Install log for 'rncl'

* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘rncl’ ...
** this is package ‘rncl’ version ‘0.8.9’
** package ‘rncl’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’
using C++ compiler: ‘g++-15 (Debian 15.2.0-12) 15.2.0’
make[1]: Entering directory '/tmp/RtmpPrngSD/R.INSTALL2167de5a0deb2d/rncl/src'
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GetNCL.cpp -o GetNCL.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c collapse_singles.cpp -o collapse_singles.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxsassumptionsblock.cpp -o nxsassumptionsblock.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxsblock.cpp -o nxsblock.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxscharactersblock.cpp -o nxscharactersblock.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxscxxdiscretematrix.cpp -o nxscxxdiscretematrix.o
In file included from nxscxxdiscretematrix.cpp:20:
In copy constructor ‘constexpr NxsCharacterPattern::NxsCharacterPattern(const NxsCharacterPattern&)’,
    inlined from ‘constexpr _Tp* std::construct_at(_Tp*, _Args&& ...) [with _Tp = NxsCharacterPattern; _Args = {const NxsCharacterPattern&}]’ at /usr/include/c++/15/bits/stl_construct.h:110:9,
    inlined from ‘static constexpr void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = NxsCharacterPattern; _Args = {const NxsCharacterPattern&}; _Tp = std::_Rb_tree_node<NxsCharacterPattern>]’ at /usr/include/c++/15/bits/alloc_traits.h:676:21,
    inlined from ‘void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_construct_node(_Node_ptr, _Args&& ...) [with _Args = {const NxsCharacterPattern&}; _Key = NxsCharacterPattern; _Val = NxsCharacterPattern; _KeyOfValue = std::_Identity<NxsCharacterPattern>; _Compare = std::less<NxsCharacterPattern>; _Alloc = std::allocator<NxsCharacterPattern>]’ at /usr/include/c++/15/bits/stl_tree.h:1237:37,
    inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Node_ptr std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const NxsCharacterPattern&}; _Key = NxsCharacterPattern; _Val = NxsCharacterPattern; _KeyOfValue = std::_Identity<NxsCharacterPattern>; _Compare = std::less<NxsCharacterPattern>; _Alloc = std::allocator<NxsCharacterPattern>]’ at /usr/include/c++/15/bits/stl_tree.h:1254:21,
    inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Node_ptr std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Alloc_node::operator()(_Arg&&) const [with _Arg = const NxsCharacterPattern&; _Key = NxsCharacterPattern; _Val = NxsCharacterPattern; _KeyOfValue = std::_Identity<NxsCharacterPattern>; _Compare = std::less<NxsCharacterPattern>; _Alloc = std::allocator<NxsCharacterPattern>]’ at /usr/include/c++/15/bits/stl_tree.h:1136:32,
    inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_(_Base_ptr, _Base_ptr, _Arg&&, _NodeGen&) [with _Arg = const NxsCharacterPattern&; _NodeGen = std::_Rb_tree<NxsCharacterPattern, NxsCharacterPattern, std::_Identity<NxsCharacterPattern>, std::less<NxsCharacterPattern>, std::allocator<NxsCharacterPattern> >::_Alloc_node; _Key = NxsCharacterPattern; _Val = NxsCharacterPattern; _KeyOfValue = std::_Identity<NxsCharacterPattern>; _Compare = std::less<NxsCharacterPattern>; _Alloc = std::allocator<NxsCharacterPattern>]’ at /usr/include/c++/15/bits/stl_tree.h:2481:14,
    inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(const_iterator, _Arg&&, _NodeGen&) [with _Arg = const NxsCharacterPattern&; _NodeGen = std::_Rb_tree<NxsCharacterPattern, NxsCharacterPattern, std::_Identity<NxsCharacterPattern>, std::less<NxsCharacterPattern>, std::allocator<NxsCharacterPattern> >::_Alloc_node; _Key = NxsCharacterPattern; _Val = NxsCharacterPattern; _KeyOfValue = std::_Identity<NxsCharacterPattern>; _Compare = std::less<NxsCharacterPattern>; _Alloc = std::allocator<NxsCharacterPattern>]’ at /usr/include/c++/15/bits/stl_tree.h:2905:19,
    inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(const_iterator, _Arg&&) [with _Arg = const NxsCharacterPattern&; _Key = NxsCharacterPattern; _Val = NxsCharacterPattern; _KeyOfValue = std::_Identity<NxsCharacterPattern>; _Compare = std::less<NxsCharacterPattern>; _Alloc = std::allocator<NxsCharacterPattern>]’ at /usr/include/c++/15/bits/stl_tree.h:1686:28,
    inlined from ‘std::set<_Key, _Compare, _Alloc>::iterator std::set<_Key, _Compare, _Alloc>::insert(const_iterator, const value_type&) [with _Key = NxsCharacterPattern; _Compare = std::less<NxsCharacterPattern>; _Alloc = std::allocator<NxsCharacterPattern>]’ at /usr/include/c++/15/bits/stl_set.h:571:38,
    inlined from ‘unsigned int NxsCompressDiscreteMatrix(const NxsCXXDiscreteMatrix&, std::set<NxsCharacterPattern>&, std::vector<const NxsCharacterPattern*>*, const NxsUnsignedSet*, const NxsUnsignedSet*)’ at nxscxxdiscretematrix.cpp:193:87:
ncl/nxscxxdiscretematrix.h:179:7: warning: ‘patternTemp.NxsCharacterPattern::patternIndex’ may be used uninitialized [-Wmaybe-uninitialized]
  179 | class NxsCharacterPattern
      |       ^~~~~~~~~~~~~~~~~~~
nxscxxdiscretematrix.cpp: In function ‘unsigned int NxsCompressDiscreteMatrix(const NxsCXXDiscreteMatrix&, std::set<NxsCharacterPattern>&, std::vector<const NxsCharacterPattern*>*, const NxsUnsignedSet*, const NxsUnsignedSet*)’:
nxscxxdiscretematrix.cpp:167:29: note: ‘patternTemp’ declared here
  167 |         NxsCharacterPattern patternTemp;
      |                             ^~~~~~~~~~~
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxsdatablock.cpp -o nxsdatablock.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxsdistancedatum.cpp -o nxsdistancedatum.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxsdistancesblock.cpp -o nxsdistancesblock.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxsemptyblock.cpp -o nxsemptyblock.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxsexception.cpp -o nxsexception.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxsmultiformat.cpp -o nxsmultiformat.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxspublicblocks.cpp -o nxspublicblocks.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxsreader.cpp -o nxsreader.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxssetreader.cpp -o nxssetreader.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxsstring.cpp -o nxsstring.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxstaxaassociationblock.cpp -o nxstaxaassociationblock.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxstaxablock.cpp -o nxstaxablock.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxstoken.cpp -o nxstoken.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxstreesblock.cpp -o nxstreesblock.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nxsunalignedblock.cpp -o nxsunalignedblock.o
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c rncl_init.c -o rncl_init.o
g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o rncl.so GetNCL.o RcppExports.o collapse_singles.o nxsassumptionsblock.o nxsblock.o nxscharactersblock.o nxscxxdiscretematrix.o nxsdatablock.o nxsdistancedatum.o nxsdistancesblock.o nxsemptyblock.o nxsexception.o nxsmultiformat.o nxspublicblocks.o nxsreader.o nxssetreader.o nxsstring.o nxstaxaassociationblock.o nxstaxablock.o nxstoken.o nxstreesblock.o nxsunalignedblock.o rncl_init.o -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpPrngSD/R.INSTALL2167de5a0deb2d/rncl/src'
make[1]: Entering directory '/tmp/RtmpPrngSD/R.INSTALL2167de5a0deb2d/rncl/src'
make[1]: Leaving directory '/tmp/RtmpPrngSD/R.INSTALL2167de5a0deb2d/rncl/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-rncl/00new/rncl/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 (rncl)