Install log for 'scellpam'

* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘scellpam’ ...
** this is package ‘scellpam’ version ‘1.4.6.2’
** package ‘scellpam’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-15 (Debian 15.2.0-13) 15.2.0’
make[1]: Entering directory '/tmp/Rtmps5KJT3/R.INSTALL296f81650d44c4/scellpam/src'
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c biodatatojmat.cpp -o biodatatojmat.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c buildresults.cpp -o buildresults.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c csvtojmat.cpp -o csvtojmat.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c debugpar.cpp -o debugpar.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c diftimehelper.cpp -o diftimehelper.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c dissimmat.cpp -o dissimmat.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c dissimmat_full.cpp -o dissimmat_full.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c dissimmat_sparse.cpp -o dissimmat_sparse.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c fastpam.cpp -o fastpam.o
In file included from /usr/include/c++/15/bits/stl_iterator.h:78,
                 from /usr/include/c++/15/bits/stl_algobase.h:67,
                 from /usr/include/c++/15/bits/specfun.h:43,
                 from /usr/include/c++/15/cmath:3913,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/platform/compiler.h:37,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/r/headers.h:67,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:30,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp.h:27,
                 from ../inst/include/fastpam.h:22,
                 from fastpam.cpp:19:
In function ‘constexpr _Tp* std::construct_at(_Tp*, _Args&& ...) [with _Tp = unsigned int; _Args = {const unsigned int&}]’,
    inlined from ‘static constexpr void std::allocator_traits<std::allocator<_Up> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = unsigned int; _Args = {const unsigned int&}; _Tp = unsigned int]’ at /usr/include/c++/15/bits/alloc_traits.h:676:21,
    inlined from ‘constexpr void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const unsigned int&}; _Tp = unsigned int; _Alloc = std::allocator<unsigned int>]’ at /usr/include/c++/15/bits/vector.tcc:586:26,
    inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = unsigned int; _Alloc = std::allocator<unsigned int>]’ at /usr/include/c++/15/bits/stl_vector.h:1427:21,
    inlined from ‘void FastPAM<disttype>::LAB() [with disttype = float]’ at fastpam.cpp:814:22:
/usr/include/c++/15/bits/stl_construct.h:110:16: warning: ‘initial_best’ may be used uninitialized [-Wmaybe-uninitialized]
  110 |         return ::new(__loc) _Tp(std::forward<_Args>(__args)...);
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fastpam.cpp: In member function ‘void FastPAM<disttype>::LAB() [with disttype = float]’:
fastpam.cpp:796:15: note: ‘initial_best’ was declared here
  796 |     indextype initial_best;
      |               ^~~~~~~~~~~~
In function ‘constexpr _Tp* std::construct_at(_Tp*, _Args&& ...) [with _Tp = unsigned int; _Args = {const unsigned int&}]’,
    inlined from ‘static constexpr void std::allocator_traits<std::allocator<_Up> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = unsigned int; _Args = {const unsigned int&}; _Tp = unsigned int]’ at /usr/include/c++/15/bits/alloc_traits.h:676:21,
    inlined from ‘constexpr void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const unsigned int&}; _Tp = unsigned int; _Alloc = std::allocator<unsigned int>]’ at /usr/include/c++/15/bits/vector.tcc:586:26,
    inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = unsigned int; _Alloc = std::allocator<unsigned int>]’ at /usr/include/c++/15/bits/stl_vector.h:1427:21,
    inlined from ‘void FastPAM<disttype>::LAB() [with disttype = double]’ at fastpam.cpp:814:22:
/usr/include/c++/15/bits/stl_construct.h:110:16: warning: ‘initial_best’ may be used uninitialized [-Wmaybe-uninitialized]
  110 |         return ::new(__loc) _Tp(std::forward<_Args>(__args)...);
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fastpam.cpp: In member function ‘void FastPAM<disttype>::LAB() [with disttype = double]’:
fastpam.cpp:796:15: note: ‘initial_best’ was declared here
  796 |     indextype initial_best;
      |               ^~~~~~~~~~~~
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c filternames.cpp -o filternames.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c filtersil.cpp -o filtersil.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c fullmatrix.cpp -o fullmatrix.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c jmatrix.cpp -o jmatrix.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c jmatrixaux.cpp -o jmatrixaux.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c mainfastpam.cpp -o mainfastpam.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c matgetcols.cpp -o matgetcols.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c matgetdiag.cpp -o matgetdiag.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c matgetrows.cpp -o matgetrows.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c matinfo.cpp -o matinfo.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c matmetadata.cpp -o matmetadata.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c matwrite.cpp -o matwrite.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c memhelper.cpp -o memhelper.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c silhouette.cpp -o silhouette.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c sparsematrix.cpp -o sparsematrix.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c symmetricmatrix.cpp -o symmetricmatrix.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c threadhelper.cpp -o threadhelper.o
g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o scellpam.so RcppExports.o biodatatojmat.o buildresults.o csvtojmat.o debugpar.o diftimehelper.o dissimmat.o dissimmat_full.o dissimmat_sparse.o fastpam.o filternames.o filtersil.o fullmatrix.o jmatrix.o jmatrixaux.o mainfastpam.o matgetcols.o matgetdiag.o matgetrows.o matinfo.o matmetadata.o matwrite.o memhelper.o silhouette.o sparsematrix.o symmetricmatrix.o threadhelper.o -lpthread -O2 -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmps5KJT3/R.INSTALL296f81650d44c4/scellpam/src'
make[1]: Entering directory '/tmp/Rtmps5KJT3/R.INSTALL296f81650d44c4/scellpam/src'
make[1]: Leaving directory '/tmp/Rtmps5KJT3/R.INSTALL296f81650d44c4/scellpam/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-scellpam/00new/scellpam/libs
** R
** 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 (scellpam)