* installing *source* package ‘nlmixr’ ... ** package ‘nlmixr’ successfully unpacked and MD5 sums checked ** using staged installation --------[begin src/Makevars]-------- # -*- mode: makefile-gmake -*- ARMA=`"$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'` BH=`"$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e 'cat(file.path(find.package("BH"),"include"))'` RCPP=`"$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'` EG=`"$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'` SH=`"$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e 'cat(file.path(find.package("StanHeaders"),"include"))'` CXX_STD = CXX14 CXX14STD = -std=gnu++14 PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) PKG_CXXFLAGS = -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -isystem"$(BH)" -isystem"$(EG)" -isystem"$(SH)" -isystem"$(RCPP)" -isystem"$(ARMA)" $(SHLIB_OPENMP_CXXFLAGS) SHLIB_LDFLAGS = $(SHLIB_CXXLDFLAGS) SHLIB_LD = $(SHLIB_CXXLD) SOURCES_C = init.c rprintf.c merge3.c lbfgsR.c utilc.c SOURCES_CPP = inner.cpp npde.cpp shrink.cpp ires.cpp res.cpp cwres.cpp censResid.cpp cholse.cpp saem.cpp neldermead.cpp resid.cpp slice.cpp RcppExportMod.cpp ode_cmt1.cpp RcppExports.cpp OBJECTS = $(SOURCES_CPP:.cpp=.o) $(SOURCES_C:.c=.o) all: $(SHLIB) $(SHLIB): $(OBJECTS) --------[end src/Makevars]-------- ** libs make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/nlmixr/src' /usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("BH"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("StanHeaders"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -fopenmp -fpic -O3 -Wall -pedantic -frtti -c inner.cpp -o inner.o inner.cpp:100:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ focei_options inner.cpp:107:22: note: type is not C-compatible due to this default member initializer double *etaUpper = NULL; ^~~~ /usr/local/clang15/lib/clang/15.0.1/include/stddef.h:84:18: note: expanded from macro 'NULL' # define NULL __null ^~~~~~ inner.cpp:306:3: note: type is given name 'focei_options' for linkage purposes by this typedef declaration } focei_options; ^ inner.cpp:310:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ focei_ind inner.cpp:347:14: note: type is not C-compatible due to this default member initializer int doChol=1; ^ inner.cpp:354:3: note: type is given name 'focei_ind' for linkage purposes by this typedef declaration } focei_ind; ^ inner.cpp:436:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ rxSolveF inner.cpp:442:17: note: type is not C-compatible due to this default member initializer t_dydt dydt = NULL; ^~~~ /usr/local/clang15/lib/clang/15.0.1/include/stddef.h:84:18: note: expanded from macro 'NULL' # define NULL __null ^~~~~~ inner.cpp:455:3: note: type is given name 'rxSolveF' for linkage purposes by this typedef declaration } rxSolveF; ^ inner.cpp:754:9: warning: variable 'gillRet' set but not used [-Wunused-but-set-variable] int gillRet; ^ inner.cpp:772:12: warning: unused variable 'fv' [-Wunused-variable] double fv; ^ inner.cpp:887:30: warning: unused variable 'fpm2' [-Wunused-variable] double f, err, r, fpm, fpm2, rp = 0,lnr, limit, dv,dv0, curT; ^ inner.cpp:2925:26: warning: variable 'k' set but not used [-Wunused-but-set-variable] unsigned int i, j = 0, k = 0, ii=0, jj = 0, iA=0, iB=0, iH=0, iVid=0; ^ 7 warnings generated. /usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("BH"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("StanHeaders"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -fopenmp -fpic -O3 -Wall -pedantic -frtti -c npde.cpp -o npde.o In file included from npde.cpp:2: ./npde.h:29:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ calcNpdeInfoId ./npde.h:52:23: note: type is not C-compatible due to this default member initializer unsigned int warn = 0; ^ ./npde.h:53:3: note: type is given name 'calcNpdeInfoId' for linkage purposes by this typedef declaration } calcNpdeInfoId; ^ npde.cpp:128:15: warning: variable 'hi' set but not used [-Wunused-but-set-variable] double low, hi, low2, hi2; ^ 2 warnings generated. /usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("BH"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("StanHeaders"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -fopenmp -fpic -O3 -Wall -pedantic -frtti -c shrink.cpp -o shrink.o /usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("BH"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("StanHeaders"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -fopenmp -fpic -O3 -Wall -pedantic -frtti -c ires.cpp -o ires.o /usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("BH"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("StanHeaders"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -fopenmp -fpic -O3 -Wall -pedantic -frtti -c res.cpp -o res.o /usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("BH"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("StanHeaders"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -fopenmp -fpic -O3 -Wall -pedantic -frtti -c cwres.cpp -o cwres.o /usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("BH"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("StanHeaders"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -fopenmp -fpic -O3 -Wall -pedantic -frtti -c censResid.cpp -o censResid.o /usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("BH"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("StanHeaders"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -fopenmp -fpic -O3 -Wall -pedantic -frtti -c cholse.cpp -o cholse.o /usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("BH"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("StanHeaders"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -fopenmp -fpic -O3 -Wall -pedantic -frtti -c saem.cpp -o saem.o saem.cpp:1428:16: warning: unused variable 'nNanWarn' [-Wunused-variable] unsigned int nNanWarn=0; ^ 1 warning generated. /usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("BH"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("StanHeaders"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -fopenmp -fpic -O3 -Wall -pedantic -frtti -c neldermead.cpp -o neldermead.o /usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("BH"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("StanHeaders"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -fopenmp -fpic -O3 -Wall -pedantic -frtti -c resid.cpp -o resid.o /usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("BH"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("StanHeaders"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -fopenmp -fpic -O3 -Wall -pedantic -frtti -c slice.cpp -o slice.o /usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("BH"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("StanHeaders"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -fopenmp -fpic -O3 -Wall -pedantic -frtti -c RcppExportMod.cpp -o RcppExportMod.o /usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("BH"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("StanHeaders"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -fopenmp -fpic -O3 -Wall -pedantic -frtti -c ode_cmt1.cpp -o ode_cmt1.o /usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("BH"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppEigen"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("StanHeaders"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("Rcpp"),"include"))'`" -isystem"`"/data/gannet/ripley/R/R-clang/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'`" -fopenmp -fpic -O3 -Wall -pedantic -frtti -c RcppExports.cpp -o RcppExports.o /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c init.c -o init.o init.c:58:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] SEXP _nlmixr_freeFocei(); ^ void init.c:145:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] void rxOptionsFreeFocei(); ^ void 2 warnings generated. /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c rprintf.c -o rprintf.o /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c merge3.c -o merge3.o /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c lbfgsR.c -o lbfgsR.o /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/RxODE/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/lbfgsb3c/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c utilc.c -o utilc.o In file included from utilc.c:13: /data/gannet/ripley/R/test-clang/RxODE/include/RxODE.h:49:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] typedef void (*t_ode_current)(); ^ void /data/gannet/ripley/R/test-clang/RxODE/include/RxODE.h:299:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] typedef rx_solve *(*t_get_solve)(); ^ void /data/gannet/ripley/R/test-clang/RxODE/include/RxODE.h:301:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] typedef void *(*t_assignFuns)(); ^ void /data/gannet/ripley/R/test-clang/RxODE/include/RxODE.h:303:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] rx_solve *getRxSolve_(); ^ void /data/gannet/ripley/R/test-clang/RxODE/include/RxODE.h:304:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] rx_solve *getRxSolve2_(); ^ void /data/gannet/ripley/R/test-clang/RxODE/include/RxODE.h:312:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] SEXP RxODE_par_df(); ^ void 6 warnings generated. /usr/local/clang15/bin/clang++ -std=gnu++14 -shared -L/usr/local/clang/lib64 -L/usr/local/clang15/lib -L/usr/local/lib64 -o nlmixr.so inner.o npde.o shrink.o ires.o res.o cwres.o censResid.o cholse.o saem.o neldermead.o resid.o slice.o RcppExportMod.o ode_cmt1.o RcppExports.o init.o rprintf.o merge3.o lbfgsR.o utilc.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lgfortran -lm -lquadmath -fopenmp make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/nlmixr/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/nlmixr/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/nlmixr/src' installing to /data/gannet/ripley/R/packages/tests-clang/nlmixr.Rcheck/00LOCK-nlmixr/00new/nlmixr/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (nlmixr)