* installing *source* package ‘rxode2parse’ ... ** package ‘rxode2parse’ successfully unpacked and MD5 sums checked ** using staged installation --------[begin src/Makevars]-------- # -*- mode: makefile-gmake -*- BH=/data/gannet/ripley/R/test-clang/BH/include RCPP=/data/gannet/ripley/R/test-clang/Rcpp/include EG=/data/gannet/ripley/R/test-clang/RcppEigen/include SH=-isystem'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' CXX_STD = CXX17 ################################################################################ ## Package library flags. PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) -L'/data/gannet/ripley/R/test-clang/RcppParallel/lib/' -Wl,-rpath,'/data/gannet/ripley/R/test-clang/RcppParallel/lib/' -ltbb -ltbbmalloc # Release options PKG_CFLAGS = -D_isrxode2parse_ PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -D_isrxode2parse_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"$(BH)" -isystem"$(EG)" $(SH) -isystem"$(RCPP)" --------[end src/Makevars]-------- --------[begin R/RxODE_md5.R]-------- rxode2parse.md5 <- "c18ff1a2f151e2d8b856bbe21daf2be7" --------[end R/RxODE_md5.R]-------- ** libs using C compiler: ‘clang version 18.1.4’ using C++ compiler: ‘clang version 18.1.4’ using C++17 make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rxode2parse/src' /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2parse_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -isystem"/data/gannet/ripley/R/test-clang/RcppEigen/include" -isystem'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -isystem"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_isrxode2parse_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c codegen.c -o codegen.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2parse_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -isystem"/data/gannet/ripley/R/test-clang/RcppEigen/include" -isystem'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -isystem"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c etTran.cpp -o etTran.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2parse_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -isystem"/data/gannet/ripley/R/test-clang/RcppEigen/include" -isystem'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -isystem"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c fast_factor.cpp -o fast_factor.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_isrxode2parse_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c genModelVars.c -o genModelVars.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_isrxode2parse_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c getOption.c -o getOption.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_isrxode2parse_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c init.c -o init.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_isrxode2parse_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c lincmt.c -o lincmt.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2parse_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -isystem"/data/gannet/ripley/R/test-clang/RcppEigen/include" -isystem'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -isystem"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c lincmtB.cpp -o lincmtB.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_isrxode2parse_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c parseLinCmt.c -o parseLinCmt.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_isrxode2parse_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c print_node.c -o print_node.o In file included from lincmtB.cpp:108: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:56: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun/elt_multiply.hpp:9: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun/multiply.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 57 | struct ops_partials_edge> { | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 45 | class ops_partials_edge; | ^~~~~ | struct /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2parse_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -isystem"/data/gannet/ripley/R/test-clang/RcppEigen/include" -isystem'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -isystem"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c qs.cpp -o qs.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_isrxode2parse_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c sbuf.c -o sbuf.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_isrxode2parse_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c strncmpi.c -o strncmpi.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_isrxode2parse_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c tran.c -o tran.o In file included from tran.c:28: ./tran.g.d_parser.h:3:9: warning: 'printf' macro redefined [-Wmacro-redefined] 3 | #define printf Rprintf | ^ /usr/include/bits/stdio2.h:89:11: note: previous definition is here 89 | # define printf(...) \ | ^ In file included from lincmtB.cpp:108: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:201: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /usr/local/clang/include/boost/numeric/odeint.hpp:25: In file included from /usr/local/clang/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /usr/local/clang/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /usr/local/clang/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /usr/local/clang/include/boost/units/quantity.hpp:29: In file included from /usr/local/clang/include/boost/units/conversion.hpp:17: In file included from /usr/local/clang/include/boost/units/detail/conversion_impl.hpp:20: In file included from /usr/local/clang/include/boost/units/heterogeneous_system.hpp:34: /usr/local/clang/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token] 166 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /usr/local/clang/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 197 | | ^ In file included from lincmtB.cpp:108: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:201: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /usr/local/clang/include/boost/numeric/odeint.hpp:25: In file included from /usr/local/clang/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /usr/local/clang/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /usr/local/clang/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /usr/local/clang/include/boost/units/quantity.hpp:29: In file included from /usr/local/clang/include/boost/units/conversion.hpp:17: In file included from /usr/local/clang/include/boost/units/detail/conversion_impl.hpp:20: In file included from /usr/local/clang/include/boost/units/heterogeneous_system.hpp:35: In file included from /usr/local/clang/include/boost/units/dimension.hpp:21: /usr/local/clang/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token] 125 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /usr/local/clang/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 197 | | ^ In file included from lincmtB.cpp:108: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:201: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /usr/local/clang/include/boost/numeric/odeint.hpp:25: In file included from /usr/local/clang/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /usr/local/clang/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /usr/local/clang/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /usr/local/clang/include/boost/units/quantity.hpp:29: In file included from /usr/local/clang/include/boost/units/conversion.hpp:17: In file included from /usr/local/clang/include/boost/units/detail/conversion_impl.hpp:20: In file included from /usr/local/clang/include/boost/units/heterogeneous_system.hpp:35: In file included from /usr/local/clang/include/boost/units/dimension.hpp:21: In file included from /usr/local/clang/include/boost/units/detail/dimension_list.hpp:131: /usr/local/clang/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token] 49 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /usr/local/clang/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 197 | | ^ In file included from lincmtB.cpp:108: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:201: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /usr/local/clang/include/boost/numeric/odeint.hpp:25: In file included from /usr/local/clang/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /usr/local/clang/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /usr/local/clang/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /usr/local/clang/include/boost/units/quantity.hpp:29: In file included from /usr/local/clang/include/boost/units/conversion.hpp:17: In file included from /usr/local/clang/include/boost/units/detail/conversion_impl.hpp:20: In file included from /usr/local/clang/include/boost/units/heterogeneous_system.hpp:39: In file included from /usr/local/clang/include/boost/units/detail/linear_algebra.hpp:20: /usr/local/clang/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token] 75 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /usr/local/clang/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 197 | | ^ In file included from lincmtB.cpp:108: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:201: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /usr/local/clang/include/boost/numeric/odeint.hpp:25: In file included from /usr/local/clang/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /usr/local/clang/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /usr/local/clang/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /usr/local/clang/include/boost/units/quantity.hpp:29: In file included from /usr/local/clang/include/boost/units/conversion.hpp:17: In file included from /usr/local/clang/include/boost/units/detail/conversion_impl.hpp:20: In file included from /usr/local/clang/include/boost/units/heterogeneous_system.hpp:40: In file included from /usr/local/clang/include/boost/units/detail/unscale.hpp:28: /usr/local/clang/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token] 139 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /usr/local/clang/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 197 | | ^ In file included from lincmtB.cpp:108: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:201: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /usr/local/clang/include/boost/numeric/odeint.hpp:25: In file included from /usr/local/clang/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /usr/local/clang/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /usr/local/clang/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /usr/local/clang/include/boost/units/quantity.hpp:29: In file included from /usr/local/clang/include/boost/units/conversion.hpp:17: In file included from /usr/local/clang/include/boost/units/detail/conversion_impl.hpp:20: /usr/local/clang/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token] 120 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /usr/local/clang/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 197 | | ^ In file included from lincmtB.cpp:108: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:201: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /usr/local/clang/include/boost/numeric/odeint.hpp:25: In file included from /usr/local/clang/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /usr/local/clang/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /usr/local/clang/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /usr/local/clang/include/boost/units/quantity.hpp:29: In file included from /usr/local/clang/include/boost/units/conversion.hpp:17: In file included from /usr/local/clang/include/boost/units/detail/conversion_impl.hpp:21: /usr/local/clang/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token] 99 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /usr/local/clang/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 197 | | ^ In file included from lincmtB.cpp:108: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:201: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /usr/local/clang/include/boost/numeric/odeint.hpp:25: In file included from /usr/local/clang/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /usr/local/clang/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /usr/local/clang/include/boost/numeric/odeint/util/unit_helper.hpp:23: /usr/local/clang/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token] 495 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /usr/local/clang/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 197 | | ^ 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2parse_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -isystem"/data/gannet/ripley/R/test-clang/RcppEigen/include" -isystem'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -isystem"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c udf.cpp -o udf.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_isrxode2parse_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c utilc.c -o utilc.o In file included from lincmtB.cpp:187: ./../inst/include/rxode2parseGetTime.h:223:9: warning: unused variable 'curEvid' [-Wunused-variable] 223 | int curEvid = getEvid(ind, ind->idose[*endIdx+1]); | ^~~~~~~ 10 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o rxode2parse.so RcppExports.o codegen.o etTran.o fast_factor.o genModelVars.o getOption.o init.o lincmt.o lincmtB.o parseLinCmt.o print_node.o qs.o sbuf.o strncmpi.o tran.o udf.o utilc.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortran_main -lFortranRuntime -lFortranDecimal -lm -fopenmp -L/data/gannet/ripley/R/test-clang/RcppParallel/lib/ -Wl,-rpath,/data/gannet/ripley/R/test-clang/RcppParallel/lib/ -ltbb -ltbbmalloc make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rxode2parse/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rxode2parse/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rxode2parse/src' installing to /data/gannet/ripley/R/packages/tests-clang/rxode2parse.Rcheck/00LOCK-rxode2parse/00new/rxode2parse/libs ** R ** 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 (rxode2parse)