* 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 18.1.2’
using C++ compiler: ‘clang version 18.1.2’
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
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<ViewElt, Op, require_st_arithmetic<Op>> {
| ^
/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
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:200:
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 | <boost/typeof/incr_registration_group.hpp>
| ^
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:200:
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 | <boost/typeof/incr_registration_group.hpp>
| ^
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:200:
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 | <boost/typeof/incr_registration_group.hpp>
| ^
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:200:
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 | <boost/typeof/incr_registration_group.hpp>
| ^
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:200:
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 | <boost/typeof/incr_registration_group.hpp>
| ^
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:200:
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 | <boost/typeof/incr_registration_group.hpp>
| ^
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:200:
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 | <boost/typeof/incr_registration_group.hpp>
| ^
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:200:
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 | <boost/typeof/incr_registration_group.hpp>
| ^
/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
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]);
| ^~~~~~~
/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
/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(...) \
| ^
/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
1 warning generated.
/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
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)