* installing *source* package ‘nlmixr2est’ ...
** this is package ‘nlmixr2est’ version ‘7.0.2’
** package ‘nlmixr2est’ successfully unpacked and MD5 sums checked
** using staged installation
--------[begin src/Makevars]--------
# -*- mode: makefile-gmake -*-
ARMA=/data/localhost/ripley/R/test-dev/RcppArmadillo/include
BH=/data/localhost/ripley/R/test-dev/BH/include
RCPP=/data/localhost/ripley/R/test-dev/Rcpp/include
RXP=/data/localhost/ripley/R/test-dev/rxode2/include
EG=/data/localhost/ripley/R/test-dev/RcppEigen/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"$(RXP)" -I"$(EG)" $(SHLIB_OPENMP_CXXFLAGS) -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE
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 odeSwap.cpp imp.cpp npCommon.cpp npag.cpp npb.cpp foceiGrad.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 vaeEncoder.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) 16.1.1 20260515 (Red Hat 16.1.1-2)’
using C++ compiler: ‘g++ (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’
using C++17
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/nlmixr2est/src'
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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 nlm.cpp:6:
censEst.h: In function ‘void censNormalPartials(double, double, double, double, double, int, double*)’:
censEst.h:308:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
308 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:267:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
267 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:388:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
388 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:347:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
347 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:506:14: warning: unused variable ‘rx_expr_48’ [-Wunused-variable]
506 | double rx_expr_48 = erf(rx_expr_44);
| ^~~~~~~~~~
censEst.h:507:14: warning: unused variable ‘rx_expr_49’ [-Wunused-variable]
507 | double rx_expr_49 = erf(rx_expr_46);
| ^~~~~~~~~~
censEst.h:433:12: warning: unused variable ‘rx_expr_29’ [-Wunused-variable]
433 | double rx_expr_29 = erf(rx_expr_26);
| ^~~~~~~~~~
censEst.h:434:12: warning: unused variable ‘rx_expr_30’ [-Wunused-variable]
434 | double rx_expr_30 = erf(rx_expr_28);
| ^~~~~~~~~~
censEst.h:630:14: warning: unused variable ‘rx_expr_34’ [-Wunused-variable]
630 | double rx_expr_34 = erf(rx_expr_31);
| ^~~~~~~~~~
censEst.h:595:12: warning: unused variable ‘rx_expr_18’ [-Wunused-variable]
595 | double rx_expr_18 = erf(rx_expr_17);
| ^~~~~~~~~~
nlm.cpp: In function ‘Rcpp::RObject nlmSetup(Rcpp::Environment)’:
nlm.cpp:284:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
284 | for (int i = 0; i < nlmOp.ntheta; ++i) {
| ~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘Rcpp::RObject nlmScalePar(Rcpp::RObject)’:
nlm.cpp:303:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
303 | for (int i = 0; i < nlmOp.ntheta; i++) {
| ~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘Rcpp::NumericVector nlmUnscalePar(Rcpp::NumericVector)’:
nlm.cpp:313:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
313 | for (int i = 0; i < nlmOp.ntheta; i++) {
| ~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘arma::mat nlmSolveGradId(arma::vec&, int)’:
nlm.cpp:556:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
556 | for (int ii = 0; ii < nlmOp.ntheta; ++ii) {
| ~~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘Rcpp::NumericVector nlmGetScaleC(arma::vec&, double)’:
nlm.cpp:715:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
715 | for(int i = 0; i < nlmOp.ntheta; ++i) {
| ~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘Rcpp::NumericVector solveGradNls(arma::vec&, int)’:
nlm.cpp:768:12: warning: unused variable ‘llik’ [-Wunused-variable]
768 | double llik;
| ^~~~
nlm.cpp: In function ‘Rcpp::RObject nlmAdjustHessian(Rcpp::RObject, arma::vec)’:
nlm.cpp:1108:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1108 | for (int i = 0; i < nlmOp.ntheta; ++i) {
| ~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘Rcpp::RObject nlmAdjustCov(Rcpp::RObject, arma::vec)’:
nlm.cpp:1122:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1122 | for (int i = 0; i < nlmOp.ntheta; ++i) {
| ~~^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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:8:
censEst.h: In function ‘void censNormalPartials(double, double, double, double, double, int, double*)’:
censEst.h:308:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
308 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:267:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
267 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:388:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
388 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:347:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
347 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:506:14: warning: unused variable ‘rx_expr_48’ [-Wunused-variable]
506 | double rx_expr_48 = erf(rx_expr_44);
| ^~~~~~~~~~
censEst.h:507:14: warning: unused variable ‘rx_expr_49’ [-Wunused-variable]
507 | double rx_expr_49 = erf(rx_expr_46);
| ^~~~~~~~~~
censEst.h:433:12: warning: unused variable ‘rx_expr_29’ [-Wunused-variable]
433 | double rx_expr_29 = erf(rx_expr_26);
| ^~~~~~~~~~
censEst.h:434:12: warning: unused variable ‘rx_expr_30’ [-Wunused-variable]
434 | double rx_expr_30 = erf(rx_expr_28);
| ^~~~~~~~~~
censEst.h:630:14: warning: unused variable ‘rx_expr_34’ [-Wunused-variable]
630 | double rx_expr_34 = erf(rx_expr_31);
| ^~~~~~~~~~
censEst.h:595:12: warning: unused variable ‘rx_expr_18’ [-Wunused-variable]
595 | double rx_expr_18 = erf(rx_expr_17);
| ^~~~~~~~~~
inner.cpp: In function ‘bool etaInBound(double*)’:
inner.cpp:760:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
760 | for (int j = 0; j < op_focei.neta; j++) em(j, 0) = eta[j];
| ~~^~~~~~~~~~~~~~~
inner.cpp: In function ‘arma::vec shi21LikTheta(arma::vec&, int)’:
inner.cpp:1622:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1622 | if ((int)_fdRefEta.size() == op_focei.neta) {
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
inner.cpp:1623:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1623 | for (int i = 0; i < op_focei.neta; ++i) {
| ~~^~~~~~~~~~~~~~~
inner.cpp: In function ‘double likInner0(double*, int)’:
inner.cpp:1860:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1860 | for (int ii = 0; ii < op_focei.neta; ++ii) {
| ~~~^~~~~~~~~~~~~~~
inner.cpp:1891:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1891 | for (int ii = 0; ii < op_focei.neta; ++ii) {
| ~~~^~~~~~~~~~~~~~~
inner.cpp: In function ‘double LikInner2(double*, int, int)’:
inner.cpp:2629:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2629 | for (; curi < _aqn; curi++) {
| ~~~~~^~~~~~
inner.cpp: In function ‘int innerOpt1(int, int)’:
inner.cpp:2767:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2767 | for (int _j = 0; _j < op_focei.neta; _j++) {
| ~~~^~~~~~~~~~~~~~~
inner.cpp:2797:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2797 | for (int j = 0; j < op_focei.neta; j++) etaNew[j] = fInd->eta[j];
| ~~^~~~~~~~~~~~~~~
inner.cpp:2801:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2801 | for (int j = 0; j < op_focei.neta; j++)
| ~~^~~~~~~~~~~~~~~
inner.cpp: In function ‘void innerOpt()’:
inner.cpp:3811:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
3811 | for (int id = 0; id < getRxNsubAndMix(rx); id++){
| ~~~^~~~~~~~~~~~~~~~~~~~~
inner.cpp: In function ‘void foceiSetupEta_(Rcpp::NumericMatrix)’:
inner.cpp:5472:26: warning: variable ‘k’ set but not used [-Wunused-but-set-variable=]
5472 | unsigned int i, j = 0, k = 0, ii=0, jj = 0, iA=0, iB=0, iH=0, iVid=0, iLO=0;
| ^
inner.cpp:5472:59: warning: variable ‘iH’ set but not used [-Wunused-but-set-variable=]
5472 | unsigned int i, j = 0, k = 0, ii=0, jj = 0, iA=0, iB=0, iH=0, iVid=0, iLO=0;
| ^~
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:6057:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
6057 | if (etaMat1.ncol() != op_focei.neta){
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
inner.cpp: In function ‘double foceiOfvOptim(int, double*, void*)’:
inner.cpp:6784:7: warning: unused variable ‘finalize’ [-Wunused-variable]
6784 | int finalize = 0, i = 0;
| ^~~~~~~~
inner.cpp: In function ‘void outerGradNumOptim(int, double*, double*, void*)’:
inner.cpp:6851:7: warning: unused variable ‘finalize’ [-Wunused-variable]
6851 | int finalize=0, i = 0;
| ^~~~~~~~
inner.cpp: In function ‘void parHistData(Rcpp::Environment, bool)’:
inner.cpp:9093:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
9093 | for (i = 0; i < min2(op_focei.nparsPrint+1, vals.n_cols); i++){
| ^
inner.cpp: In function ‘void foceiFinalizeTables(Rcpp::Environment)’:
inner.cpp:9228:12: warning: unused variable ‘k’ [-Wunused-variable]
9228 | int j=0, k=0, l=0;
| ^
inner.cpp:9228:17: warning: unused variable ‘l’ [-Wunused-variable]
9228 | int j=0, k=0, l=0;
| ^
inner.cpp: In function ‘Rcpp::NumericVector foceiIndLik_(Rcpp::NumericVector, Rcpp::IntegerVector)’:
inner.cpp:11743:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
11743 | for (int i = 0; i < op_focei.neta; ++i) {
| ~~^~~~~~~~~~~~~~~
inner.cpp: In function ‘Rcpp::NumericMatrix foceiOuterFdInd_(Rcpp::IntegerVector, Rcpp::NumericMatrix)’:
inner.cpp:11921:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
11921 | for (int i = 0; i < op_focei.neta; ++i) {
| ~~^~~~~~~~~~~~~~~
inner.cpp:12009:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
12009 | for (int i = 0; i < op_focei.neta; ++i) {
| ~~^~~~~~~~~~~~~~~
inner.cpp:12160:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
12160 | for (int i = 0; i < op_focei.neta; ++i) {
| ~~^~~~~~~~~~~~~~~
inner.cpp:12106:12: warning: unused variable ‘hCentral’ [-Wunused-variable]
12106 | double hCentral = hs[hs.size() / 2];
| ^~~~~~~~
inner.cpp: In function ‘void outerSolveFill(int, rxSolveF*, const std::vector<double>&, const arma::mat&, const OuterCols&, int, rx_solving_options*, int, int, std::vector<VaeOuterE>&)’:
inner.cpp:12290:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12290 | for (int d = 0; d < C.f1.size(); ++d) E.a(ko, C.fDirIdx[d]) = lhs[C.f1[d]];
| ~~^~~~~~~~~~~~~
inner.cpp:12291:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12291 | for (int r = 0; r < C.f2.size(); ++r) {
| ~~^~~~~~~~~~~~~
inner.cpp:12297:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12297 | for (int d = 0; d < C.rvar1.size(); ++d) E.aR(ko, d) = lhs[C.rvar1[d]];
| ~~^~~~~~~~~~~~~~~~
inner.cpp:12298:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12298 | for (int r = 0; r < C.rvar2.size(); ++r) {
| ~~^~~~~~~~~~~~~~~~
inner.cpp:12305:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12305 | for (int d = 0; d < r1.size(); ++d) E.RsigDir(ko, d, s) = lhs[r1[d]];
| ~~^~~~~~~~~~~
inner.cpp:12307:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12307 | for (int r = 0; r < C.rsig2.size(); ++r) {
| ~~^~~~~~~~~~~~~~~~
inner.cpp: In function ‘bool analyticOuterGradDirect(double*, double*)’:
inner.cpp:13201:12: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘unsigned int’ [-Wsign-compare]
13201 | if (neta != op_focei.neta || (int)G.gMap.size() != npars) return declineHere(103);
| ~~~~~^~~~~~~~~~~~~~~~
inner.cpp: In function ‘Rcpp::List vaeTrainCpp_(Rcpp::List, Rcpp::List, Rcpp::List, int, Rcpp::NumericVector, int, Rcpp::NumericVector, Rcpp::CharacterVector, Rcpp::List, Rcpp::RObject, Rcpp::IntegerVector)’:
inner.cpp:18085:47: warning: comparison of integer expressions of different signedness: ‘arma::uword’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare]
18085 | sReg[k] = regIdx[j]; sMap[k] = (j < (int)regErrMapV.n_elem) ? regErrMapV[j] : -1;
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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 odeSwap.cpp -o odeSwap.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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 imp.cpp -o imp.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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 npCommon.cpp -o npCommon.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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 npag.cpp -o npag.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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 npb.cpp -o npb.o
inner.cpp: In function ‘Rcpp::List nlmixr2Gill83_(Rcpp::Function, Rcpp::NumericVector, Rcpp::Environment, Rcpp::LogicalVector, double, int, double, double, bool)’:
inner.cpp:7147:13: warning: ‘gillF’ may be used uninitialized [-Wmaybe-uninitialized]
7147 | fN[i] = gillF;
inner.cpp:7140:10: note: ‘gillF’ was declared here
7140 | double gillF;
| ^~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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 foceiGrad.cpp -o foceiGrad.o
In file included from foceiGrad.cpp:15:
censEst.h: In function ‘void censNormalPartials(double, double, double, double, double, int, double*)’:
censEst.h:308:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
308 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:267:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
267 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:388:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
388 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:347:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
347 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:506:14: warning: unused variable ‘rx_expr_48’ [-Wunused-variable]
506 | double rx_expr_48 = erf(rx_expr_44);
| ^~~~~~~~~~
censEst.h:507:14: warning: unused variable ‘rx_expr_49’ [-Wunused-variable]
507 | double rx_expr_49 = erf(rx_expr_46);
| ^~~~~~~~~~
censEst.h:433:12: warning: unused variable ‘rx_expr_29’ [-Wunused-variable]
433 | double rx_expr_29 = erf(rx_expr_26);
| ^~~~~~~~~~
censEst.h:434:12: warning: unused variable ‘rx_expr_30’ [-Wunused-variable]
434 | double rx_expr_30 = erf(rx_expr_28);
| ^~~~~~~~~~
censEst.h:630:14: warning: unused variable ‘rx_expr_34’ [-Wunused-variable]
630 | double rx_expr_34 = erf(rx_expr_31);
| ^~~~~~~~~~
censEst.h:595:12: warning: unused variable ‘rx_expr_18’ [-Wunused-variable]
595 | double rx_expr_18 = erf(rx_expr_17);
| ^~~~~~~~~~
foceiGrad.cpp: In lambda function:
foceiGrad.cpp:514:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
514 | for (int l = 0; l < neta; l++) for (int m = 0; m < neta; m++) { double s = 0.0; for (int o = 0; o < nobs; o++) s += v[o] * a(o, l) * a(o, m); M(l, m) = s; } return M; };
| ^~~
foceiGrad.cpp:514:162: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
514 | for (int l = 0; l < neta; l++) for (int m = 0; m < neta; m++) { double s = 0.0; for (int o = 0; o < nobs; o++) s += v[o] * a(o, l) * a(o, m); M(l, m) = s; } return M; };
| ^~~~~~
foceiGrad.cpp: In lambda function:
foceiGrad.cpp:721:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
721 | for (int l = 0; l < neta; l++) for (int s = 0; s < ndir; s++) M(l, s) = Tn(l, dOf(p), s); return M; };
| ^~~
foceiGrad.cpp:721:95: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
721 | for (int l = 0; l < neta; l++) for (int s = 0; s < ndir; s++) M(l, s) = Tn(l, dOf(p), s); return M; };
| ^~~~~~
foceiGrad.cpp: In function ‘arma::mat foceiRSubjectFoceFR_(const arma::mat&, const arma::cube&, const arma::cube&, const arma::mat&, const arma::mat&, const arma::cube&, const arma::cube&, const arma::mat&, const arma::mat&, const arma::ivec&, const arma::vec&, const arma::vec&, const arma::vec&, const arma::vec&, const arma::vec&, const arma::mat&, const arma::cube&, const arma::cube&, const arma::mat&, int, int, int, int, const arma::ivec&)’:
foceiGrad.cpp:875:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
875 | for (int o = 0; o < nobs; o++) v += a(o, l) * a(o, m) * iR[o]; Ht(l, m) += v; }
| ^~~
foceiGrad.cpp:875:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
875 | for (int o = 0; o < nobs; o++) v += a(o, l) * a(o, m) * iR[o]; Ht(l, m) += v; }
| ^~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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
In file included from censEst.cpp:2:
censEst.h: In function ‘void censNormalPartials(double, double, double, double, double, int, double*)’:
censEst.h:308:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
308 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:267:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
267 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:388:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
388 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:347:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
347 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:506:14: warning: unused variable ‘rx_expr_48’ [-Wunused-variable]
506 | double rx_expr_48 = erf(rx_expr_44);
| ^~~~~~~~~~
censEst.h:507:14: warning: unused variable ‘rx_expr_49’ [-Wunused-variable]
507 | double rx_expr_49 = erf(rx_expr_46);
| ^~~~~~~~~~
censEst.h:433:12: warning: unused variable ‘rx_expr_29’ [-Wunused-variable]
433 | double rx_expr_29 = erf(rx_expr_26);
| ^~~~~~~~~~
censEst.h:434:12: warning: unused variable ‘rx_expr_30’ [-Wunused-variable]
434 | double rx_expr_30 = erf(rx_expr_28);
| ^~~~~~~~~~
censEst.h:630:14: warning: unused variable ‘rx_expr_34’ [-Wunused-variable]
630 | double rx_expr_34 = erf(rx_expr_31);
| ^~~~~~~~~~
censEst.h:595:12: warning: unused variable ‘rx_expr_18’ [-Wunused-variable]
595 | double rx_expr_18 = erf(rx_expr_17);
| ^~~~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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 saem.cpp:12:
censEst.h: In function ‘void censNormalPartials(double, double, double, double, double, int, double*)’:
censEst.h:308:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
308 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:267:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
267 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:388:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
388 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:347:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
347 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:506:14: warning: unused variable ‘rx_expr_48’ [-Wunused-variable]
506 | double rx_expr_48 = erf(rx_expr_44);
| ^~~~~~~~~~
censEst.h:507:14: warning: unused variable ‘rx_expr_49’ [-Wunused-variable]
507 | double rx_expr_49 = erf(rx_expr_46);
| ^~~~~~~~~~
censEst.h:433:12: warning: unused variable ‘rx_expr_29’ [-Wunused-variable]
433 | double rx_expr_29 = erf(rx_expr_26);
| ^~~~~~~~~~
censEst.h:434:12: warning: unused variable ‘rx_expr_30’ [-Wunused-variable]
434 | double rx_expr_30 = erf(rx_expr_28);
| ^~~~~~~~~~
censEst.h:630:14: warning: unused variable ‘rx_expr_34’ [-Wunused-variable]
630 | double rx_expr_34 = erf(rx_expr_31);
| ^~~~~~~~~~
censEst.h:595:12: warning: unused variable ‘rx_expr_18’ [-Wunused-variable]
595 | double rx_expr_18 = erf(rx_expr_17);
| ^~~~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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 /data/localhost/ripley/R/test-dev/BH/include/boost/bind/mem_fn.hpp:23,
from /data/localhost/ripley/R/test-dev/BH/include/boost/mem_fn.hpp:22,
from /data/localhost/ripley/R/test-dev/BH/include/boost/function/function_template.hpp:16,
from /data/localhost/ripley/R/test-dev/BH/include/boost/function.hpp:16,
from /data/localhost/ripley/R/test-dev/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /data/localhost/ripley/R/test-dev/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /data/localhost/ripley/R/test-dev/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /data/localhost/ripley/R/test-dev/BH/include/boost/algorithm/string/split.hpp:16,
from /data/localhost/ripley/R/test-dev/BH/include/boost/algorithm/string.hpp:23,
from res.cpp:4:
/data/localhost/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++/16/memory:80,
from /data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo:38,
from /data/localhost/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:51,
from /data/localhost/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
from armahead.h:11,
from res.h:4,
from res.cpp:2:
/usr/include/c++/16/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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/rxode2/include' -I/usr/local/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -I"/data/localhost/ripley/R/test-dev/BH/include" -I"/data/localhost/ripley/R/test-dev/Rcpp/include" -I"/data/localhost/ripley/R/test-dev/RcppArmadillo/include" -I"/data/localhost/ripley/R/test-dev/rxode2/include" -I"/data/localhost/ripley/R/test-dev/RcppEigen/include" -fopenmp -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -DARMA_DONT_USE_OPENMP -DEIGEN_DONT_PARALLELIZE -DNLMIXR2EST_HAS_SETINDCMT -DNLMIXR2EST_HAS_ESSHAPE -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 vaeEncoder.cpp -o vaeEncoder.o
gcc -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/BH/include' -I'/data/localhost/ripley/R/test-dev/n1qn1/include' -I'/data/localhost/ripley/R/test-dev/lbfgsb3c/include' -I'/data/localhost/ripley/R/test-dev/lotri/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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 odeSwap.o imp.o npCommon.o npag.o npb.o foceiGrad.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 vaeEncoder.o init.o rprintf.o merge3.o lbfgsR.o utilc.o -llapack -L/data/localhost/ripley/R/R-devel/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath -fopenmp
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/nlmixr2est/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/nlmixr2est/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/nlmixr2est/src'
installing to /data/localhost/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)