* installing *source* package ‘LOMAR’ ...
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 17.0.6 (2)’
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG -I. -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DBOOST_DISABLE_THREADS -fpic  -g -O3 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27:
In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:128:
In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/routines.h:26:
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
   53 |         Rprintf("%.*s", num, s);
      |                  ~~^~   ~~~
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
   57 |         REprintf("%.*s", num, s);
      |                   ~~^~   ~~~
In file included from RcppExports.cpp:4:
In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27:
In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:181:
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
   30 |     Rf_warningcall(call, s.c_str());
      |                          ^~~~~~~~~
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this
   30 |     Rf_warningcall(call, s.c_str());
      |                          ^
      |                          "%s", 
3 warnings generated.
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG -I. -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DBOOST_DISABLE_THREADS -fpic  -g -O3 -Wall -pedantic -c diag.cpp -o diag.o
In file included from diag.cpp:6:
In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27:
In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:128:
In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/routines.h:26:
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
   53 |         Rprintf("%.*s", num, s);
      |                  ~~^~   ~~~
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
   57 |         REprintf("%.*s", num, s);
      |                   ~~^~   ~~~
In file included from diag.cpp:6:
In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27:
In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:181:
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
   30 |     Rf_warningcall(call, s.c_str());
      |                          ^~~~~~~~~
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this
   30 |     Rf_warningcall(call, s.c_str());
      |                          ^
      |                          "%s", 
In file included from diag.cpp:9:
In file included from ./tdautils/ripsL2.h:5:
In file included from ./topology/rips.h:6:
In file included from ./topology/simplex.h:221:
./topology/simplex.hpp:12:1: warning: 'BoundaryIterator' defined as a struct here but previously declared as a class; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
   12 | struct Simplex<V,T>::BoundaryIterator: public boost::iterator_adaptor<BoundaryIterator,                                 // Derived
      | ^
./topology/simplex.h:47:9: note: did you mean struct here?
   47 |         class BoundaryIterator;
      |         ^~~~~
      |         struct
In file included from diag.cpp:9:
In file included from ./tdautils/ripsL2.h:5:
./topology/rips.h:181:3: warning: 'ComparePair' defined as a struct here but previously declared as a class; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
  181 |   struct Rips<Distances_, Simplex_>::ComparePair:
      |   ^
./topology/rips.h:34:9: note: did you mean struct here?
   34 |         class               ComparePair;       
      |         ^~~~~
      |         struct
In file included from diag.cpp:9:
In file included from ./tdautils/ripsL2.h:7:
In file included from ./topology/static-persistence.h:22:
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/progress.hpp:23:1: warning: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead. [-W#pragma-messages]
   23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
      | ^
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^
<scratch space>:136:2: note: expanded from here
  136 |  message("This header is deprecated. Use " "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" " instead.")
      |  ^
In file included from diag.cpp:9:
In file included from ./tdautils/ripsL2.h:7:
In file included from ./topology/static-persistence.h:22:
In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/progress.hpp:25:
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/timer.hpp:21:1: warning: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead. [-W#pragma-messages]
   21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
      | ^
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
   23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
      |                                     ^
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^
<scratch space>:139:2: note: expanded from here
  139 |  message("This header is deprecated. Use " "the facilities in <boost/timer/timer.hpp>" " instead.")
      |  ^
In file included from diag.cpp:9:
In file included from ./tdautils/ripsL2.h:9:
In file included from ./topology/persistence-diagram.h:176:
In file included from ./topology/persistence-diagram.hpp:143:
In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/scoped_ptr.hpp:13:
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/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/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS>' requested here
   61 |     typedef typename G::vertex_descriptor vertex_descriptor;
      |                      ^
./topology/persistence-diagram.hpp:163:40: note: in instantiation of template class 'boost::graph_traits<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS>>' requested here
  163 |     typedef         std::vector<boost::graph_traits<Graph>::vertex_descriptor>                  MatchingVector;
      |                                        ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/13/../../../../include/c++/13/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/13/../../../../include/x86_64-linux-gnu/c++/13/bits/c++config.h:106:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST'
  106 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT)
      |                                             ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/13/../../../../include/x86_64-linux-gnu/c++/13/bits/c++config.h:98:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST'
   98 |   __attribute__ ((__deprecated__ ("use '" ALT "' instead")))
      |                   ^
In file included from diag.cpp:9:
In file included from ./tdautils/ripsL2.h:9:
In file included from ./topology/persistence-diagram.h:176:
In file included from ./topology/persistence-diagram.hpp:143:
In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/scoped_ptr.hpp:13:
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::archive::detail::basic_oarchive_impl>' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/archive/detail/basic_oarchive.hpp:49:44: note: in instantiation of template class 'boost::scoped_ptr<boost::archive::detail::basic_oarchive_impl>' requested here
   49 |     boost::scoped_ptr<basic_oarchive_impl> pimpl;
      |                                            ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/13/../../../../include/c++/13/backward/auto_ptr.h:291:7: note: 'auto_ptr<boost::archive::detail::basic_oarchive_impl>' has been explicitly marked deprecated here
  291 |     } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr");
      |       ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/13/../../../../include/x86_64-linux-gnu/c++/13/bits/c++config.h:106:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST'
  106 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT)
      |                                             ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/13/../../../../include/x86_64-linux-gnu/c++/13/bits/c++config.h:98:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST'
   98 |   __attribute__ ((__deprecated__ ("use '" ALT "' instead")))
      |                   ^
In file included from diag.cpp:9:
In file included from ./tdautils/ripsL2.h:9:
In file included from ./topology/persistence-diagram.h:176:
In file included from ./topology/persistence-diagram.hpp:143:
In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/scoped_ptr.hpp:13:
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::archive::detail::basic_iarchive_impl>' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/archive/detail/basic_iarchive.hpp:51:44: note: in instantiation of template class 'boost::scoped_ptr<boost::archive::detail::basic_iarchive_impl>' requested here
   51 |     boost::scoped_ptr<basic_iarchive_impl> pimpl;
      |                                            ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/13/../../../../include/c++/13/backward/auto_ptr.h:291:7: note: 'auto_ptr<boost::archive::detail::basic_iarchive_impl>' has been explicitly marked deprecated here
  291 |     } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr");
      |       ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/13/../../../../include/x86_64-linux-gnu/c++/13/bits/c++config.h:106:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST'
  106 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT)
      |                                             ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/13/../../../../include/x86_64-linux-gnu/c++/13/bits/c++config.h:98:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST'
   98 |   __attribute__ ((__deprecated__ ("use '" ALT "' instead")))
      |                   ^
In file included from diag.cpp:13:
./tdautils/gridUtils.h:183:13: warning: unused variable 'value' [-Wunused-variable]
  183 |      double value, value2;  // max of value and value 2 is the fcn value. 
      |             ^~~~~
./tdautils/gridUtils.h:183:20: warning: unused variable 'value2' [-Wunused-variable]
  183 |      double value, value2;  // max of value and value 2 is the fcn value. 
      |                    ^~~~~~
In file included from diag.cpp:26:
./kde.h:21:16: warning: unused variable 'pi' [-Wunused-variable]
   21 |   const double pi = 3.141592653589793;
      |                ^~
In file included from diag.cpp:9:
In file included from ./tdautils/ripsL2.h:8:
In file included from ./topology/dynamic-persistence.h:332:
./topology/dynamic-persistence.hpp:60:73: warning: unused typedef 'TrailIterator' [-Wunused-local-typedef]
   60 |     typedef                 typename Element::Trail::iterator           TrailIterator;
      |                                                                         ^
14 warnings generated.
clang++-17 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-clang-17/lib -Wl,-O1 -o LOMAR.so RcppExports.o diag.o -lgmp -L/home/hornik/tmp/R-d-clang-17/lib -lR
installing to /srv/hornik/tmp/CRAN/LOMAR.Rcheck/00LOCK-LOMAR/00new/LOMAR/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 (LOMAR)