* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘glymotif’ ...
** this is package ‘glymotif’ version ‘1.0.0’
** package ‘glymotif’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 23.1.2 (1)’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp5CmUzd/R.INSTALL5cb0137c0b22/glymotif/src'
clang++-23 -std=gnu++20 -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/BH/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c RcppExports.cpp -o RcppExports.o
clang++-23 -std=gnu++20 -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/BH/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c extract-motifs.cpp -o extract-motifs.o
clang++-23 -std=gnu++20 -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/BH/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c structure-matcher.cpp -o structure-matcher.o
structure-matcher.cpp:126:31: warning: trigraph ignored [-Wtrigraphs]
  126 |       informative|=links[e]!="??-?";
      |                               ^
structure-matcher.cpp:281:44: warning: trigraph ignored [-Wtrigraphs]
  281 |           localized.informative|=a.token!="??-?";
      |                                            ^
2 warnings generated.
clang++-23 -std=gnu++20 -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/BH/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c vf2.cpp -o vf2.o
In file included from vf2.cpp:9:
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:63:31: warning: 'auto_ptr<boost::no_property>' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   63 |     explicit scoped_ptr( std::auto_ptr<T> p ) noexcept : px( p.release() )
      |                               ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:411:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
  411 |     property_ptr m_property;
      |                  ^
vf2.cpp:38:5: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::no_property, boost::property<boost::edge_index_t, int>>' requested here
   38 |     Graph::vertex_descriptor motif_vertex,
      |     ^
/usr/lib/gcc/x86_64-linux-gnu/16/../../../../include/c++/16/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/lib/gcc/x86_64-linux-gnu/16/../../../../include/x86_64-linux-gnu/c++/16/bits/c++config.h:120:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST'
  120 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT)
      |                                             ^
/usr/lib/gcc/x86_64-linux-gnu/16/../../../../include/x86_64-linux-gnu/c++/16/bits/c++config.h:112:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST'
  112 |   __attribute__ ((__deprecated__ ("use '" ALT "' instead")))
      |                   ^
1 warning generated.
clang++-23 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o glymotif.so RcppExports.o extract-motifs.o structure-matcher.o vf2.o -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp5CmUzd/R.INSTALL5cb0137c0b22/glymotif/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp5CmUzd/R.INSTALL5cb0137c0b22/glymotif/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp5CmUzd/R.INSTALL5cb0137c0b22/glymotif/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-glymotif/00new/glymotif/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (glymotif)