* installing *source* package ‘nlmixr2est’ ...
** this is package ‘nlmixr2est’ version ‘6.0.1’
** package ‘nlmixr2est’ successfully unpacked and MD5 sums checked
** using staged installation
--------[begin src/Makevars]--------
# -*- mode: makefile-gmake -*-
ARMA=/data/gannet/ripley/R/test-dev/RcppArmadillo/include
BH=/data/gannet/ripley/R/test-dev/BH/include
RCPP=/data/gannet/ripley/R/test-dev/Rcpp/include
RXP=/data/gannet/ripley/R/test-dev/rxode2/include
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 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP
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 rxcmp.cpp
OBJECTS = $(SOURCES_CPP:.cpp=.o) $(SOURCES_C:.c=.o)
all: $(SHLIB)
$(SHLIB): $(OBJECTS)
--------[end src/Makevars]--------
** libs
specified C++17
using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
using C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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
In file included from uninformativeEtas.cpp:2:
armahead.h:4:9: warning: ‘ARMA_DONT_USE_OPENMP’ redefined
4 | #define ARMA_DONT_USE_OPENMP // Known to cause speed problems
| ^~~~~~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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
In file included from nlm.cpp:4:
armahead.h:4:9: warning: ‘ARMA_DONT_USE_OPENMP’ redefined
4 | #define ARMA_DONT_USE_OPENMP // Known to cause speed problems
| ^~~~~~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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
In file included from filterNormalLike.cpp:10:
armahead.h:4:9: warning: ‘ARMA_DONT_USE_OPENMP’ redefined
4 | #define ARMA_DONT_USE_OPENMP // Known to cause speed problems
| ^~~~~~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
nlm.cpp: In function ‘Rcpp::RObject nlmSetup(Rcpp::Environment)’:
nlm.cpp:267:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
267 | for (int i = 0; i < nlmOp.ntheta; ++i) {
| ~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘Rcpp::RObject nlmScalePar(Rcpp::RObject)’:
nlm.cpp:286:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
286 | for (int i = 0; i < nlmOp.ntheta; i++) {
| ~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘Rcpp::NumericVector nlmUnscalePar(Rcpp::NumericVector)’:
nlm.cpp:296:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
296 | for (int i = 0; i < nlmOp.ntheta; i++) {
| ~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘arma::mat nlmSolveGradId(arma::vec&, int)’:
nlm.cpp:509:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
509 | if (kk > nlmOp.ntheta) break; // skip rx_pred_f_ and rx_r_ lhs values
| ~~~^~~~~~~~~~~~~~
nlm.cpp:547:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
547 | for (int ii = 0; ii < nlmOp.ntheta; ++ii) {
| ~~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘Rcpp::NumericVector nlmGetScaleC(arma::vec&, double)’:
nlm.cpp:638:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
638 | for(int i = 0; i < nlmOp.ntheta; ++i) {
| ~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘Rcpp::NumericVector solveGradNls(arma::vec&, int)’:
nlm.cpp:691:12: warning: unused variable ‘llik’ [-Wunused-variable]
691 | double llik;
| ^~~~
nlm.cpp: In function ‘Rcpp::RObject nlmAdjustHessian(Rcpp::RObject, arma::vec)’:
nlm.cpp:1012:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1012 | for (int i = 0; i < nlmOp.ntheta; ++i) {
| ~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘Rcpp::RObject nlmAdjustCov(Rcpp::RObject, arma::vec)’:
nlm.cpp:1026:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1026 | for (int i = 0; i < nlmOp.ntheta; ++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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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
In file included from inner.cpp:5:
armahead.h:4:9: warning: ‘ARMA_DONT_USE_OPENMP’ redefined
4 | #define ARMA_DONT_USE_OPENMP // Known to cause speed problems
| ^~~~~~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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
In file included from shi21.cpp:11:
armahead.h:4:9: warning: ‘ARMA_DONT_USE_OPENMP’ redefined
4 | #define ARMA_DONT_USE_OPENMP // Known to cause speed problems
| ^~~~~~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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
In file included from nearPD.cpp:5:
armahead.h:4:9: warning: ‘ARMA_DONT_USE_OPENMP’ redefined
4 | #define ARMA_DONT_USE_OPENMP // Known to cause speed problems
| ^~~~~~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
inner.cpp: In function ‘double likInner0(double*, int)’:
inner.cpp:1113:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1113 | for (int ii = 0; ii < op_focei.neta; ++ii) {
| ~~~^~~~~~~~~~~~~~~
inner.cpp:1139:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1139 | for (int ii = 0; ii < op_focei.neta; ++ii) {
| ~~~^~~~~~~~~~~~~~~
inner.cpp: In function ‘double LikInner2(double*, int, int)’:
inner.cpp:1744:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1744 | for (; curi < _aqn; curi++) {
| ~~~~~^~~~~~
inner.cpp: In function ‘void innerOpt()’:
inner.cpp:2500:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
2500 | for (int id = 0; id < getRxNsubAndMix(rx); id++){
| ~~~^~~~~~~~~~~~~~~~~~~~~
inner.cpp: In function ‘Rcpp::NumericVector foceiSetup_(const Rcpp::RObject&, const Rcpp::RObject&, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::Nullable<Rcpp::Vector<10, Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::Vector<10, Rcpp::PreserveStorage> >, Rcpp::RObject, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::Matrix<14> >, Rcpp::Nullable<Rcpp::Vector<19> >)’:
inner.cpp:4050:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
4050 | if (etaMat1.ncol() != op_focei.neta){
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
inner.cpp: In function ‘double foceiOfvOptim(int, double*, void*)’:
inner.cpp:4677:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
4677 | if (op_focei.useColor && op_focei.printNcol + i > op_focei.npars){
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
inner.cpp:4719:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
4719 | if (op_focei.useColor && op_focei.printNcol + i >= op_focei.npars){
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
inner.cpp: In function ‘void outerGradNumOptim(int, double*, double*, void*)’:
inner.cpp:4813:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
4813 | if (op_focei.useColor && op_focei.printNcol + i >= op_focei.npars){
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
inner.cpp:50:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
50 | #define min2( a , b ) ( (a) < (b) ? (a) : (b) )
| ~~~~^~~~~
inner.cpp:4835:22: note: in expansion of macro ‘min2’
4835 | foceiPrintLine(min2(op_focei.npars, op_focei.printNcol));
| ^~~~
inner.cpp: In function ‘void parHistData(Rcpp::Environment, bool)’:
inner.cpp:6520:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
6520 | for (i = 0; i < op_focei.npars; i++){
| ~~^~~~~~~~~~~~~~~~
inner.cpp:6573:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
6573 | for (i = 0; i < min2(op_focei.npars+1, vals.n_cols); i++){
| ^
inner.cpp: In function ‘Rcpp::Environment foceiFitCpp_(Rcpp::Environment)’:
inner.cpp:50:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
50 | #define min2( a , b ) ( (a) < (b) ? (a) : (b) )
| ~~~~^~~~~
inner.cpp:7393:20: note: in expansion of macro ‘min2’
7393 | foceiPrintLine(min2(op_focei.npars, op_focei.printNcol));
| ^~~~
inner.cpp:7397:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
7397 | for (i = 0; i < op_focei.npars; i++){
| ~~^~~~~~~~~~~~~~~~
inner.cpp:7406:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
7406 | if ((i + 1) != op_focei.npars && (i + 1) % op_focei.printNcol == 0){
| ~~~~~~~~^~~~~~~~~~~~~~~~~
inner.cpp:7407:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
7407 | if (op_focei.useColor && op_focei.printNcol + i >= op_focei.npars){
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
inner.cpp:50:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
50 | #define min2( a , b ) ( (a) < (b) ? (a) : (b) )
| ~~~~^~~~~
inner.cpp:7429:22: note: in expansion of macro ‘min2’
7429 | foceiPrintLine(min2(op_focei.npars, op_focei.printNcol));
| ^~~~
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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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
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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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
inner.cpp: In function ‘Rcpp::List nlmixr2Gill83_(Rcpp::Function, Rcpp::NumericVector, Rcpp::Environment, Rcpp::LogicalVector, double, int, double, double, bool)’:
inner.cpp:5035:13: warning: ‘gillF’ may be used uninitialized [-Wmaybe-uninitialized]
5035 | fN[i] = gillF;
inner.cpp:5028:10: note: ‘gillF’ was declared here
5028 | 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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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
In file included from npde.h:7,
from npde.cpp:2:
armahead.h:4:9: warning: ‘ARMA_DONT_USE_OPENMP’ redefined
4 | #define ARMA_DONT_USE_OPENMP // Known to cause speed problems
| ^~~~~~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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
In file included from shrink.h:5,
from shrink.cpp:2:
armahead.h:4:9: warning: ‘ARMA_DONT_USE_OPENMP’ redefined
4 | #define ARMA_DONT_USE_OPENMP // Known to cause speed problems
| ^~~~~~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
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:130:15: warning: variable ‘hi’ set but not used [-Wunused-but-set-variable]
130 | 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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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
In file included from res.h:4,
from ires.h:4,
from ires.cpp:2:
armahead.h:4:9: warning: ‘ARMA_DONT_USE_OPENMP’ redefined
4 | #define ARMA_DONT_USE_OPENMP // Known to cause speed problems
| ^~~~~~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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
In file included from res.h:4,
from res.cpp:2:
armahead.h:4:9: warning: ‘ARMA_DONT_USE_OPENMP’ redefined
4 | #define ARMA_DONT_USE_OPENMP // Known to cause speed problems
| ^~~~~~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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
In file included from res.h:4,
from cwres.cpp:2:
armahead.h:4:9: warning: ‘ARMA_DONT_USE_OPENMP’ redefined
4 | #define ARMA_DONT_USE_OPENMP // Known to cause speed problems
| ^~~~~~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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 censResid.h:3,
from censResid.cpp:2:
armahead.h:4:9: warning: ‘ARMA_DONT_USE_OPENMP’ redefined
4 | #define ARMA_DONT_USE_OPENMP // Known to cause speed problems
| ^~~~~~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
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:4:
/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++/15/memory:80,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:38,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:51,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
from armahead.h:12:
/usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here
58 | template<typename> class auto_ptr;
| ^~~~~~~~
res.cpp: In function ‘void calculateDfFull(arma::Col<int>&, arma::mat&, Rcpp::List&, int&, unsigned int&)’:
res.cpp:11:7: warning: unused variable ‘idSize’ [-Wunused-variable]
11 | 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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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
In file included from cholse.cpp:2:
armahead.h:4:9: warning: ‘ARMA_DONT_USE_OPENMP’ redefined
4 | #define ARMA_DONT_USE_OPENMP // Known to cause speed problems
| ^~~~~~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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
In file included from resid.cpp:2:
armahead.h:4:9: warning: ‘ARMA_DONT_USE_OPENMP’ redefined
4 | #define ARMA_DONT_USE_OPENMP // Known to cause speed problems
| ^~~~~~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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++ -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"/data/gannet/ripley/R/test-dev/BH/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/rxode2/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -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 rxcmp.cpp -o rxcmp.o
In file included from rxcmp.cpp:4:
armahead.h:4:9: warning: ‘ARMA_DONT_USE_OPENMP’ redefined
4 | #define ARMA_DONT_USE_OPENMP // Known to cause speed problems
| ^~~~~~~~~~~~~~~~~~~~
<command-line>: note: this is the location of the previous definition
gcc -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 -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 -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 -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 -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 rxcmp.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)