html
MIfitHMM html
MIpool html
XBloop_rcpp html
allProbs html
checkPar0 html
circAngles html
crawlMerge html
crawlWrap html
crwData html
crwHierData html
crwHierSim html
crwSim html
dbern_rcpp html
dbeta_rcpp html
dcat_rcpp html
dexp_rcpp html
dgamma_rcpp html
distAngle html
dlnorm_rcpp html
dlogis_rcpp html
dmvnorm_rcpp html
dnbinom_rcpp html
dnorm_rcpp html
dpois_rcpp html
dt_rcpp html
dvm_rcpp html
dweibull_rcpp html
dwrpcauchy_rcpp html
exampleData html
expandPar html
fitHMM html
formatHierHMM html
getCovNames html
getDM_rcpp html
getPar html
getPar0 html
getParDM html
getTrProbs html
is.HMMfits html
is.crwData html
is.crwHierData html
is.crwHierSim html
is.crwSim html
is.miHMM html
is.miSum html
is.momentuHMM html
is.momentuHMMData html
is.momentuHierHMM html
is.momentuHierHMMData html
logAlpha html
logBeta html
miHMM html
miSum html
mixtureProbs html
momentuHMM html
momentuHMMData html
momentuHierHMM html
momentuHierHMMData html
n2w html
nLogLike html
nLogLike_rcpp html
parDef html
plot.crwData html
plot.miHMM html
plot.miSum html
plot.momentuHMM html
plot.momentuHMMData html
plotPR html
plotSat html
plotSpatialCov html
plotStates html
plotStationary html
prepData html
print.miHMM html
print.miSum html
print.momentuHMM html
pseudoRes html
randomEffects html
setModelName html
setStateNames html
simData html
simObsData html
stateProbs html
stationary html
summary.momentuHMMData html
timeInStates html
trMatrix_rcpp html
turnAngle html
viterbi html
w2n html
** 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)