* installing *source* package ‘dgtf’ ...
** this is package ‘dgtf’ version ‘0.1.0’
** package ‘dgtf’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘clang version 23.1.4’
using C++17
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/dgtf/src'
/usr/local/clang23/bin/clang++ -std=gnu++17 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/RcppProgress/include' -I'/data/localhost/ripley/R/test-clang/pg/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppExports.cpp -o RcppExports.o
/usr/local/clang23/bin/clang++ -std=gnu++17 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/RcppProgress/include' -I'/data/localhost/ripley/R/test-clang/pg/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c export.cpp -o export.o
In file included from export.cpp:2:
In file included from ./Model.h:6:
In file included from ./ErrDist.h:6:
In file included from ./distributions.h:5:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/math/special_functions/beta.hpp:23:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/math/special_functions/gamma.hpp:27:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/math/constants/constants.hpp:18:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/math/tools/convert_from_string.hpp:23:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/lexical_cast.hpp:33:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/lexical_cast/try_lexical_convert.hpp:31:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:47:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/container/container_fwd.hpp:65:
/data/localhost/ripley/R/test-clang/BH/include/boost/container/detail/std_fwd.hpp:29:1: warning: unused attribute '__exclude_from_explicit_instantiation__' in '#pragma clang attribute push' region [-Wpragma-clang-attribute]
29 | BOOST_MOVE_STD_NS_BEG
| ^
/data/localhost/ripley/R/test-clang/BH/include/boost/move/detail/std_ns_begin.hpp:21:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
21 | #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:74:39: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
74 | # define _LIBCPP_BEGIN_NAMESPACE_STD _LIBCPP_BEGIN_UNVERSIONED_NAMESPACE_STD inline namespace _LIBCPP_ABI_NAMESPACE {
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:70:40: note: expanded from macro '_LIBCPP_BEGIN_UNVERSIONED_NAMESPACE_STD'
70 | _LIBCPP_PUSH_EXTENSION_DIAGNOSTICS _LIBCPP_END_EXPLICIT_ABI_ANNOTATIONS namespace _LIBCPP_NAMESPACE_VISIBILITY std {
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:51:3: note: expanded from macro '_LIBCPP_END_EXPLICIT_ABI_ANNOTATIONS'
51 | _Pragma(_LIBCPP_TOSTRING(clang attribute _LibcxxExplicitABIAnnotations.push( \
| ^
<scratch space>:319:69: note: expanded from here
319 | clang attribute _LibcxxExplicitABIAnnotations.push( __attribute__((__exclude_from_explicit_instantiation__, __visibility__("hidden"), __abi_tag__("nqe230104"))), apply_to = function)
| ^
/data/localhost/ripley/R/test-clang/BH/include/boost/container/detail/std_fwd.hpp:61:1: note: '#pragma clang attribute push' regions ends here
61 | BOOST_MOVE_STD_NS_END
| ^
/data/localhost/ripley/R/test-clang/BH/include/boost/move/detail/std_ns_begin.hpp:22:34: note: expanded from macro 'BOOST_MOVE_STD_NS_END'
22 | #define BOOST_MOVE_STD_NS_END _LIBCPP_END_NAMESPACE_STD
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:75:39: note: expanded from macro '_LIBCPP_END_NAMESPACE_STD'
75 | # define _LIBCPP_END_NAMESPACE_STD } _LIBCPP_END_UNVERSIONED_NAMESPACE_STD
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:72:51: note: expanded from macro '_LIBCPP_END_UNVERSIONED_NAMESPACE_STD'
72 | # define _LIBCPP_END_UNVERSIONED_NAMESPACE_STD } _LIBCPP_BEGIN_EXPLICIT_ABI_ANNOTATIONS _LIBCPP_POP_EXTENSION_DIAGNOSTICS
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:57:48: note: expanded from macro '_LIBCPP_BEGIN_EXPLICIT_ABI_ANNOTATIONS'
57 | #define _LIBCPP_BEGIN_EXPLICIT_ABI_ANNOTATIONS _Pragma("clang attribute _LibcxxExplicitABIAnnotations.pop")
| ^
<scratch space>:321:8: note: expanded from here
321 | clang attribute _LibcxxExplicitABIAnnotations.pop
| ^
In file included from export.cpp:2:
In file included from ./Model.h:6:
In file included from ./ErrDist.h:6:
In file included from ./distributions.h:5:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/math/special_functions/beta.hpp:23:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/math/special_functions/gamma.hpp:27:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/math/constants/constants.hpp:18:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/math/tools/convert_from_string.hpp:23:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/lexical_cast.hpp:33:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/lexical_cast/try_lexical_convert.hpp:31:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:47:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/container/container_fwd.hpp:65:
/data/localhost/ripley/R/test-clang/BH/include/boost/container/detail/std_fwd.hpp:29:1: warning: unused attribute '__visibility__' in '#pragma clang attribute push' region [-Wpragma-clang-attribute]
29 | BOOST_MOVE_STD_NS_BEG
| ^
/data/localhost/ripley/R/test-clang/BH/include/boost/move/detail/std_ns_begin.hpp:21:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
21 | #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:74:39: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
74 | # define _LIBCPP_BEGIN_NAMESPACE_STD _LIBCPP_BEGIN_UNVERSIONED_NAMESPACE_STD inline namespace _LIBCPP_ABI_NAMESPACE {
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:70:40: note: expanded from macro '_LIBCPP_BEGIN_UNVERSIONED_NAMESPACE_STD'
70 | _LIBCPP_PUSH_EXTENSION_DIAGNOSTICS _LIBCPP_END_EXPLICIT_ABI_ANNOTATIONS namespace _LIBCPP_NAMESPACE_VISIBILITY std {
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:51:3: note: expanded from macro '_LIBCPP_END_EXPLICIT_ABI_ANNOTATIONS'
51 | _Pragma(_LIBCPP_TOSTRING(clang attribute _LibcxxExplicitABIAnnotations.push( \
| ^
<scratch space>:319:110: note: expanded from here
319 | clang attribute _LibcxxExplicitABIAnnotations.push( __attribute__((__exclude_from_explicit_instantiation__, __visibility__("hidden"), __abi_tag__("nqe230104"))), apply_to = function)
| ^
/data/localhost/ripley/R/test-clang/BH/include/boost/container/detail/std_fwd.hpp:61:1: note: '#pragma clang attribute push' regions ends here
61 | BOOST_MOVE_STD_NS_END
| ^
/data/localhost/ripley/R/test-clang/BH/include/boost/move/detail/std_ns_begin.hpp:22:34: note: expanded from macro 'BOOST_MOVE_STD_NS_END'
22 | #define BOOST_MOVE_STD_NS_END _LIBCPP_END_NAMESPACE_STD
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:75:39: note: expanded from macro '_LIBCPP_END_NAMESPACE_STD'
75 | # define _LIBCPP_END_NAMESPACE_STD } _LIBCPP_END_UNVERSIONED_NAMESPACE_STD
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:72:51: note: expanded from macro '_LIBCPP_END_UNVERSIONED_NAMESPACE_STD'
72 | # define _LIBCPP_END_UNVERSIONED_NAMESPACE_STD } _LIBCPP_BEGIN_EXPLICIT_ABI_ANNOTATIONS _LIBCPP_POP_EXTENSION_DIAGNOSTICS
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:57:48: note: expanded from macro '_LIBCPP_BEGIN_EXPLICIT_ABI_ANNOTATIONS'
57 | #define _LIBCPP_BEGIN_EXPLICIT_ABI_ANNOTATIONS _Pragma("clang attribute _LibcxxExplicitABIAnnotations.pop")
| ^
<scratch space>:321:8: note: expanded from here
321 | clang attribute _LibcxxExplicitABIAnnotations.pop
| ^
In file included from export.cpp:2:
In file included from ./Model.h:6:
In file included from ./ErrDist.h:6:
In file included from ./distributions.h:5:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/math/special_functions/beta.hpp:23:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/math/special_functions/gamma.hpp:27:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/math/constants/constants.hpp:18:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/math/tools/convert_from_string.hpp:23:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/lexical_cast.hpp:33:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/lexical_cast/try_lexical_convert.hpp:31:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:47:
In file included from /data/localhost/ripley/R/test-clang/BH/include/boost/container/container_fwd.hpp:65:
/data/localhost/ripley/R/test-clang/BH/include/boost/container/detail/std_fwd.hpp:29:1: warning: unused attribute '__abi_tag__' in '#pragma clang attribute push' region [-Wpragma-clang-attribute]
29 | BOOST_MOVE_STD_NS_BEG
| ^
/data/localhost/ripley/R/test-clang/BH/include/boost/move/detail/std_ns_begin.hpp:21:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
21 | #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:74:39: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
74 | # define _LIBCPP_BEGIN_NAMESPACE_STD _LIBCPP_BEGIN_UNVERSIONED_NAMESPACE_STD inline namespace _LIBCPP_ABI_NAMESPACE {
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:70:40: note: expanded from macro '_LIBCPP_BEGIN_UNVERSIONED_NAMESPACE_STD'
70 | _LIBCPP_PUSH_EXTENSION_DIAGNOSTICS _LIBCPP_END_EXPLICIT_ABI_ANNOTATIONS namespace _LIBCPP_NAMESPACE_VISIBILITY std {
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:51:3: note: expanded from macro '_LIBCPP_END_EXPLICIT_ABI_ANNOTATIONS'
51 | _Pragma(_LIBCPP_TOSTRING(clang attribute _LibcxxExplicitABIAnnotations.push( \
| ^
<scratch space>:319:136: note: expanded from here
319 | clang attribute _LibcxxExplicitABIAnnotations.push( __attribute__((__exclude_from_explicit_instantiation__, __visibility__("hidden"), __abi_tag__("nqe230104"))), apply_to = function)
| ^
/data/localhost/ripley/R/test-clang/BH/include/boost/container/detail/std_fwd.hpp:61:1: note: '#pragma clang attribute push' regions ends here
61 | BOOST_MOVE_STD_NS_END
| ^
/data/localhost/ripley/R/test-clang/BH/include/boost/move/detail/std_ns_begin.hpp:22:34: note: expanded from macro 'BOOST_MOVE_STD_NS_END'
22 | #define BOOST_MOVE_STD_NS_END _LIBCPP_END_NAMESPACE_STD
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:75:39: note: expanded from macro '_LIBCPP_END_NAMESPACE_STD'
75 | # define _LIBCPP_END_NAMESPACE_STD } _LIBCPP_END_UNVERSIONED_NAMESPACE_STD
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:72:51: note: expanded from macro '_LIBCPP_END_UNVERSIONED_NAMESPACE_STD'
72 | # define _LIBCPP_END_UNVERSIONED_NAMESPACE_STD } _LIBCPP_BEGIN_EXPLICIT_ABI_ANNOTATIONS _LIBCPP_POP_EXTENSION_DIAGNOSTICS
| ^
/usr/local/clang23/bin/../include/c++/v1/__configuration/namespace.h:57:48: note: expanded from macro '_LIBCPP_BEGIN_EXPLICIT_ABI_ANNOTATIONS'
57 | #define _LIBCPP_BEGIN_EXPLICIT_ABI_ANNOTATIONS _Pragma("clang attribute _LibcxxExplicitABIAnnotations.pop")
| ^
<scratch space>:321:8: note: expanded from here
321 | clang attribute _LibcxxExplicitABIAnnotations.pop
| ^
In file included from export.cpp:2:
In file included from ./Model.h:6:
In file included from ./ErrDist.h:6:
In file included from ./distributions.h:6:
./utils.h:61:8: warning: unused variable 'is_zero' [-Wunused-variable]
61 | bool is_zero = input.is_zero();
| ^~~~~~~
./utils.h:65:8: warning: unused variable 'is_negative' [-Wunused-variable]
65 | bool is_negative = arma::any(arma::vectorise(input) < -EPS);
| ^~~~~~~~~~~
In file included from export.cpp:2:
In file included from ./Model.h:6:
In file included from ./ErrDist.h:6:
./distributions.h:398:16: warning: unused variable 'a_plus_b_sq' [-Wunused-variable]
398 | double a_plus_b_sq = std::pow(a_plus_b, 2.);
| ^~~~~~~~~~~
./distributions.h:399:16: warning: unused variable 'a_times_b' [-Wunused-variable]
399 | double a_times_b = alpha * beta;
| ^~~~~~~~~
In file included from export.cpp:2:
./Model.h:677:16: warning: variable 'npop' set but not used [-Wunused-but-set-variable]
677 | double npop = 1.;
| ^
./Model.h:830:28: warning: unused variable 'p' [-Wunused-variable]
830 | const unsigned int p = theta.n_rows;
| ^
./Model.h:970:28: warning: unused variable 'p' [-Wunused-variable]
970 | const unsigned int p = theta.n_rows;
| ^
In file included from export.cpp:4:
In file included from ./SequentialMonteCarlo.h:14:
./ImportanceDensity.h:343:24: warning: unused variable 'nT' [-Wunused-variable]
343 | const unsigned int nT = y.n_elem - 1;
| ^~
In file included from export.cpp:4:
./SequentialMonteCarlo.h:509:18: warning: unused variable 'compose' [-Wunused-variable]
509 | auto compose = [](const arma::uvec &a, const arma::uvec &b)
| ^~~~~~~
./SequentialMonteCarlo.h:2896:22: warning: unused variable 'print_time' [-Wunused-variable]
2896 | bool print_time = (t == nT - 2);
| ^~~~~~~~~~
./SequentialMonteCarlo.h:2881:18: warning: unused variable 'nonnegative_par1' [-Wunused-variable]
2881 | bool nonnegative_par1 = (dist_list[prior_par1.name] != AVAIL::Dist::gaussian);
| ^~~~~~~~~~~~~~~~
./SequentialMonteCarlo.h:2882:18: warning: unused variable 'withinone_par1' [-Wunused-variable]
2882 | bool withinone_par1 = (dist_list[prior_par1.name] == AVAIL::Dist::beta);
| ^~~~~~~~~~~~~~
./SequentialMonteCarlo.h:2884:18: warning: unused variable 'nonnegative_par2' [-Wunused-variable]
2884 | bool nonnegative_par2 = (dist_list[prior_par2.name] != AVAIL::Dist::gaussian);
| ^~~~~~~~~~~~~~~~
./SequentialMonteCarlo.h:2885:18: warning: unused variable 'withinone_par2' [-Wunused-variable]
2885 | bool withinone_par2 = (dist_list[prior_par2.name] == AVAIL::Dist::beta);
| ^~~~~~~~~~~~~~
In file included from export.cpp:5:
./MCMC.h:417:24: warning: variable 'logps' set but not used [-Wunused-but-set-variable]
417 | double logps = 0.;
| ^
In file included from export.cpp:6:
./VariationalBayes.h:859:24: warning: unused variable 'log_cond_marg' [-Wunused-variable]
859 | double log_cond_marg = SMC::SequentialMonteCarlo::auxiliary_filter0(
| ^~~~~~~~~~~~~
In file included from export.cpp:2:
./Model.h:612:12: warning: private field '_y0' is not used [-Wunused-private-field]
612 | double _y0 = 0.;
| ^
./Model.h:613:12: warning: private field '_mu0' is not used [-Wunused-private-field]
613 | double _mu0 = 1.;
| ^
21 warnings generated.
/usr/local/clang23/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang23/lib -L/usr/local/clang23/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o dgtf.so RcppExports.o export.o -L/data/localhost/ripley/R/R-clang/lib -lRlapack -L/data/localhost/ripley/R/R-clang/lib -lRblas -lflang_rt.runtime -lm
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang/dgtf/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/dgtf/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang/dgtf/src'
installing to /data/localhost/ripley/R/packages/tests-clang/dgtf.Rcheck/00LOCK-dgtf/00new/dgtf/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (dgtf)