Install log for 'pcalg'

* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘pcalg’ ...
** package ‘pcalg’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Debian clang version 18.1.0 (rc4-1)’
using C++ compiler: ‘Debian clang version 18.1.0 (rc4-1)’
make[1]: Entering directory '/tmp/RtmppqL3bs/R.INSTALL280d2450fac9dc/pcalg/src'
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O3 -Wall -pedantic  -c constraint.cpp -o constraint.o
In file included from constraint.cpp:8:
In file included from ../inst/include/pcalg/constraint.hpp:8:
../inst/include/pcalg/armaLapack.hpp:17:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
   17 | #define NDEBUG
      |         ^
<command line>:1:9: note: previous definition is here
    1 | #define NDEBUG 1
      |         ^
In file included from constraint.cpp:8:
In file included from ../inst/include/pcalg/constraint.hpp:10:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/scoped_ptr.hpp:13:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<boost::no_property>' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   75 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
  408 |     property_ptr m_property;
      |                  ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list<boost::setS, boost::vecS, boost::undirectedS>' requested here
   61 |     typedef typename G::vertex_descriptor vertex_descriptor;
      |                      ^
../inst/include/pcalg/constraint.hpp:14:16: note: in instantiation of template class 'boost::graph_traits<boost::adjacency_list<boost::setS, boost::vecS, boost::undirectedS>>' requested here
   14 | typedef boost::graph_traits<InternalUndirectedGraph>::out_edge_iterator UndirOutEdgeIter;
      |                ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/backward/auto_ptr.h:291:7: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
  291 |     } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr");
      |       ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:108:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST'
  108 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT)
      |                                             ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:100:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST'
  100 |   __attribute__ ((__deprecated__ ("use '" ALT "' instead")))
      |                   ^
2 warnings generated.
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O3 -Wall -pedantic  -c gies.cpp -o gies.o
In file included from gies.cpp:21:
In file included from ../inst/include/pcalg/constraint.hpp:8:
../inst/include/pcalg/armaLapack.hpp:17:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
   17 | #define NDEBUG
      |         ^
<command line>:1:9: note: previous definition is here
    1 | #define NDEBUG 1
      |         ^
In file included from gies.cpp:12:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/scoped_ptr.hpp:13:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<boost::no_property>' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   75 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
  408 |     property_ptr m_property;
      |                  ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list<boost::setS, boost::vecS, boost::undirectedS>' requested here
   61 |     typedef typename G::vertex_descriptor vertex_descriptor;
      |                      ^
../inst/include/pcalg/constraint.hpp:14:16: note: in instantiation of template class 'boost::graph_traits<boost::adjacency_list<boost::setS, boost::vecS, boost::undirectedS>>' requested here
   14 | typedef boost::graph_traits<InternalUndirectedGraph>::out_edge_iterator UndirOutEdgeIter;
      |                ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/backward/auto_ptr.h:291:7: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
  291 |     } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr");
      |       ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:108:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST'
  108 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT)
      |                                             ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:100:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST'
  100 |   __attribute__ ((__deprecated__ ("use '" ALT "' instead")))
      |                   ^
2 warnings generated.
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O3 -Wall -pedantic  -c greedy.cpp -o greedy.o
In file included from greedy.cpp:8:
In file included from ../inst/include/pcalg/greedy.hpp:11:
In file included from ../inst/include/pcalg/score.hpp:12:
../inst/include/pcalg/armaLapack.hpp:17:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
   17 | #define NDEBUG
      |         ^
<command line>:1:9: note: previous definition is here
    1 | #define NDEBUG 1
      |         ^
In file included from greedy.cpp:8:
In file included from ../inst/include/pcalg/greedy.hpp:18:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/scoped_ptr.hpp:13:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<boost::no_property>' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   75 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
  408 |     property_ptr m_property;
      |                  ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list<boost::setS, boost::vecS, boost::bidirectionalS>' requested here
   61 |     typedef typename G::vertex_descriptor vertex_descriptor;
      |                      ^
../inst/include/pcalg/greedy.hpp:57:16: note: in instantiation of template class 'boost::graph_traits<boost::adjacency_list<boost::setS, boost::vecS, boost::bidirectionalS>>' requested here
   57 | typedef boost::graph_traits<InternalEssentialGraph>::vertex_descriptor vertex_t;
      |                ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/backward/auto_ptr.h:291:7: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
  291 |     } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr");
      |       ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:108:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST'
  108 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT)
      |                                             ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:100:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST'
  100 |   __attribute__ ((__deprecated__ ("use '" ALT "' instead")))
      |                   ^
greedy.cpp:862:30: warning: unused variable 'vi' [-Wunused-variable]
  862 |         std::vector<uint>::iterator vi;
      |                                     ^~
3 warnings generated.
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c init.c -o init.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O3 -Wall -pedantic  -c score.cpp -o score.o
In file included from score.cpp:6:
In file included from ../inst/include/pcalg/score.hpp:12:
../inst/include/pcalg/armaLapack.hpp:17:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
   17 | #define NDEBUG
      |         ^
<command line>:1:9: note: previous definition is here
    1 | #define NDEBUG 1
      |         ^
In file included from score.cpp:7:
In file included from ../inst/include/pcalg/greedy.hpp:18:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/scoped_ptr.hpp:13:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<boost::no_property>' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   75 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
  408 |     property_ptr m_property;
      |                  ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list<boost::setS, boost::vecS, boost::bidirectionalS>' requested here
   61 |     typedef typename G::vertex_descriptor vertex_descriptor;
      |                      ^
../inst/include/pcalg/greedy.hpp:57:16: note: in instantiation of template class 'boost::graph_traits<boost::adjacency_list<boost::setS, boost::vecS, boost::bidirectionalS>>' requested here
   57 | typedef boost::graph_traits<InternalEssentialGraph>::vertex_descriptor vertex_t;
      |                ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/backward/auto_ptr.h:291:7: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
  291 |     } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr");
      |       ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:108:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST'
  108 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT)
      |                                             ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:100:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST'
  100 |   __attribute__ ((__deprecated__ ("use '" ALT "' instead")))
      |                   ^
score.cpp:170:29: warning: unused variable 'vi' [-Wunused-variable]
  170 |         std::vector<int>::iterator vi;
      |                                    ^~
3 warnings generated.
clang++-18 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o pcalg.so constraint.o gies.o greedy.o init.o score.o -llapack -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lRblas -L/usr/lib/llvm-18/lib -lFortran_main -lFortranRuntime -lFortranDecimal -lm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmppqL3bs/R.INSTALL280d2450fac9dc/pcalg/src'
make[1]: Entering directory '/tmp/RtmppqL3bs/R.INSTALL280d2450fac9dc/pcalg/src'
make[1]: Leaving directory '/tmp/RtmppqL3bs/R.INSTALL280d2450fac9dc/pcalg/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-pcalg/00new/pcalg/libs
** R
** data
** 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 (pcalg)