* installing *source* package ‘rxode2parse’ ...
** package ‘rxode2parse’ successfully unpacked and MD5 sums checked
** using staged installation
--------[begin src/Makevars]--------
# -*- mode: makefile-gmake -*-
BH=/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include
RCPP=/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include
EG=/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include
SH=-isystem'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/src'
CXX_STD = CXX17
################################################################################
## Package library flags.
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) -L'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/lib/' -Wl,-rpath,'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/dparser/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include -D_isrxode2parse_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/dparser/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include -D_isrxode2parse_ -fPIC -falign-functions=64 -Wall -g -O2 -c codegen.c -o codegen.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/dparser/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include -D_isrxode2parse_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c etTran.cpp -o etTran.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/dparser/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include -D_isrxode2parse_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c fast_factor.cpp -o fast_factor.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/dparser/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include -D_isrxode2parse_ -fPIC -falign-functions=64 -Wall -g -O2 -c genModelVars.c -o genModelVars.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/dparser/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include -D_isrxode2parse_ -fPIC -falign-functions=64 -Wall -g -O2 -c getOption.c -o getOption.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/dparser/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include -D_isrxode2parse_ -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/dparser/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include -D_isrxode2parse_ -fPIC -falign-functions=64 -Wall -g -O2 -c lincmt.c -o lincmt.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/dparser/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include -D_isrxode2parse_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c lincmtB.cpp -o lincmtB.o
In file included from lincmtB.cpp:108:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math.hpp:19:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/rev/fun.hpp:56:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/rev/fun/elt_multiply.hpp:9:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/rev/fun/multiply.hpp:7:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/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]
struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> {
^
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
class ops_partials_edge;
^~~~~
struct
In file included from lincmtB.cpp:187:
./../inst/include/rxode2parseGetTime.h:223:9: warning: unused variable 'curEvid' [-Wunused-variable]
int curEvid = getEvid(ind, ind->idose[*endIdx+1]);
^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/dparser/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include -D_isrxode2parse_ -fPIC -falign-functions=64 -Wall -g -O2 -c parseLinCmt.c -o parseLinCmt.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/dparser/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include -D_isrxode2parse_ -fPIC -falign-functions=64 -Wall -g -O2 -c print_node.c -o print_node.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/dparser/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include -D_isrxode2parse_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c qs.cpp -o qs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/dparser/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include -D_isrxode2parse_ -fPIC -falign-functions=64 -Wall -g -O2 -c sbuf.c -o sbuf.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/dparser/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include -D_isrxode2parse_ -fPIC -falign-functions=64 -Wall -g -O2 -c strncmpi.c -o strncmpi.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/dparser/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include -D_isrxode2parse_ -fPIC -falign-functions=64 -Wall -g -O2 -c tran.c -o tran.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/dparser/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include -D_isrxode2parse_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c udf.cpp -o udf.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/dparser/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include' -I/opt/R/arm64/include -D_isrxode2parse_ -fPIC -falign-functions=64 -Wall -g -O2 -c utilc.c -o utilc.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -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/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -L/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/lib/ -Wl,-rpath,/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Volumes/Builds/packages/big-sur-arm64/results/4.4/rxode2parse.Rcheck/00LOCK-rxode2parse/00new/rxode2parse/libs
** generating debug symbols (dSYM)
** 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)