* installing *source* package ‘nlmixr2est’ ...
** this is package ‘nlmixr2est’ version ‘7.2.1’
** 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_CPPFLAGS = -DR_NO_REMAP
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
SHLIB_LDFLAGS = $(SHLIB_CXXLDFLAGS)
SHLIB_LD = $(SHLIB_CXXLD)
SOURCES_C = init.c rprintf.c lbfgsR.c utilc.c
SOURCES_CPP = uninformativeEtas.cpp covShortcut.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 RcppExportMod.cpp RcppExports.cpp rxcmp.cpp vaeEncoder.cpp
OBJECTS = $(SOURCES_CPP:.cpp=.o) $(SOURCES_C:.c=.o)
all: $(SHLIB)
$(SHLIB): $(OBJECTS)
# Rebuild every object when any header changes. Without this the objects have
# no header dependencies at all, so editing a shared header leaves stale objects
# linking against the previous signature -- which fails at LOAD time with an
# undefined symbol, or silently keeps running the OLD code, long after a build
# that reported success.
#
# MUST come after `all:` -- the first target in a makefile is the default goal,
# so putting this above it makes the first OBJECT the default and every build
# silently compiles that one file and stops, producing no shared object at all.
#
# -I../inst/include is on the compile line above and sources do include from
# there (nlmixr2est.h, nlmixr2estLikContrib.h, lin_cmt.hpp), so those headers
# need covering too, or the same stale-object failure stays open for exactly
# the headers that cross the package boundary.
HEADERS = armahead.h censEst.h censResid.h covShortcut.h cwres.h evaluate.h fdHess.h foceiGrad.h \
imp.h impQrng.h inner.h ires.h likContribUtil.h logSumExp.h \
nearPD.h nmMcmcRng.h nmParallel.h nmParallelCore.h nmSeqSeed.h \
np.h npCommon.h npde.h odeSwap.h res.h rxProtect.h rxomp.h scale.h \
shi21.h shrink.h solveWarnHelper.h truncNorm.h \
trustHessianUpdate.h utilc.h vaeEncoder.h \
../inst/include/lin_cmt.hpp ../inst/include/nlmixr2est.h \
../inst/include/nlmixr2estFoceiPtr.h \
../inst/include/nlmixr2estLikContrib.h \
../inst/include/nlmixr2estLikContribPtr.h \
../inst/include/nlmixr2estNlmPtr.h \
../inst/include/nlmixr2est_RcppExports.h \
../inst/include/nlmixr2est_types.h
$(OBJECTS): $(HEADERS)
--------[end src/Makevars]--------
** libs
specified C++17
using C compiler: ‘gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
using C++ compiler: ‘g++ (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
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 -DR_NO_REMAP -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/RcppTrust/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 -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 -DR_NO_REMAP -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/RcppTrust/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 -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 covShortcut.cpp -o covShortcut.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -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/RcppTrust/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 -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 -DR_NO_REMAP -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/RcppTrust/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 -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:392:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
392 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:351:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
351 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:472:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
472 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:431:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
431 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:590:14: warning: unused variable ‘rx_expr_48’ [-Wunused-variable]
590 | double rx_expr_48 = erf(rx_expr_44);
| ^~~~~~~~~~
censEst.h:591:14: warning: unused variable ‘rx_expr_49’ [-Wunused-variable]
591 | double rx_expr_49 = erf(rx_expr_46);
| ^~~~~~~~~~
censEst.h:517:12: warning: unused variable ‘rx_expr_29’ [-Wunused-variable]
517 | double rx_expr_29 = erf(rx_expr_26);
| ^~~~~~~~~~
censEst.h:518:12: warning: unused variable ‘rx_expr_30’ [-Wunused-variable]
518 | double rx_expr_30 = erf(rx_expr_28);
| ^~~~~~~~~~
censEst.h:714:14: warning: unused variable ‘rx_expr_34’ [-Wunused-variable]
714 | double rx_expr_34 = erf(rx_expr_31);
| ^~~~~~~~~~
censEst.h:679:12: warning: unused variable ‘rx_expr_18’ [-Wunused-variable]
679 | double rx_expr_18 = erf(rx_expr_17);
| ^~~~~~~~~~
nlm.cpp: In function ‘Rcpp::RObject nlmSetup(Rcpp::Environment)’:
nlm.cpp:345:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
345 | for (int i = 0; i < nlmOp.ntheta; ++i) {
| ~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘Rcpp::RObject nlmScalePar(Rcpp::RObject)’:
nlm.cpp:369:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
369 | for (int i = 0; i < nlmOp.ntheta; i++) {
| ~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘Rcpp::NumericVector nlmUnscalePar(Rcpp::NumericVector)’:
nlm.cpp:405:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
405 | for (int i = 0; i < nlmOp.ntheta; i++) {
| ~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘arma::mat nlmSolveGradId(arma::vec&, int)’:
nlm.cpp:680:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
680 | for (int ii = 0; ii < nlmOp.ntheta; ++ii) {
| ~~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘Rcpp::NumericVector nlmGetScaleC(arma::vec&, double)’:
nlm.cpp:842:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
842 | for(int i = 0; i < nlmOp.ntheta; ++i) {
| ~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘Rcpp::RObject nlmAdjustCov(Rcpp::RObject, arma::vec)’:
nlm.cpp:1370:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1370 | for (int i = 0; i < nlmOp.ntheta; ++i) {
| ~~^~~~~~~~~~~~~~
nlm.cpp: In function ‘int nlmixr2NlmEval(const double*, int, double*, double*)’:
nlm.cpp:1415:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1415 | if (ntheta != nlmOp.ntheta || theta == NULL ||
| ~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -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/RcppTrust/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 -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:9:
censEst.h: In function ‘void censNormalPartials(double, double, double, double, double, int, double*)’:
censEst.h:392:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
392 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:351:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
351 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:472:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
472 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:431:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
431 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:590:14: warning: unused variable ‘rx_expr_48’ [-Wunused-variable]
590 | double rx_expr_48 = erf(rx_expr_44);
| ^~~~~~~~~~
censEst.h:591:14: warning: unused variable ‘rx_expr_49’ [-Wunused-variable]
591 | double rx_expr_49 = erf(rx_expr_46);
| ^~~~~~~~~~
censEst.h:517:12: warning: unused variable ‘rx_expr_29’ [-Wunused-variable]
517 | double rx_expr_29 = erf(rx_expr_26);
| ^~~~~~~~~~
censEst.h:518:12: warning: unused variable ‘rx_expr_30’ [-Wunused-variable]
518 | double rx_expr_30 = erf(rx_expr_28);
| ^~~~~~~~~~
censEst.h:714:14: warning: unused variable ‘rx_expr_34’ [-Wunused-variable]
714 | double rx_expr_34 = erf(rx_expr_31);
| ^~~~~~~~~~
censEst.h:679:12: warning: unused variable ‘rx_expr_18’ [-Wunused-variable]
679 | double rx_expr_18 = erf(rx_expr_17);
| ^~~~~~~~~~
inner.cpp: In function ‘bool etaInBound(double*)’:
inner.cpp:1397:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1397 | for (int j = 0; j < op_focei.neta; j++) em(j, 0) = eta[j];
| ~~^~~~~~~~~~~~~~~
inner.cpp: In function ‘void fdPinRefEtaForce(focei_ind*, rx_solving_options_ind*, const std::vector<double>&)’:
inner.cpp:2484:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2484 | if ((int)refEta.size() == op_focei.neta) {
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
inner.cpp:2485:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2485 | for (int i = 0; i < op_focei.neta; ++i) {
| ~~^~~~~~~~~~~~~~~
inner.cpp: In function ‘double likInner0(double*, int)’:
inner.cpp:2896:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2896 | for (int ii = 0; ii < op_focei.neta; ++ii) {
| ~~~^~~~~~~~~~~~~~~
inner.cpp:2950:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2950 | for (int ii = 0; ii < op_focei.neta; ++ii) {
| ~~~^~~~~~~~~~~~~~~
inner.cpp: In function ‘double LikInner2(double*, int, int)’:
inner.cpp:3975:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
3975 | for (; curi < _aqn; curi++) {
| ~~~~~^~~~~~
inner.cpp: In function ‘int innerOpt1(int, int)’:
inner.cpp:4191:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
4191 | for (int _j = 0; _j < op_focei.neta; _j++) {
| ~~~^~~~~~~~~~~~~~~
inner.cpp:4228:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
4228 | for (int j = 0; j < op_focei.neta; j++) etaNew[j] = fInd->eta[j];
| ~~^~~~~~~~~~~~~~~
inner.cpp:4232:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
4232 | for (int j = 0; j < op_focei.neta; j++)
| ~~^~~~~~~~~~~~~~~
inner.cpp: In function ‘void fillEtaRestartSamples(rx_solve*)’:
inner.cpp:5953:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
5953 | for (int j = 0; j < op_focei.neta; ++j) {
| ~~^~~~~~~~~~~~~~~
inner.cpp:5976:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
5976 | for (int j = 0; j < op_focei.neta; ++j) z[j] = rxNormEng(0.0, 1.0);
| ~~^~~~~~~~~~~~~~~
inner.cpp: In function ‘void innerOpt()’:
inner.cpp:6043:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
6043 | if (nCopy > op_focei.neta) nCopy = op_focei.neta;
| ~~~~~~^~~~~~~~~~~~~~~
inner.cpp:6046:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
6046 | if (nCopy < op_focei.neta) {
| ~~~~~~^~~~~~~~~~~~~~~
inner.cpp:6061:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
6061 | for (int id = 0; id < getRxNsubAndMix(rx); id++){
| ~~~^~~~~~~~~~~~~~~~~~~~~
inner.cpp: In function ‘void foceiSetupNoEta_()’:
inner.cpp:8401:29: warning: unused variable ‘ind’ [-Wunused-variable]
8401 | rx_solving_options_ind *ind = getSolvingOptionsInd(rx, i);
| ^~~
inner.cpp: In function ‘void foceiSetupEta_(Rcpp::NumericMatrix)’:
inner.cpp:8537:17: warning: variable ‘k’ set but not used [-Wunused-but-set-variable=]
8537 | size_t j = 0, k = 0, ii=0, jj = 0, iA=0, iB=0, iH=0, iVid=0;
| ^
inner.cpp:8537:50: warning: variable ‘iH’ set but not used [-Wunused-but-set-variable=]
8537 | size_t j = 0, k = 0, ii=0, jj = 0, iA=0, iB=0, iH=0, iVid=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:9663:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
9663 | if (etaMat1.ncol() != op_focei.neta){
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
inner.cpp: In function ‘double foceiOfvOptim(int, double*, void*)’:
inner.cpp:10494:7: warning: unused variable ‘finalize’ [-Wunused-variable]
10494 | int finalize = 0, i = 0;
| ^~~~~~~~
inner.cpp: In function ‘void outerGradNumOptim(int, double*, double*, void*)’:
inner.cpp:10604:7: warning: unused variable ‘finalize’ [-Wunused-variable]
10604 | int finalize=0, i = 0;
| ^~~~~~~~
inner.cpp: In function ‘void foceiFinalizeTables(Rcpp::Environment)’:
inner.cpp:13158:12: warning: unused variable ‘k’ [-Wunused-variable]
13158 | int j=0, k=0, l=0;
| ^
inner.cpp:13158:17: warning: unused variable ‘l’ [-Wunused-variable]
13158 | int j=0, k=0, l=0;
| ^
inner.cpp: In function ‘Rcpp::Environment foceiFitCpp_(Rcpp::Environment)’:
inner.cpp:15066:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
15066 | for (int j = 0; j < op_focei.neta; ++j) {
| ~~^~~~~~~~~~~~~~~
inner.cpp: In function ‘void foceiFdOmegaSteps(Rcpp::NumericMatrix, Rcpp::NumericMatrix, const std::vector<int, std::allocator<int> >&, arma::vec&, arma::vec&, std::vector<double>&, int, int, int, bool, double)’:
inner.cpp:16921:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
16921 | for (int i = 0; i < op_focei.npars; ++i) {
| ~~^~~~~~~~~~~~~~~~
inner.cpp: In function ‘Rcpp::NumericMatrix foceiOuterFdIndCore(Rcpp::IntegerVector, Rcpp::NumericMatrix, const FdIndPoint&)’:
inner.cpp:17272:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
17272 | if ((int)e.size() == op_focei.neta) src = &e;
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
inner.cpp:17275:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
17275 | for (int i = 0; i < op_focei.neta; ++i) _fdThRefEta[q][(size_t)i] = (*src)[(size_t)i];
| ~~^~~~~~~~~~~~~~~
inner.cpp:17277:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
17277 | for (int i = 0; i < op_focei.neta; ++i) _fdThRefEta[q][(size_t)i] = fI->saveEta[i];
| ~~^~~~~~~~~~~~~~~
inner.cpp:17280:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
17280 | for (int i = 0; i < op_focei.neta; ++i) {
| ~~^~~~~~~~~~~~~~~
inner.cpp:17302:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
17302 | for (int i = 0; i < op_focei.npars; ++i) {
| ~~^~~~~~~~~~~~~~~~
inner.cpp: In lambda function:
inner.cpp:17674:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17674 | for (int d = 0; d < C.f1.size(); ++d) E.a(ko, C.fDirIdx[d]) = lhs[C.f1[d]];
| ~~^~~~~~~~~~~~~
inner.cpp:17675:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17675 | for (int r = 0; r < C.f2.size(); ++r) {
| ~~^~~~~~~~~~~~~
inner.cpp:17681:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17681 | for (int d = 0; d < C.rvar1.size(); ++d) E.aR(ko, d) = lhs[C.rvar1[d]];
| ~~^~~~~~~~~~~~~~~~
inner.cpp:17682:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17682 | for (int r = 0; r < C.rvar2.size(); ++r) {
| ~~^~~~~~~~~~~~~~~~
inner.cpp:17689:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17689 | for (int d = 0; d < r1.size(); ++d) E.RsigDir(ko, d, s) = lhs[r1[d]];
| ~~^~~~~~~~~~~
inner.cpp:17691:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17691 | for (int r = 0; r < C.rsig2.size(); ++r) {
| ~~^~~~~~~~~~~~~~~~
inner.cpp: In function ‘bool gradPooledCore(const FoceiGradPooledSetup&, const std::vector<double>&, const arma::mat&, const arma::mat&, const arma::cube&, const arma::vec&, int, arma::vec&, arma::cube&, double&)’:
inner.cpp:19042:61: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
19042 | if (!flagged.empty() && npAll > 0 && (int)G.gMap.size() == op_focei.npars) {
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
inner.cpp: In function ‘bool analyticOuterGradDirect(double*, double*)’:
inner.cpp:19375:12: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘unsigned int’ [-Wsign-compare]
19375 | if (neta != op_focei.neta || (int)G.gMap.size() != npars) return declineHere(103);
| ~~~~~^~~~~~~~~~~~~~~~
inner.cpp: In function ‘Rcpp::RObject foceiGradPooledDirect_(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::List, Rcpp::NumericVector, int)’:
inner.cpp:19446:12: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘unsigned int’ [-Wsign-compare]
19446 | if (neta != op_focei.neta) return R_NilValue;
| ~~~~~^~~~~~~~~~~~~~~~
inner.cpp: In function ‘int foceiDimsFlags(rx_solving_options*)’:
inner.cpp:21915:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
21915 | for (int k = 0; k < op_focei.neta; ++k) {
| ~~^~~~~~~~~~~~~~~
inner.cpp: In function ‘int nlmixr2FoceiSetOmegaInv(const double*, int)’:
inner.cpp:21974:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
21974 | if (omegaInv == NULL || neta != op_focei.neta || neta <= 0) return -2;
| ~~~~~^~~~~~~~~~~~~~~~
inner.cpp: In function ‘int foceiCondBatchCheck(const double*, const double*, int, int)’:
inner.cpp:22042:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
22042 | if (neta != op_focei.neta || neta <= 0 || op_focei.fo == 1) return -2;
| ~~~~~^~~~~~~~~~~~~~~~
inner.cpp:22044:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
22044 | if (nid != (int)getRxNsub(rx) * (op_focei.mixIdxN + 1)) return -2;
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:24320:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
24320 | for (int m = 0; m < op_focei.mixIdxN; ++m) mixThIdx[m] = op_focei.mixIdx[m] - 1;
| ~~^~~~~~~~~~~~~~~~~~
inner.cpp:25629:47: warning: comparison of integer expressions of different signedness: ‘arma::uword’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare]
25629 | sReg[k] = regIdx[j]; sMap[k] = (j < (int)regErrMapV.n_elem) ? regErrMapV[j] : -1;
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
inner.cpp: In function ‘bool foceiHessianSensitivitySupport(int)’:
inner.cpp:26061:12: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘unsigned int’ [-Wsign-compare]
26061 | g.neta == op_focei.neta && (int)g.gMap.size() == n && !g.nLam &&
| ~~~~~~~^~~~~~~~~~~~~~~~
In file included from nmParallel.h:32,
from inner.cpp:28:
nmParallelCore.h: In instantiation of ‘void nmForEach(int, int, bool, nmFlags, F&&) [with Scope = nmNoScope; F = vaeTrainCpp_(Rcpp::List, Rcpp::List, Rcpp::List, int, Rcpp::NumericVector, int, Rcpp::NumericVector, Rcpp::CharacterVector, Rcpp::List, Rcpp::RObject, Rcpp::IntegerVector)::<lambda(int)>&]’:
nmParallelCore.h:83:19: required from ‘void nmForEach(int, int, bool, F&&) [with Scope = nmNoScope; F = vaeTrainCpp_(Rcpp::List, Rcpp::List, Rcpp::List, int, Rcpp::NumericVector, int, Rcpp::NumericVector, Rcpp::CharacterVector, Rcpp::List, Rcpp::RObject, Rcpp::IntegerVector)::<lambda(int)>]’
83 | nmForEach<Scope>(n, cores, par, nmDefault, body);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
inner.cpp:24937:16: required from here
24937 | nmForEach(zDim, cores, cores > 1, [&](int k) {
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24938 | if (isFreeR[k]) return;
| ~~~~~~~~~~~~~~~~~~~~~~~
24939 | // fixed structural theta: hold the intercept at ini, add no covariates
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24940 | if (zPopFixR[k]) { intercept[k] = zPop[k]; zPopMat.col(k).fill(zPop[k]); return; }
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24941 | // GLS offset response + conditional variance (both no-ops when diagonal)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24942 | arma::vec yk = (covSelectSmooth ? s1.col(k) : last.mu.col(k)) + covOffset.col(k);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24943 | // pinCovariates: restrict this dim's candidate columns to its allowed
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24944 | // (model-declared) covariates. A reduced design [1 | covMat.cols(allowed)]
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24945 | // is searched, then the chosen reduced indices are mapped back to global
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24946 | // covariate columns. No allowed columns -> intercept-only fit.
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24947 | arma::uvec allowedG;
| ~~~~~~~~~~~~~~~~~~~~
24948 | arma::mat Xk;
| ~~~~~~~~~~~~~
24949 | if (haveCovAllow) {
| ~~~~~~~~~~~~~~~~~~~
24950 | std::vector<arma::uword> av;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24951 | for (int j = 0; j < nCov; ++j) if (covAllow(k, j) == 1) av.push_back((arma::uword)j);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24952 | // A mask that allows only PART of a block leaves that block
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24953 | // unsatisfiable -- it can never be selected whole, and its allowed
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24954 | // columns would sit in the design as dead weight the search keeps
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24955 | // pricing. Drop such blocks outright.
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24956 | if (!covBlock.empty()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~
24957 | std::vector<arma::uword> keep;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24958 | for (size_t t = 0; t < av.size(); ++t) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24959 | const int bt = covBlock[(size_t)av[t]];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24960 | bool whole = true;
| ~~~~~~~~~~~~~~~~~~
24961 | if (bt >= 0) {
| ~~~~~~~~~~~~~~
24962 | for (int j = 0; j < nCov && whole; ++j) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24963 | if (covBlock[(size_t)j] == bt && covAllow(k, j) != 1) whole = false;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24964 | }
| ~
24965 | }
| ~
24966 | if (whole) keep.push_back(av[t]);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24967 | }
| ~
24968 | av.swap(keep);
| ~~~~~~~~~~~~~~
24969 | }
| ~
24970 | allowedG = arma::uvec(av);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
24971 | Xk.set_size(N, 1 + allowedG.n_elem);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24972 | Xk.col(0).ones();
| ~~~~~~~~~~~~~~~~~
24973 | if (allowedG.n_elem > 0) Xk.cols(1, allowedG.n_elem) = covMat.cols(allowedG);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24974 | }
| ~
24975 | const arma::mat& Xuse = haveCovAllow ? Xk : X;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24976 | // the group ids must follow the design actually searched, so subset them
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24977 | // to the allowed columns alongside Xk
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24978 | std::vector<int> grpK;
| ~~~~~~~~~~~~~~~~~~~~~~
24979 | if (!covGroup.empty()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~
24980 | if (haveCovAllow) {
| ~~~~~~~~~~~~~~~~~~~
24981 | grpK.resize(allowedG.n_elem);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24982 | for (size_t s = 0; s < allowedG.n_elem; ++s) grpK[s] = covGroup[(size_t)allowedG[s]];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24983 | } else {
| ~~~~~~~~
24984 | grpK = covGroup;
| ~~~~~~~~~~~~~~~~
24985 | }
| ~
24986 | }
| ~
24987 | const std::vector<int>* grpP = grpK.empty() ? nullptr : &grpK;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24988 | // block ids follow the design actually searched, exactly as the groups do
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24989 | std::vector<int> blkK;
| ~~~~~~~~~~~~~~~~~~~~~~
24990 | if (!covBlock.empty()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~
24991 | if (haveCovAllow) {
| ~~~~~~~~~~~~~~~~~~~
24992 | blkK.resize(allowedG.n_elem);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24993 | for (size_t s = 0; s < allowedG.n_elem; ++s) blkK[s] = covBlock[(size_t)allowedG[s]];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24994 | } else {
| ~~~~~~~~
24995 | blkK = covBlock;
| ~~~~~~~~~~~~~~~~
24996 | }
| ~
24997 | }
| ~
24998 | const std::vector<int>* blkP = blkK.empty() ? nullptr : &blkK;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24999 | // cluster ids follow the design actually searched, exactly as the groups
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25000 | // and blocks do
| ~~~~~~~~~~~~~~~~
25001 | std::vector<int> cluK;
| ~~~~~~~~~~~~~~~~~~~~~~
25002 | if (!covCluster.empty()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
25003 | if (haveCovAllow) {
| ~~~~~~~~~~~~~~~~~~~
25004 | cluK.resize(allowedG.n_elem);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25005 | for (size_t s = 0; s < allowedG.n_elem; ++s) cluK[s] = covCluster[(size_t)allowedG[s]];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25006 | } else {
| ~~~~~~~~
25007 | cluK = covCluster;
| ~~~~~~~~~~~~~~~~~~
25008 | }
| ~
25009 | }
| ~
25010 | VaeSubsetFit fit = (haveL0 && covSelMode[k] == 1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25011 | // covVar[k] (not omega[k]): the GLS conditional variance 1/P_kk for a
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25012 | // correlated block, which reduces to omega[k] when Omega is diagonal.
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25013 | // grpP is main's mutual-exclusion grouping -- both are wanted here.
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25014 | ? vaeCandidateSubsetL0(yk, Xuse, covVar[k], covPenalty, cands[(size_t)k], true,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25015 | grpP, blkP)
| ~~~~~~~~~~~
25016 | : vaeBestSubsetL0(yk, Xuse, covVar[k], covPenalty, bnbStrategy, grpP, blkP);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25017 | std::vector<int> useSel = fit.sel;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25018 | arma::vec useCoef = fit.coef;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25019 | if (!cluK.empty()) {
| ~~~~~~~~~~~~~~~~~~~~
25020 | // "Clearly beats" is measured in the search's OWN currency: one
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25021 | // covariate's L0 cost. An exchange between two columns the design
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25022 | // cannot tell apart (abs(cor) at or above the cut) has to be worth as
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25023 | // much as admitting a covariate before it displaces the incumbent.
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25024 | // That needs no threshold of its own, and it can only ever veto a
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25025 | // SWAP -- never an addition or a removal -- so a real covariate
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25026 | // effect still enters and leaves on the search's terms.
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25027 | const double margin = covPenalty;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25028 | double useScore = vaeScoreSupport(yk, Xuse, covVar[k], covPenalty,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25029 | grpP, blkP, useSel, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25030 | if (selPrevSet[(size_t)k] &&
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25031 | vaeClusterSwapOnly(useSel, selPrev[(size_t)k], cluK)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25032 | arma::vec incCoef;
| ~~~~~~~~~~~~~~~~~~
25033 | const double incScore =
| ~~~~~~~~~~~~~~~~~~~~~~~
25034 | vaeScoreSupport(yk, Xuse, covVar[k], covPenalty, grpP, blkP,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25035 | selPrev[(size_t)k], &incCoef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25036 | if (R_FINITE(incScore) && incScore - useScore <= margin) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25037 | useSel = selPrev[(size_t)k];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25038 | useCoef = incCoef;
| ~~~~~~~~~~~~~~~~~~
25039 | useScore = incScore;
| ~~~~~~~~~~~~~~~~~~~~
25040 | ++hystN[(size_t)k];
| ~~~~~~~~~~~~~~~~~~~
25041 | }
| ~
25042 | }
| ~
25043 | // Near ties: which cluster mates would have come within the same
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25044 | // margin had they been chosen instead? One single-column exchange at
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25045 | // a time, scored through the leaf evaluator, so an exchange that is
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25046 | // infeasible (two shapes of one covariate, half a hockey stick) drops
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25047 | // out on its own. Recorded against GLOBAL covariate columns.
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25048 | std::vector<int>& tS = tieSel[(size_t)k];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25049 | std::vector<int>& tM = tieMate[(size_t)k];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25050 | std::vector<double>& tD = tieDelta[(size_t)k];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25051 | tS.clear(); tM.clear(); tD.clear();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25052 | std::vector<char> inSup(cluK.size(), 0);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25053 | for (size_t s = 0; s < useSel.size(); ++s) inSup[(size_t)useSel[s]] = 1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25054 | for (size_t s = 0; s < useSel.size(); ++s) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25055 | const int j = useSel[s];
| ~~~~~~~~~~~~~~~~~~~~~~~~
25056 | if ((size_t)j >= cluK.size() || cluK[(size_t)j] < 0) continue;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25057 | for (size_t m = 0; m < cluK.size(); ++m) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25058 | if ((int)m == j || inSup[m] != 0 || cluK[m] != cluK[(size_t)j]) continue;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25059 | std::vector<int> t = useSel;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25060 | t[s] = (int)m;
| ~~~~~~~~~~~~~~
25061 | std::sort(t.begin(), t.end());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25062 | const double sc = vaeScoreSupport(yk, Xuse, covVar[k], covPenalty,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25063 | grpP, blkP, t, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~
25064 | if (!R_FINITE(sc) || sc - useScore > margin) continue;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25065 | tS.push_back(haveCovAllow ? (int)allowedG[(size_t)j] : j);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25066 | tM.push_back(haveCovAllow ? (int)allowedG[m] : (int)m);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25067 | tD.push_back(sc - useScore);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25068 | }
| ~
25069 | }
| ~
25070 | }
| ~
25071 | selPrev[(size_t)k] = useSel;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25072 | selPrevSet[(size_t)k] = 1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
25073 | arma::vec bestCoef = useCoef;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25074 | double ic = bestCoef[0];
| ~~~~~~~~~~~~~~~~~~~~~~~~
25075 | if (R_FINITE(zPopLower[k]) && ic < zPopLower[k]) ic = zPopLower[k];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25076 | if (R_FINITE(zPopUpper[k]) && ic > zPopUpper[k]) ic = zPopUpper[k];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25077 | intercept[k] = ic; bestCoef[0] = ic;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25078 | arma::uvec bestCols = vaeSubsetCols(useSel);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25079 | for (size_t s = 0; s < useSel.size(); ++s) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25080 | int gj = haveCovAllow ? (int)allowedG[useSel[s]] : useSel[s];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25081 | beta(k, gj) = bestCoef[s + 1]; selected(k, gj) = 1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25082 | }
| ~
25083 | zPopMat.col(k) = Xuse.cols(bestCols) * bestCoef;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25084 | });
| ~~
nmParallelCore.h:61:15: warning: unused variable ‘_nmScope’ [-Wunused-variable]
61 | Scope _nmScope;
| ^~~~~~~~
nmParallelCore.h:68:15: warning: unused variable ‘_nmScope’ [-Wunused-variable]
68 | Scope _nmScope;
| ^~~~~~~~
nmParallelCore.h: In instantiation of ‘void nmForEach(int, int, bool, nmFlags, F&&) [with Scope = nmNoScope; F = vaeTrainCpp_(Rcpp::List, Rcpp::List, Rcpp::List, int, Rcpp::NumericVector, int, Rcpp::NumericVector, Rcpp::CharacterVector, Rcpp::List, Rcpp::RObject, Rcpp::IntegerVector)::<lambda(int)>&]’:
nmParallelCore.h:83:19: required from ‘void nmForEach(int, int, bool, F&&) [with Scope = nmNoScope; F = vaeTrainCpp_(Rcpp::List, Rcpp::List, Rcpp::List, int, Rcpp::NumericVector, int, Rcpp::NumericVector, Rcpp::CharacterVector, Rcpp::List, Rcpp::RObject, Rcpp::IntegerVector)::<lambda(int)>]’
83 | nmForEach<Scope>(n, cores, par, nmDefault, body);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
inner.cpp:25189:22: required from here
25189 | nmForEach(nG, cores, cores > 1 && nG > 1, [&](int gi) {
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25190 | const std::vector<int>& G = groups[(size_t)gi];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25191 | if (G.size() < 2) return;
| ~~~~~~~~~~~~~~~~~~~~~~~~~
25192 | if ((int)G.size() > phiMaxDim) { gBig[gi] = 1; return; }
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25193 | // an exception must never cross an OpenMP region; a group that
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25194 | // fails numerically simply does nothing, which is the conservative
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25195 | // answer anyway
| ~~~~~~~~~~~~~~~~
25196 | try {
| ~~~~~
25197 | // current supports, and the blocks in play anywhere in the group
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25198 | std::vector<std::vector<int> > sup(G.size());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25199 | std::vector<int> bag;
| ~~~~~~~~~~~~~~~~~~~~~
25200 | for (size_t a = 0; a < G.size(); ++a) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25201 | for (int j = 0; j < nCov; ++j) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25202 | if (selected(G[a], j)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~
25203 | sup[a].push_back(j);
| ~~~~~~~~~~~~~~~~~~~~
25204 | const int bb = fc.blockOf[(size_t)j];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25205 | if (std::find(bag.begin(), bag.end(), bb) == bag.end()) bag.push_back(bb);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25206 | }
| ~
25207 | }
| ~
25208 | }
| ~
25209 | std::sort(bag.begin(), bag.end());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25210 | if (bag.empty()) return;
| ~~~~~~~~~~~~~~~~~~~~~~~~
25211 | // a candidate support must be block-complete, group-feasible and
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25212 | // allowed on the dim it lands on
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25213 | auto feasible = [&](int k, const std::vector<int>& s) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25214 | if (!vaeGroupOk(fc, s) || !vaeBlockOk(fc, s)) return false;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25215 | if (haveCovAllow) {
| ~~~~~~~~~~~~~~~~~~~
25216 | for (size_t t = 0; t < s.size(); ++t) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25217 | if (covAllow(k, s[t]) != 1) return false;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25218 | }
| ~
25219 | }
| ~
25220 | return true;
| ~~~~~~~~~~~~
25221 | };
| ~~
25222 | auto addBlk = [&](std::vector<int> s, int b) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25223 | const std::vector<int>& cols = fc.blocks[(size_t)b];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25224 | s.insert(s.end(), cols.begin(), cols.end());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25225 | std::sort(s.begin(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25226 | return s;
| ~~~~~~~~~
25227 | };
| ~~
25228 | auto dropBlk = [&](const std::vector<int>& s, int b) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25229 | std::vector<int> t;
| ~~~~~~~~~~~~~~~~~~~
25230 | for (size_t u2 = 0; u2 < s.size(); ++u2) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25231 | if (fc.blockOf[(size_t)s[u2]] != b) t.push_back(s[u2]);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25232 | }
| ~
25233 | return t;
| ~~~~~~~~~
25234 | };
| ~~
25235 | auto hasBlk = [&](const std::vector<int>& s, int b) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25236 | for (size_t u2 = 0; u2 < s.size(); ++u2) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25237 | if (fc.blockOf[(size_t)s[u2]] == b) return true;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25238 | }
| ~
25239 | return false;
| ~~~~~~~~~~~~~
25240 | };
| ~~
25241 | // score an assignment, re-scoring with any binding intercept HELD:
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25242 | // the per-dim path clamps after scoring, so without this a move
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25243 | // could win on a score its written parameters never achieve
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25244 | auto scoreOf = [&](const std::vector<std::vector<int> >& s,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25245 | std::vector<arma::vec>* th) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25246 | bool cl = false;
| ~~~~~~~~~~~~~~~~
25247 | double q = vaeJointScore(jc, G, s, th, nullptr, &cl);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25248 | if (!cl || !R_FINITE(q)) return q;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25249 | std::vector<arma::vec> t0;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
25250 | vaeJointScore(jc, G, s, &t0, nullptr, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25251 | std::vector<double> fixv(G.size(), NA_REAL);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25252 | for (size_t a = 0; a < G.size(); ++a) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25253 | const int k = G[a];
| ~~~~~~~~~~~~~~~~~~~
25254 | if (t0.size() <= a || t0[a].n_elem == 0) continue;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25255 | if (R_FINITE(zPopLower[k]) && t0[a][0] < zPopLower[k]) fixv[a] = zPopLower[k];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25256 | else if (R_FINITE(zPopUpper[k]) && t0[a][0] > zPopUpper[k]) fixv[a] = zPopUpper[k];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25257 | }
| ~
25258 | ++gClamp[gi];
| ~~~~~~~~~~~~~
25259 | return vaeJointScore(jc, G, s, th, &fixv, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25260 | };
| ~~
25261 | std::vector<arma::vec> thCur;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25262 | double best = scoreOf(sup, &thCur);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25263 | if (!R_FINITE(best)) return;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25264 | bool moved = false;
| ~~~~~~~~~~~~~~~~~~~
25265 | for (int pass = 0; pass < 20; ++pass) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25266 | double bestScore = best;
| ~~~~~~~~~~~~~~~~~~~~~~~~
25267 | std::vector<std::vector<int> > bestSup;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25268 | std::vector<arma::vec> bestTh;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25269 | bool have = false;
| ~~~~~~~~~~~~~~~~~~
25270 | // MOVE b from k to k', ADD b to k', DROP b from k -- a fixed
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25271 | // enumeration, with best-improvement acceptance so the winner does
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25272 | // not depend on that order
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
25273 | for (size_t a = 0; a < G.size(); ++a) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25274 | for (size_t t = 0; t < bag.size(); ++t) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25275 | const int b = bag[t];
| ~~~~~~~~~~~~~~~~~~~~~
25276 | const bool inA = hasBlk(sup[a], b);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25277 | for (size_t c2 = 0; c2 < G.size(); ++c2) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25278 | if (c2 == a || !inA) continue;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25279 | if (hasBlk(sup[c2], b)) continue;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25280 | std::vector<std::vector<int> > cand = sup;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25281 | cand[a] = dropBlk(sup[a], b);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25282 | cand[c2] = addBlk(sup[c2], b);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25283 | if (!feasible(G[a], cand[a]) || !feasible(G[c2], cand[c2])) continue;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25284 | std::vector<arma::vec> th;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
25285 | ++gTest[gi];
| ~~~~~~~~~~~~
25286 | double q = scoreOf(cand, &th);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25287 | if (R_FINITE(q) && (q < bestScore ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25288 | (q == bestScore && have && vaeJointSelLess(cand, bestSup)))) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25289 | have = true; bestScore = q; bestSup = cand; bestTh = th;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25290 | }
| ~
25291 | }
| ~
25292 | if (!inA) { // ADD
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25293 | std::vector<std::vector<int> > cand = sup;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25294 | cand[a] = addBlk(sup[a], b);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25295 | if (feasible(G[a], cand[a])) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25296 | std::vector<arma::vec> th;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
25297 | ++gTest[gi];
| ~~~~~~~~~~~~
25298 | double q = scoreOf(cand, &th);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25299 | if (R_FINITE(q) && (q < bestScore ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25300 | (q == bestScore && have && vaeJointSelLess(cand, bestSup)))) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25301 | have = true; bestScore = q; bestSup = cand; bestTh = th;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25302 | }
| ~
25303 | }
| ~
25304 | } else { // DROP
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25305 | std::vector<std::vector<int> > cand = sup;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25306 | cand[a] = dropBlk(sup[a], b);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25307 | if (feasible(G[a], cand[a])) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25308 | std::vector<arma::vec> th;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
25309 | ++gTest[gi];
| ~~~~~~~~~~~~
25310 | double q = scoreOf(cand, &th);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25311 | if (R_FINITE(q) && (q < bestScore ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25312 | (q == bestScore && have && vaeJointSelLess(cand, bestSup)))) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25313 | have = true; bestScore = q; bestSup = cand; bestTh = th;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25314 | }
| ~
25315 | }
| ~
25316 | }
| ~
25317 | }
| ~
25318 | }
| ~
25319 | if (!have || !(bestScore < best)) break;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25320 | sup = bestSup; thCur = bestTh; best = bestScore;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25321 | moved = true; ++gMove[gi];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
25322 | }
| ~
25323 | // Write back ONLY when something was accepted. The joint refit is a
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25324 | // GLS solve, not the per-dim OLS the loop ran, so re-deriving "the
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25325 | // same" answer would differ in the last bits and perturb every
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25326 | // downstream fit. Only not writing guarantees the no-op.
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25327 | if (!moved) return;
| ~~~~~~~~~~~~~~~~~~~
25328 | for (size_t a = 0; a < G.size(); ++a) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25329 | const int k = G[a];
| ~~~~~~~~~~~~~~~~~~~
25330 | if (thCur.size() <= a || thCur[a].n_elem == 0) continue;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25331 | double ic = thCur[a][0];
| ~~~~~~~~~~~~~~~~~~~~~~~~
25332 | if (R_FINITE(zPopLower[k]) && ic < zPopLower[k]) ic = zPopLower[k];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25333 | if (R_FINITE(zPopUpper[k]) && ic > zPopUpper[k]) ic = zPopUpper[k];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25334 | arma::vec th = thCur[a];
| ~~~~~~~~~~~~~~~~~~~~~~~~
25335 | th[0] = ic;
| ~~~~~~~~~~~
25336 | intercept[k] = ic;
| ~~~~~~~~~~~~~~~~~~
25337 | beta.row(k).zeros();
| ~~~~~~~~~~~~~~~~~~~~
25338 | selected.row(k).zeros();
| ~~~~~~~~~~~~~~~~~~~~~~~~
25339 | for (size_t s2 = 0; s2 < sup[a].size(); ++s2) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25340 | beta(k, sup[a][s2]) = th[s2 + 1];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25341 | selected(k, sup[a][s2]) = 1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25342 | }
| ~
25343 | zPopMat.col(k) = vaeJointZ(jc, sup[a]) * th;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25344 | // the near-tie report was computed against the support the
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25345 | // per-dim pass chose; this dim no longer has that support, and a
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25346 | // stale alternative is worse than none
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25347 | tieSel[(size_t)k].clear();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
25348 | tieMate[(size_t)k].clear();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
25349 | tieDelta[(size_t)k].clear();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25350 | // Same staleness, stronger consequence: selPrev is the hysteresis
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25351 | // INCUMBENT, and it still holds the support this pass just
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25352 | // overruled. Left alone, the next iteration could adopt it back
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25353 | // -- a report going stale only misinforms, an incumbent going
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25354 | // stale changes the selection. Dropping it (rather than
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25355 | // translating sup[a] into the per-dim REDUCED index space, whose
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25356 | // allow-mask and block-dropping map is local to that loop) means
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25357 | // the next iteration simply re-seeds from whatever it chooses,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25358 | // which is the same path the first iteration takes.
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25359 | selPrev[(size_t)k].clear();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
25360 | selPrevSet[(size_t)k] = 0;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
25361 | }
| ~
25362 | } catch (...) {
| ~~~~~~~~~~~~~~~
25363 | // leave this group exactly as the per-dim pass left it
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
25364 | }
| ~
25365 | });
| ~~
nmParallelCore.h:61:15: warning: unused variable ‘_nmScope’ [-Wunused-variable]
61 | Scope _nmScope;
| ^~~~~~~~
nmParallelCore.h:68:15: warning: unused variable ‘_nmScope’ [-Wunused-variable]
68 | Scope _nmScope;
| ^~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -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/RcppTrust/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 -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 -DR_NO_REMAP -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/RcppTrust/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 -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 -DR_NO_REMAP -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/RcppTrust/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 -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 -DR_NO_REMAP -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/RcppTrust/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 -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 -DR_NO_REMAP -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/RcppTrust/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 -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
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -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/RcppTrust/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 -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:16:
censEst.h: In function ‘void censNormalPartials(double, double, double, double, double, int, double*)’:
censEst.h:392:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
392 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:351:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
351 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:472:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
472 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:431:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
431 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:590:14: warning: unused variable ‘rx_expr_48’ [-Wunused-variable]
590 | double rx_expr_48 = erf(rx_expr_44);
| ^~~~~~~~~~
censEst.h:591:14: warning: unused variable ‘rx_expr_49’ [-Wunused-variable]
591 | double rx_expr_49 = erf(rx_expr_46);
| ^~~~~~~~~~
censEst.h:517:12: warning: unused variable ‘rx_expr_29’ [-Wunused-variable]
517 | double rx_expr_29 = erf(rx_expr_26);
| ^~~~~~~~~~
censEst.h:518:12: warning: unused variable ‘rx_expr_30’ [-Wunused-variable]
518 | double rx_expr_30 = erf(rx_expr_28);
| ^~~~~~~~~~
censEst.h:714:14: warning: unused variable ‘rx_expr_34’ [-Wunused-variable]
714 | double rx_expr_34 = erf(rx_expr_31);
| ^~~~~~~~~~
censEst.h:679:12: warning: unused variable ‘rx_expr_18’ [-Wunused-variable]
679 | double rx_expr_18 = erf(rx_expr_17);
| ^~~~~~~~~~
foceiGrad.cpp: In lambda function:
foceiGrad.cpp:288:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
288 | 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:288:162: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
288 | 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:586:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
586 | for (int s = 0; s < neta; s++) D(l, s) = C.Tn(l, s, t); return D; };
| ^~~
foceiGrad.cpp:586:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
586 | for (int s = 0; s < neta; s++) D(l, s) = C.Tn(l, s, t); return D; };
| ^~~~~~
foceiGrad.cpp:585:46: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
585 | auto dHD = [&](int t) { mat D(neta, neta); for (int l = 0; l < neta; l++)
| ^~~
foceiGrad.cpp:586:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
586 | for (int s = 0; s < neta; s++) D(l, s) = C.Tn(l, s, t); return D; };
| ^~~~~~
foceiGrad.cpp: In lambda function:
foceiGrad.cpp:685:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
685 | 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:685:95: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
685 | 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:854:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
854 | for (int o = 0; o < nobs; o++) v += a(o, l) * a(o, m) * iR[o]; Ht(l, m) += v; }
| ^~~
foceiGrad.cpp:854:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
854 | for (int o = 0; o < nobs; o++) v += a(o, l) * a(o, m) * iR[o]; Ht(l, m) += v; }
| ^~
In file included from foceiGrad.cpp:14:
nmParallelCore.h: In instantiation of ‘void nmForEach(int, int, bool, nmFlags, F&&) [with Scope = nmNoScope; F = foceiRAllFR_(const arma::mat&, const arma::cube&, const arma::cube&, 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::mat&, const arma::ivec&, const arma::mat&, const arma::cube&, const arma::cube&, const arma::mat&, int, int, int, int, const arma::ivec&, int)::<lambda(int)>]’:
foceiGrad.cpp:761:12: required from here
761 | nmForEach(nsub, ncores, ncores > 1, nmStatic, [&](int i) {
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
762 | try {
| ~~~~~
763 | int o0 = obsOffset[i], o1 = obsOffset[i + 1] - 1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
764 | mat dvi = hasDv ? mat(dvSens.rows(o0, o1)) : mat(o1 - o0 + 1, 0);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
765 | mat dv2i = hasDv ? mat(dvSens2.rows(o0, o1)) : mat(o1 - o0 + 1, 0);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
766 | ivec censi = hasCens ? ivec(censv.subvec(o0, o1)) : ivec();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
767 | vec limi = hasCens ? vec(limv.subvec(o0, o1)) : vec();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
768 | Rall.slice(i) = foceiRSubjectFR_(a.rows(o0, o1), A.rows(o0, o1), Ath.rows(o0, o1),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
769 | aR.rows(o0, o1), AR.rows(o0, o1), AthR.rows(o0, o1), dvi, dv2i, censi, limi,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
770 | fv.subvec(o0, o1), yv.subvec(o0, o1), Rv.subvec(o0, o1),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
771 | ehat.row(i).t(), Oi, dOi, d2Oi, d2LD,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
772 | neta, ndir, ndirP, nom, dirP);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
773 | } catch (...) {
| ~~~~~~~~~~~~~~~
774 | Rall.slice(i).fill(datum::nan);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
775 | }
| ~
776 | });
| ~~
nmParallelCore.h:61:15: warning: unused variable ‘_nmScope’ [-Wunused-variable]
61 | Scope _nmScope;
| ^~~~~~~~
nmParallelCore.h:68:15: warning: unused variable ‘_nmScope’ [-Wunused-variable]
68 | Scope _nmScope;
| ^~~~~~~~
nmParallelCore.h: In instantiation of ‘void nmForEach(int, int, bool, nmFlags, F&&) [with Scope = nmNoScope; F = foceiRAllFoceFR_(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::mat&, const arma::ivec&, const arma::mat&, const arma::cube&, const arma::cube&, const arma::mat&, int, int, int, int, const arma::ivec&, int)::<lambda(int)>]’:
foceiGrad.cpp:968:12: required from here
968 | nmForEach(nsub, ncores, ncores > 1, nmStatic, [&](int i) {
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
969 | try {
| ~~~~~
970 | int o0 = obsOffset[i], o1 = obsOffset[i + 1] - 1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
971 | mat dvi = hasDv ? mat(dvSens.rows(o0, o1)) : mat(o1 - o0 + 1, 0);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
972 | mat dv2i = hasDv ? mat(dvSens2.rows(o0, o1)) : mat(o1 - o0 + 1, 0);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
973 | ivec censi = hasCens ? ivec(censv.subvec(o0, o1)) : ivec();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
974 | vec limi = hasCens ? vec(limv.subvec(o0, o1)) : vec();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
975 | Rall.slice(i) = foceiRSubjectFoceFR_(a.rows(o0, o1), A.rows(o0, o1), Ath.rows(o0, o1),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
976 | aRe.rows(o0, o1), aRc.rows(o0, o1), ARe.rows(o0, o1), ARc.rows(o0, o1), dvi, dv2i,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
977 | censi, limi, fv.subvec(o0, o1), yv.subvec(o0, o1), R0v.subvec(o0, o1),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
978 | ehat.row(i).t(), Oi, dOi, d2Oi, d2LD,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
979 | neta, ndir, ndirP, nom, dirP);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
980 | } catch (...) {
| ~~~~~~~~~~~~~~~
981 | Rall.slice(i).fill(datum::nan);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
982 | }
| ~
983 | });
| ~~
nmParallelCore.h:61:15: warning: unused variable ‘_nmScope’ [-Wunused-variable]
61 | Scope _nmScope;
| ^~~~~~~~
nmParallelCore.h:68:15: warning: unused variable ‘_nmScope’ [-Wunused-variable]
68 | Scope _nmScope;
| ^~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -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/RcppTrust/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 -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 -DR_NO_REMAP -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/RcppTrust/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 -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 -DR_NO_REMAP -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/RcppTrust/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 -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:392:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
392 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:351:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
351 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:472:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
472 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:431:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
431 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:590:14: warning: unused variable ‘rx_expr_48’ [-Wunused-variable]
590 | double rx_expr_48 = erf(rx_expr_44);
| ^~~~~~~~~~
censEst.h:591:14: warning: unused variable ‘rx_expr_49’ [-Wunused-variable]
591 | double rx_expr_49 = erf(rx_expr_46);
| ^~~~~~~~~~
censEst.h:517:12: warning: unused variable ‘rx_expr_29’ [-Wunused-variable]
517 | double rx_expr_29 = erf(rx_expr_26);
| ^~~~~~~~~~
censEst.h:518:12: warning: unused variable ‘rx_expr_30’ [-Wunused-variable]
518 | double rx_expr_30 = erf(rx_expr_28);
| ^~~~~~~~~~
censEst.h:714:14: warning: unused variable ‘rx_expr_34’ [-Wunused-variable]
714 | double rx_expr_34 = erf(rx_expr_31);
| ^~~~~~~~~~
censEst.h:679:12: warning: unused variable ‘rx_expr_18’ [-Wunused-variable]
679 | double rx_expr_18 = erf(rx_expr_17);
| ^~~~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -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/RcppTrust/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 -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 -DR_NO_REMAP -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/RcppTrust/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 -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
In file included from saem.cpp:14:
censEst.h: In function ‘void censNormalPartials(double, double, double, double, double, int, double*)’:
censEst.h:392:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
392 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:351:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
351 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:472:16: warning: unused variable ‘rx_expr_31’ [-Wunused-variable]
472 | double rx_expr_31 = erf(rx_expr_25);
| ^~~~~~~~~~
censEst.h:431:14: warning: unused variable ‘rx_expr_21’ [-Wunused-variable]
431 | double rx_expr_21 = erf(rx_expr_18);
| ^~~~~~~~~~
censEst.h:590:14: warning: unused variable ‘rx_expr_48’ [-Wunused-variable]
590 | double rx_expr_48 = erf(rx_expr_44);
| ^~~~~~~~~~
censEst.h:591:14: warning: unused variable ‘rx_expr_49’ [-Wunused-variable]
591 | double rx_expr_49 = erf(rx_expr_46);
| ^~~~~~~~~~
censEst.h:517:12: warning: unused variable ‘rx_expr_29’ [-Wunused-variable]
517 | double rx_expr_29 = erf(rx_expr_26);
| ^~~~~~~~~~
censEst.h:518:12: warning: unused variable ‘rx_expr_30’ [-Wunused-variable]
518 | double rx_expr_30 = erf(rx_expr_28);
| ^~~~~~~~~~
censEst.h:714:14: warning: unused variable ‘rx_expr_34’ [-Wunused-variable]
714 | double rx_expr_34 = erf(rx_expr_31);
| ^~~~~~~~~~
censEst.h:679:12: warning: unused variable ‘rx_expr_18’ [-Wunused-variable]
679 | double rx_expr_18 = erf(rx_expr_17);
| ^~~~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -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/RcppTrust/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 -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 -DR_NO_REMAP -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/RcppTrust/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 -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
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -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/RcppTrust/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 -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 npde.cpp:7:
nmParallelCore.h: In instantiation of ‘void nmForEach(int, int, bool, nmFlags, F&&) [with Scope = nmNoScope; F = _nlmixr2est_npdeCalc(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)::<lambda(int)>&]’:
nmParallelCore.h:83:19: required from ‘void nmForEach(int, int, bool, F&&) [with Scope = nmNoScope; F = _nlmixr2est_npdeCalc(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)::<lambda(int)>]’
83 | nmForEach<Scope>(n, cores, par, nmDefault, body);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
npde.cpp:461:14: required from here
461 | nmForEach(_nid, _cores, _doParallel, [&](int _curid) {
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
462 | unsigned int curid = (unsigned int)_curid;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
463 | // A C++ exception must never escape this OMP region -- doing so calls
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
464 | // std::terminate() and aborts R. Any per-subject numerical failure (e.g. a
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
465 | // degenerate simulated covariance) is caught here and that subject's npde
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
466 | // is set NA instead.
| ~~~~~~~~~~~~~~~~~~~~~
467 | try {
| ~~~~~
468 | calcNpdeInfoId idInfo = calcNpdeId(idLoc, sim, dvt, evid, cens, limit, censMethod, doLimit, curid, K, tolChol, ties, ru, ru2, ru3,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
469 | lambda, yj, hi, low);
| ~~~~~~~~~~~~~~~~~~~~~
470 | npde(span(idLoc[curid], idLoc[curid+1]-1)) = idInfo.npde;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
471 | npd(span(idLoc[curid], idLoc[curid+1]-1)) = idInfo.npd;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
472 | pde(span(idLoc[curid], idLoc[curid+1]-1)) = idInfo.pd;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
473 | pd(span(idLoc[curid], idLoc[curid+1]-1)) = idInfo.pd2;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
474 | epred(span(idLoc[curid], idLoc[curid+1]-1)) = idInfo.epred;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
475 | dvf(span(idLoc[curid], idLoc[curid+1]-1)) = idInfo.yobs;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
476 | eres(span(idLoc[curid], idLoc[curid+1]-1)) = idInfo.eres;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | warn[curid] = idInfo.warn;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
478 | } catch (...) {
| ~~~~~~~~~~~~~~~
479 | npde(span(idLoc[curid], idLoc[curid+1]-1)).fill(NA_REAL);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
480 | npd(span(idLoc[curid], idLoc[curid+1]-1)).fill(NA_REAL);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
481 | pde(span(idLoc[curid], idLoc[curid+1]-1)).fill(NA_REAL);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
482 | pd(span(idLoc[curid], idLoc[curid+1]-1)).fill(NA_REAL);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
483 | epred(span(idLoc[curid], idLoc[curid+1]-1)).fill(NA_REAL);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
484 | dvf(span(idLoc[curid], idLoc[curid+1]-1)).fill(NA_REAL);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
485 | eres(span(idLoc[curid], idLoc[curid+1]-1)).fill(NA_REAL);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | warn[curid] = NPDE_NPD;
| ~~~~~~~~~~~~~~~~~~~~~~~
487 | }
| ~
488 | });
| ~~
nmParallelCore.h:61:15: warning: unused variable ‘_nmScope’ [-Wunused-variable]
61 | Scope _nmScope;
| ^~~~~~~~
nmParallelCore.h:68:15: warning: unused variable ‘_nmScope’ [-Wunused-variable]
68 | Scope _nmScope;
| ^~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -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/RcppTrust/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 -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
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -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/RcppTrust/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 -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 /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 -DR_NO_REMAP -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/RcppTrust/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 -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 -DR_NO_REMAP -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/RcppTrust/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 -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 -DR_NO_REMAP -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/RcppTrust/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 -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 -DR_NO_REMAP -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/RcppTrust/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 -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 -DR_NO_REMAP -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/RcppTrust/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 -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 -DR_NO_REMAP -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/RcppTrust/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 -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 -DR_NO_REMAP -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/RcppTrust/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 -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
In file included from vaeEncoder.cpp:20:
nmParallelCore.h: In instantiation of ‘void nmForEach(int, int, bool, nmFlags, F&&) [with Scope = nmNoScope; F = vaeEncoderFwdBwdCore(const arma::cube&, const arma::ivec&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::vec&, const arma::vec&, const arma::mat&, const arma::vec&, int, const arma::mat&, const arma::mat&, bool, arma::mat&, arma::mat&, arma::cube&, arma::mat&, arma::mat&, arma::mat&, arma::vec&, arma::vec&, arma::mat&, arma::vec&, int, bool)::<lambda(int)>]’:
vaeEncoder.cpp:98:12: required from here
98 | nmForEach(N, cores, (cores > 1 && !backward) || parBwd, nmStatic, [&](int i) {
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
99 | const int Ti = lengths[i];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
100 | // forward caches for this subject
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
101 | arma::mat I(h, Ti), F(h, Ti), G(h, Ti), O(h, Ti), C(h, Ti), H(h, Ti), X(xDim, Ti);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
102 | arma::vec hPrev(h, arma::fill::zeros), cPrev(h, arma::fill::zeros);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
103 |
|
104 | for (int t = 0; t < Ti; ++t) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
105 | arma::vec xt(xDim);
| ~~~~~~~~~~~~~~~~~~~
106 | for (int d = 0; d < xDim; ++d) xt[d] = dataIn(i, t, d);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
107 | arma::vec pre = Wih * xt + bih + Whh * hPrev + bhh;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
108 | arma::vec it = vaeSigmoid(pre.subvec(0, h - 1));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
109 | arma::vec ft = vaeSigmoid(pre.subvec(h, 2 * h - 1));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
110 | arma::vec gt = arma::tanh(pre.subvec(2 * h, 3 * h - 1));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
111 | arma::vec ot = vaeSigmoid(pre.subvec(3 * h, 4 * h - 1));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
112 | arma::vec ct = ft % cPrev + it % gt;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
113 | arma::vec ht = ot % arma::tanh(ct);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
114 | I.col(t) = it; F.col(t) = ft; G.col(t) = gt; O.col(t) = ot;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
115 | C.col(t) = ct; H.col(t) = ht; X.col(t) = xt;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
116 | hPrev = ht; cPrev = ct;
| ~~~~~~~~~~~~~~~~~~~~~~~
117 | }
| ~
118 |
|
119 | arma::vec hLast = H.col(Ti - 1);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
120 | arma::vec combined(h + nCov);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
121 | combined.subvec(0, h - 1) = hLast;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
122 | if (nCov > 0) combined.subvec(h, h + nCov - 1) = covIn.row(i).t();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
123 | arma::vec out = fcW * combined + fcB;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
124 |
|
125 | arma::vec muI = out.subvec(0, zDim - 1);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
126 | arma::vec lsI = out.subvec(zDim, 2 * zDim - 1);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
127 | arma::vec lmask = (nOff > 0) ? out.subvec(2 * zDim, outDim - 1) : arma::vec();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
128 |
|
129 | arma::mat Li(zDim, zDim, arma::fill::zeros);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
130 | Li.diag() = arma::exp(lsI);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
131 | for (int k = 0; k < nOff; ++k) Li(offR[k], offC[k]) = lmask[k];
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
132 | arma::vec epsI = eps.row(i).t();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
133 | arma::vec zI = muI + Li * epsI;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
134 |
|
135 | mu.row(i) = muI.t();
| ~~~~~~~~~~~~~~~~~~~~
136 | logSigma.row(i) = lsI.t();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
137 | Lout.slice(i) = Li;
| ~~~~~~~~~~~~~~~~~~~
138 | zOut.row(i) = zI.t();
| ~~~~~~~~~~~~~~~~~~~~~
139 |
|
140 | if (!backward) return; // forward-only: this subject is done
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
141 |
|
142 | // ---- backward ----
| ~~~~~~~~~~~~~~~~~~~~~
143 | // accumulate into this thread's private partial when parBwd, else straight
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
144 | // into the shared (serial, continuous-fold) outputs
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
145 | int tid = 0;
| ~~~~~~~~~~~~
146 | #ifdef _OPENMP
| ~~~~~~~~~~~~~~
147 | if (parBwd) tid = omp_get_thread_num();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | #endif
| ~~~~~~
149 | arma::mat& aWih = parBwd ? tWih[tid] : gWih;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
150 | arma::mat& aWhh = parBwd ? tWhh[tid] : gWhh;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
151 | arma::vec& abih = parBwd ? tbih[tid] : gbih;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
152 | arma::vec& abhh = parBwd ? tbhh[tid] : gbhh;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
153 | arma::mat& aFcW = parBwd ? tFcW[tid] : gFcW;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
154 | arma::vec& aFcB = parBwd ? tFcB[tid] : gFcB;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
155 | arma::vec gZi = gZ.row(i).t();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
156 | arma::vec gMu = gZi; // dz/dmu = I
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
157 | arma::mat gL = gZi * epsI.t(); // dLoss/dL via z = mu + L eps
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
158 | arma::vec gLogSigma = gLogSigmaDirect.row(i).t() + gL.diag() % arma::exp(lsI);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
159 | arma::vec gLmask(nOff);
| ~~~~~~~~~~~~~~~~~~~~~~~
160 | for (int k = 0; k < nOff; ++k) gLmask[k] = gL(offR[k], offC[k]);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
161 |
|
162 | arma::vec gOut(outDim);
| ~~~~~~~~~~~~~~~~~~~~~~~
163 | gOut.subvec(0, zDim - 1) = gMu;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
164 | gOut.subvec(zDim, 2 * zDim - 1) = gLogSigma;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
165 | if (nOff > 0) gOut.subvec(2 * zDim, outDim - 1) = gLmask;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
166 |
|
167 | aFcB += gOut;
| ~~~~~~~~~~~~~
168 | aFcW += gOut * combined.t();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
169 | arma::vec gCombined = fcW.t() * gOut;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
170 | arma::vec dh = gCombined.subvec(0, h - 1); // grad on final hidden state
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
171 | arma::vec dc(h, arma::fill::zeros);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
172 |
|
173 | for (int t = Ti - 1; t >= 0; --t) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
174 | arma::vec tanhC = arma::tanh(C.col(t));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
175 | arma::vec doo = dh % tanhC;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
176 | dc += dh % O.col(t) % (1.0 - tanhC % tanhC);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
177 | arma::vec cPrevT = (t > 0) ? C.col(t - 1) : arma::vec(h, arma::fill::zeros);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
178 | arma::vec df = dc % cPrevT;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
179 | arma::vec di = dc % G.col(t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
180 | arma::vec dg = dc % I.col(t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
181 | arma::vec dcPrev = dc % F.col(t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
182 |
|
183 | arma::vec diPre = di % I.col(t) % (1.0 - I.col(t));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
184 | arma::vec dfPre = df % F.col(t) % (1.0 - F.col(t));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
185 | arma::vec dgPre = dg % (1.0 - G.col(t) % G.col(t));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
186 | arma::vec doPre = doo % O.col(t) % (1.0 - O.col(t));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
187 |
|
188 | arma::vec dpre(4 * h);
| ~~~~~~~~~~~~~~~~~~~~~~
189 | dpre.subvec(0, h - 1) = diPre;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
190 | dpre.subvec(h, 2 * h - 1) = dfPre;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
191 | dpre.subvec(2 * h, 3 * h - 1) = dgPre;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
192 | dpre.subvec(3 * h, 4 * h - 1) = doPre;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
193 |
|
194 | arma::vec hPrevT = (t > 0) ? H.col(t - 1) : arma::vec(h, arma::fill::zeros);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
195 | aWih += dpre * X.col(t).t();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | aWhh += dpre * hPrevT.t();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
197 | abih += dpre;
| ~~~~~~~~~~~~~
198 | abhh += dpre;
| ~~~~~~~~~~~~~
199 |
|
200 | dh = Whh.t() * dpre; // grad to h_{t-1}
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | dc = dcPrev;
| ~~~~~~~~~~~~
202 | }
| ~
203 | });
| ~~
nmParallelCore.h:61:15: warning: unused variable ‘_nmScope’ [-Wunused-variable]
61 | Scope _nmScope;
| ^~~~~~~~
nmParallelCore.h:68:15: warning: unused variable ‘_nmScope’ [-Wunused-variable]
68 | Scope _nmScope;
| ^~~~~~~~
gcc -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -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/RcppTrust/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 -DR_NO_REMAP -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/RcppTrust/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 -DR_NO_REMAP -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/RcppTrust/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 -DR_NO_REMAP -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/RcppTrust/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 covShortcut.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 RcppExportMod.o RcppExports.o rxcmp.o vaeEncoder.o init.o rprintf.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
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (nlmixr2est)