* installing *source* package ‘adapt3’ ...
** this is package ‘adapt3’ version ‘2.0.9’
** package ‘adapt3’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 23.1.1’
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/adapt3/src'
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/lefko3/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -I../inst/include/ -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c RcppExports.cpp -o RcppExports.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/lefko3/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -I../inst/include/ -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c projection.cpp -o projection.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/lefko3/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -I../inst/include/ -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c utilities.cpp -o utilities.o
In file included from projection.cpp:8:
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>:133:69: note: expanded from here
133 | clang attribute _LibcxxExplicitABIAnnotations.push( __attribute__((__exclude_from_explicit_instantiation__, __visibility__("hidden"), __abi_tag__("nqe230101"))), 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>:135:8: note: expanded from here
135 | clang attribute _LibcxxExplicitABIAnnotations.pop
| ^
In file included from projection.cpp:8:
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>:133:110: note: expanded from here
133 | clang attribute _LibcxxExplicitABIAnnotations.push( __attribute__((__exclude_from_explicit_instantiation__, __visibility__("hidden"), __abi_tag__("nqe230101"))), 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>:135:8: note: expanded from here
135 | clang attribute _LibcxxExplicitABIAnnotations.pop
| ^
In file included from projection.cpp:8:
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>:133:136: note: expanded from here
133 | clang attribute _LibcxxExplicitABIAnnotations.push( __attribute__((__exclude_from_explicit_instantiation__, __visibility__("hidden"), __abi_tag__("nqe230101"))), 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>:135:8: note: expanded from here
135 | clang attribute _LibcxxExplicitABIAnnotations.pop
| ^
In file included from utilities.cpp:7:
In file included from /data/localhost/ripley/R/test-clang/lefko3/include/LefkoUtils.h:7:
In file included from /data/localhost/ripley/R/test-clang/lefko3/include/basic_funcs/main_utils.h:7:
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>:133:69: note: expanded from here
133 | clang attribute _LibcxxExplicitABIAnnotations.push( __attribute__((__exclude_from_explicit_instantiation__, __visibility__("hidden"), __abi_tag__("nqe230101"))), 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>:135:8: note: expanded from here
135 | clang attribute _LibcxxExplicitABIAnnotations.pop
| ^
In file included from utilities.cpp:7:
In file included from /data/localhost/ripley/R/test-clang/lefko3/include/LefkoUtils.h:7:
In file included from /data/localhost/ripley/R/test-clang/lefko3/include/basic_funcs/main_utils.h:7:
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>:133:110: note: expanded from here
133 | clang attribute _LibcxxExplicitABIAnnotations.push( __attribute__((__exclude_from_explicit_instantiation__, __visibility__("hidden"), __abi_tag__("nqe230101"))), 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>:135:8: note: expanded from here
135 | clang attribute _LibcxxExplicitABIAnnotations.pop
| ^
In file included from utilities.cpp:7:
In file included from /data/localhost/ripley/R/test-clang/lefko3/include/LefkoUtils.h:7:
In file included from /data/localhost/ripley/R/test-clang/lefko3/include/basic_funcs/main_utils.h:7:
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>:133:136: note: expanded from here
133 | clang attribute _LibcxxExplicitABIAnnotations.push( __attribute__((__exclude_from_explicit_instantiation__, __visibility__("hidden"), __abi_tag__("nqe230101"))), 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>:135:8: note: expanded from here
135 | clang attribute _LibcxxExplicitABIAnnotations.pop
| ^
In file included from projection.cpp:10:
In file included from /data/localhost/ripley/R/test-clang/lefko3/include/LefkoUtils.h:8:
/data/localhost/ripley/R/test-clang/lefko3/include/basic_funcs/mat_stuff.h:1672:12: warning: variable 'esta2_used' set but not used [-Wunused-but-set-variable]
1672 | bool esta2_used {false};
| ^
/data/localhost/ripley/R/test-clang/lefko3/include/basic_funcs/mat_stuff.h:1478:9: warning: variable 'age_related_stages' set but not used [-Wunused-but-set-variable]
1478 | int age_related_stages {0};
| ^
/data/localhost/ripley/R/test-clang/lefko3/include/basic_funcs/mat_stuff.h:1479:9: warning: variable 'age_related_min_ages' set but not used [-Wunused-but-set-variable]
1479 | int age_related_min_ages {0};
| ^
In file included from projection.cpp:11:
In file included from ../inst/include/AdaptUtils.h:7:
../inst/include/basic_funcs/main_utils.h:4475:9: warning: variable 'good_max_age_values' set but not used [-Wunused-but-set-variable]
4475 | int good_max_age_values {0};
| ^
../inst/include/basic_funcs/main_utils.h:4551:9: warning: variable 'ce2_nas_length' set but not used [-Wunused-but-set-variable]
4551 | int ce2_nas_length {0};
| ^
In file included from projection.cpp:11:
In file included from ../inst/include/AdaptUtils.h:8:
../inst/include/basic_funcs/mats_utils.h:3763:9: warning: unused variable 'nostages_nounborn' [-Wunused-variable]
3763 | int nostages_nounborn = nostages - almostbornstages;
| ^~~~~~~~~~~~~~~~~
projection.cpp:5891:8: warning: variable 'pure_fleslie' set but not used [-Wunused-but-set-variable]
5891 | bool pure_fleslie {false}; // Are all function-based MPMs Leslie MPMs?
| ^
projection.cpp:5896:7: warning: variable 'stageframe_count' set but not used [-Wunused-but-set-variable]
5896 | int stageframe_count {0};
| ^
projection.cpp:5897:7: warning: variable 'stageframe_notNull_count' set but not used [-Wunused-but-set-variable]
5897 | int stageframe_notNull_count {0};
| ^
projection.cpp:5898:7: warning: variable 'supplement_count' set but not used [-Wunused-but-set-variable]
5898 | int supplement_count {0};
| ^
projection.cpp:5899:7: warning: variable 'equivalence_count' set but not used [-Wunused-but-set-variable]
5899 | int equivalence_count {0};
| ^
projection.cpp:5900:7: warning: variable 'start_count' set but not used [-Wunused-but-set-variable]
5900 | int start_count {0};
| ^
projection.cpp:5901:7: warning: variable 'tweights_count' set but not used [-Wunused-but-set-variable]
5901 | int tweights_count {0};
| ^
projection.cpp:5902:7: warning: variable 'density_count' set but not used [-Wunused-but-set-variable]
5902 | int density_count {0};
| ^
projection.cpp:5903:7: warning: variable 'entry_time_count' set but not used [-Wunused-but-set-variable]
5903 | int entry_time_count {0};
| ^
projection.cpp:5904:7: warning: variable 'density_vr_count' set but not used [-Wunused-but-set-variable]
5904 | int density_vr_count {0};
| ^
projection.cpp:5905:7: warning: variable 'sparse_vec_count' set but not used [-Wunused-but-set-variable]
5905 | int sparse_vec_count {0};
| ^
projection.cpp:5906:7: warning: variable 'found_fleslie' set but not used [-Wunused-but-set-variable]
5906 | int found_fleslie {0};
| ^
projection.cpp:7888:15: warning: variable 'maxage_NAs' set but not used [-Wunused-but-set-variable]
7888 | int maxage_NAs {0};
| ^
projection.cpp:8089:13: warning: unused variable 'current_supplement_rows' [-Wunused-variable]
8089 | int current_supplement_rows = static_cast<int>(current_supplement_df.nrows());
| ^~~~~~~~~~~~~~~~~~~~~~~
projection.cpp:6596:8: warning: unused variable 'sensitivity_bool' [-Wunused-variable]
6596 | bool sensitivity_bool {false};
| ^~~~~~~~~~~~~~~~
In file included from utilities.cpp:7:
In file included from /data/localhost/ripley/R/test-clang/lefko3/include/LefkoUtils.h:8:
/data/localhost/ripley/R/test-clang/lefko3/include/basic_funcs/mat_stuff.h:1672:12: warning: variable 'esta2_used' set but not used [-Wunused-but-set-variable]
1672 | bool esta2_used {false};
| ^
/data/localhost/ripley/R/test-clang/lefko3/include/basic_funcs/mat_stuff.h:1478:9: warning: variable 'age_related_stages' set but not used [-Wunused-but-set-variable]
1478 | int age_related_stages {0};
| ^
/data/localhost/ripley/R/test-clang/lefko3/include/basic_funcs/mat_stuff.h:1479:9: warning: variable 'age_related_min_ages' set but not used [-Wunused-but-set-variable]
1479 | int age_related_min_ages {0};
| ^
projection.cpp:12857:18: warning: unused variable 'res_fitness_test' [-Wunused-variable]
12857 | double res_fitness_test = current_round_fitness_values(0);
| ^~~~~~~~~~~~~~~~
projection.cpp:12487:12: warning: variable 'conv_test' set but not used [-Wunused-but-set-variable]
12487 | double conv_test {0.};
| ^
projection.cpp:12489:12: warning: variable 'xE' set but not used [-Wunused-but-set-variable]
12489 | double xE {0.}; // test value to keep in memory from previous expansion round
| ^
projection.cpp:12490:12: warning: variable 'xC_new' set but not used [-Wunused-but-set-variable]
12490 | double xC_new {0.}; // test value to keep in memory from previous contraction round
| ^
projection.cpp:13072:7: warning: unused variable 'optim_rows' [-Wunused-variable]
13072 | int optim_rows = static_cast<int>(final_output_df.nrows());
| ^~~~~~~~~~
projection.cpp:14912:18: warning: unused variable 'res_fitness_test' [-Wunused-variable]
14912 | double res_fitness_test = current_round_fitness_values(0);
| ^~~~~~~~~~~~~~~~
projection.cpp:14430:12: warning: variable 'conv_test' set but not used [-Wunused-but-set-variable]
14430 | double conv_test {0.};
| ^
projection.cpp:14432:12: warning: variable 'xE' set but not used [-Wunused-but-set-variable]
14432 | double xE {0.}; // test value to keep in memory from previous expansion round
| ^
projection.cpp:14433:12: warning: variable 'xC_new' set but not used [-Wunused-but-set-variable]
14433 | double xC_new {0.}; // test value to keep in memory from previous contraction round
| ^
projection.cpp:15129:7: warning: unused variable 'optim_rows' [-Wunused-variable]
15129 | int optim_rows = static_cast<int>(final_output_df.nrows());
| ^~~~~~~~~~
In file included from utilities.cpp:8:
In file included from ../inst/include/AdaptUtils.h:7:
../inst/include/basic_funcs/main_utils.h:4475:9: warning: variable 'good_max_age_values' set but not used [-Wunused-but-set-variable]
4475 | int good_max_age_values {0};
| ^
../inst/include/basic_funcs/main_utils.h:4551:9: warning: variable 'ce2_nas_length' set but not used [-Wunused-but-set-variable]
4551 | int ce2_nas_length {0};
| ^
projection.cpp:19872:7: warning: unused variable 'stageframe_count' [-Wunused-variable]
19872 | int stageframe_count {0};
| ^~~~~~~~~~~~~~~~
projection.cpp:19873:7: warning: variable 'stageframe_notNull_count' set but not used [-Wunused-but-set-variable]
19873 | int stageframe_notNull_count {0};
| ^
projection.cpp:19874:7: warning: unused variable 'supplement_count' [-Wunused-variable]
19874 | int supplement_count {0};
| ^~~~~~~~~~~~~~~~
projection.cpp:19875:7: warning: variable 'equivalence_count' set but not used [-Wunused-but-set-variable]
19875 | int equivalence_count {0};
| ^
projection.cpp:19876:7: warning: variable 'start_count' set but not used [-Wunused-but-set-variable]
19876 | int start_count {0};
| ^
projection.cpp:19877:7: warning: variable 'tweights_count' set but not used [-Wunused-but-set-variable]
19877 | int tweights_count {0};
| ^
projection.cpp:19878:7: warning: variable 'density_count' set but not used [-Wunused-but-set-variable]
19878 | int density_count {0};
| ^
projection.cpp:19880:7: warning: variable 'entry_time_count' set but not used [-Wunused-but-set-variable]
19880 | int entry_time_count {0};
| ^
projection.cpp:19881:7: warning: variable 'density_vr_count' set but not used [-Wunused-but-set-variable]
19881 | int density_vr_count {0};
| ^
projection.cpp:19882:7: warning: variable 'sparse_vec_count' set but not used [-Wunused-but-set-variable]
19882 | int sparse_vec_count {0};
| ^
projection.cpp:19894:8: warning: variable 'prebreeding_bool' set but not used [-Wunused-but-set-variable]
19894 | bool prebreeding_bool {true};
| ^
In file included from utilities.cpp:8:
In file included from ../inst/include/AdaptUtils.h:8:
../inst/include/basic_funcs/mats_utils.h:3763:9: warning: unused variable 'nostages_nounborn' [-Wunused-variable]
3763 | int nostages_nounborn = nostages - almostbornstages;
| ^~~~~~~~~~~~~~~~~
9 warnings generated.
45 warnings generated.
/usr/local/clang23/bin/clang++ -std=gnu++20 -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 adapt3.so RcppExports.o projection.o utilities.o -fopenmp -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/adapt3/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/adapt3/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang/adapt3/src'
installing to /data/localhost/ripley/R/packages/tests-clang/adapt3.Rcheck/00LOCK-adapt3/00new/adapt3/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 (adapt3)