* installing *source* package ‘nlmixr2est’ ...
** this is package ‘nlmixr2est’ version ‘3.0.4’
** package ‘nlmixr2est’ successfully unpacked and MD5 sums checked
** using staged installation
--------[begin src/Makevars]--------
# -*- mode: makefile-gmake -*-
ARMA=@ARMA@
BH=@BH@
RCPP=@RCPP@
RXP=@RXP@
CXX_STD = CXX17
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS)
PKG_CXXFLAGS = -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"$(BH)" -I"$(RCPP)" -I"$(ARMA)" -I"$(RXP)" $(SHLIB_OPENMP_CXXFLAGS) -DARMA_64BIT_WORD=1
SHLIB_LDFLAGS = $(SHLIB_CXXLDFLAGS)
SHLIB_LD = $(SHLIB_CXXLD)
SOURCES_C = init.c rprintf.c merge3.c lbfgsR.c utilc.c
SOURCES_CPP = uninformativeEtas.cpp nlm.cpp filterNormalLike.cpp inner.cpp shi21.cpp nearPD.cpp censEst.cpp saem.cpp expandNlme.cpp npde.cpp shrink.cpp ires.cpp res.cpp cwres.cpp censResid.cpp cholse.cpp neldermead.cpp resid.cpp slice.cpp RcppExportMod.cpp RcppExports.cpp
OBJECTS = $(SOURCES_CPP:.cpp=.o) $(SOURCES_C:.c=.o)
all: $(SHLIB)
$(SHLIB): $(OBJECTS)
--------[end src/Makevars]--------
** libs
using C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
using C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/nlmixr2est/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 uninformativeEtas.cpp -o uninformativeEtas.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 nlm.cpp -o nlm.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 filterNormalLike.cpp -o filterNormalLike.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 inner.cpp -o inner.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 shi21.cpp -o shi21.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 nearPD.cpp -o nearPD.o
nlm.cpp: In function ‘arma::vec nlmSolveF(arma::vec&)’:
nlm.cpp:399:7: warning: unused variable ‘cores’ [-Wunused-variable]
399 | int cores = getOpCores(op);
| ^~~~~
nlm.cpp: In function ‘arma::mat nlmSolveGrad(arma::vec&)’:
nlm.cpp:525:7: warning: unused variable ‘cores’ [-Wunused-variable]
525 | int cores = getOpCores(op);
| ^~~~~
nlm.cpp: In function ‘Rcpp::NumericVector solveGradNls(arma::vec&, int)’:
nlm.cpp:608:12: warning: unused variable ‘llik’ [-Wunused-variable]
608 | double llik;
| ^~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 censEst.cpp -o censEst.o
inner.cpp: In function ‘void parHistData(Rcpp::Environment, bool)’:
inner.cpp:37:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
37 | #define min2( a , b ) ( (a) < (b) ? (a) : (b) )
| ~~~~^~~~~
inner.cpp:5853:23: note: in expansion of macro ‘min2’
5853 | for (i = 0; i < min2(op_focei.npars+1, vals.n_cols); i++){
| ^~~~
inner.cpp:5853:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
5853 | for (i = 0; i < min2(op_focei.npars+1, vals.n_cols); i++){
| ^
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 saem.cpp -o saem.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 expandNlme.cpp -o expandNlme.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 npde.cpp -o npde.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 shrink.cpp -o shrink.o
npde.cpp: In function ‘void handleCensNpdeCdf(calcNpdeInfoId&, arma::Col<int>&, arma::vec&, int&, bool&, unsigned int, arma::vec&, arma::vec&, unsigned int&, bool&)’:
npde.cpp:129:15: warning: variable ‘hi’ set but not used [-Wunused-but-set-variable]
129 | double low, hi, low2, hi2;
| ^~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 ires.cpp -o ires.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 res.cpp -o res.o
inner.cpp: In function ‘Rcpp::List nlmixr2Gill83_(Rcpp::Function, Rcpp::NumericVector, Rcpp::Environment, Rcpp::LogicalVector, double, int, double, double, bool)’:
inner.cpp:4327:13: warning: ‘gillF’ may be used uninitialized [-Wmaybe-uninitialized]
4327 | fN[i] = gillF;
inner.cpp:4320:10: note: ‘gillF’ was declared here
4320 | double gillF;
| ^~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 cwres.cpp -o cwres.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 censResid.cpp -o censResid.o
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/bind/mem_fn.hpp:23,
from /data/gannet/ripley/R/test-dev/BH/include/boost/mem_fn.hpp:22,
from /data/gannet/ripley/R/test-dev/BH/include/boost/function/function_template.hpp:16,
from /data/gannet/ripley/R/test-dev/BH/include/boost/function.hpp:16,
from /data/gannet/ripley/R/test-dev/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /data/gannet/ripley/R/test-dev/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /data/gannet/ripley/R/test-dev/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /data/gannet/ripley/R/test-dev/BH/include/boost/algorithm/string/split.hpp:16,
from /data/gannet/ripley/R/test-dev/BH/include/boost/algorithm/string.hpp:23,
from res.cpp:3:
/data/gannet/ripley/R/test-dev/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/14/memory:78,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:38,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
from armahead.h:12,
from res.h:4,
from res.cpp:2:
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
res.cpp: In function ‘void calculateDfFull(arma::Col<int>&, arma::mat&, Rcpp::List&, int&, unsigned int&)’:
res.cpp:17:7: warning: unused variable ‘idSize’ [-Wunused-variable]
17 | int idSize = ID.size();
| ^~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 cholse.cpp -o cholse.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 neldermead.cpp -o neldermead.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 resid.cpp -o resid.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 slice.cpp -o slice.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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 RcppExportMod.cpp -o RcppExportMod.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"@BH@" -I"@RCPP@" -I"@ARMA@" -I"@RXP@" -fopenmp -DARMA_64BIT_WORD=1 -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
gcc -std=gnu23 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c init.c -o init.o
gcc -std=gnu23 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c rprintf.c -o rprintf.o
gcc -std=gnu23 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c merge3.c -o merge3.o
gcc -std=gnu23 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c lbfgsR.c -o lbfgsR.o
gcc -std=gnu23 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/n1qn1/include' -I'/data/gannet/ripley/R/test-dev/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-dev/lotri/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rxode2/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c utilc.c -o utilc.o
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o nlmixr2est.so uninformativeEtas.o nlm.o filterNormalLike.o inner.o shi21.o nearPD.o censEst.o saem.o expandNlme.o npde.o shrink.o ires.o res.o cwres.o censResid.o cholse.o neldermead.o resid.o slice.o RcppExportMod.o RcppExports.o init.o rprintf.o merge3.o lbfgsR.o utilc.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/nlmixr2est/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/nlmixr2est/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/nlmixr2est/src'
installing to /data/gannet/ripley/R/packages/tests-devel/nlmixr2est.Rcheck/00LOCK-nlmixr2est/00new/nlmixr2est/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
** 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 (nlmixr2est)