* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘som’ ...
** package ‘som’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpoc3SfY/R.INSTALL3de9fc1a60bc70/som/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c som.cc -o som.o
In file included from tntsupp.h:8,
from sub.h:1,
from SomParam.h:2,
from som.cc:4:
tnt/fmat.h: In member function ‘void TNT::Fortran_Matrix<T>::destroy() [with T = double]’:
tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘*this.TNT::Fortran_Matrix<double>::col_’ with nonzero offset 8 [-Wfree-nonheap-object]
161 | delete [] (col_);
| ^~~~~~~~~~~~~~~~
In member function ‘void TNT::Fortran_Matrix<T>::destroy() [with T = double]’,
inlined from ‘TNT::Fortran_Matrix<T>::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16,
inlined from ‘double rect_dist(TNT::Region2D<TNT::Fortran_Matrix<double> >, TNT::Region2D<TNT::Fortran_Matrix<double> >)’ at SomParam.h:11:19:
tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘<anonymous>.TNT::Fortran_Matrix<double>::col_’ with nonzero offset 8 [-Wfree-nonheap-object]
161 | delete [] (col_);
| ^~~~~~~~~~~~~~~~
In member function ‘void TNT::Fortran_Matrix<T>::destroy() [with T = double]’,
inlined from ‘TNT::Fortran_Matrix<T>::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16,
inlined from ‘TNT::Subscript find_winner(TNT::DMatrix&, TNT::Subscript, TNT::DMatrix&)’ at som.cc:12:40:
tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘<anonymous>.TNT::Fortran_Matrix<double>::col_’ with nonzero offset 8 [-Wfree-nonheap-object]
161 | delete [] (col_);
| ^~~~~~~~~~~~~~~~
In member function ‘void TNT::Fortran_Matrix<T>::destroy() [with T = double]’,
inlined from ‘TNT::Fortran_Matrix<T>::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16,
inlined from ‘TNT::Subscript find_winner(TNT::DMatrix&, TNT::Subscript, TNT::DMatrix&)’ at som.cc:16:36:
tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘<anonymous>.TNT::Fortran_Matrix<double>::col_’ with nonzero offset 8 [-Wfree-nonheap-object]
161 | delete [] (col_);
| ^~~~~~~~~~~~~~~~
In member function ‘void TNT::Fortran_Matrix<T>::destroy() [with T = double]’,
inlined from ‘TNT::Fortran_Matrix<T>::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16,
inlined from ‘void visual(TNT::DMatrix&, TNT::DMatrix&, TNT::DMatrix&, TNT::DMatrix&)’ at som.cc:57:36:
tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘<anonymous>.TNT::Fortran_Matrix<double>::col_’ with nonzero offset 8 [-Wfree-nonheap-object]
161 | delete [] (col_);
| ^~~~~~~~~~~~~~~~
In member function ‘void TNT::Fortran_Matrix<T>::destroy() [with T = double]’,
inlined from ‘TNT::Fortran_Matrix<T>::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16,
inlined from ‘int update(TNT::DMatrix&, TNT::DMatrix&, TNT::Subscript, double, TNT::DVector&)’ at som.cc:32:24:
tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘<anonymous>.TNT::Fortran_Matrix<double>::col_’ with nonzero offset 8 [-Wfree-nonheap-object]
161 | delete [] (col_);
| ^~~~~~~~~~~~~~~~
In member function ‘void TNT::Fortran_Matrix<T>::destroy() [with T = double]’,
inlined from ‘TNT::Fortran_Matrix<T>& TNT::Fortran_Matrix<T>::operator=(const TNT::Fortran_Matrix<T>&) [with T = double]’ at tnt/fmat.h:227:20,
inlined from ‘TNT::Fortran_Matrix<T>& TNT::Fortran_Matrix<T>::operator=(const TNT::Fortran_Matrix<T>&) [with T = double]’ at tnt/fmat.h:217:24,
inlined from ‘int update(TNT::DMatrix&, TNT::DMatrix&, TNT::Subscript, double, TNT::DVector&)’ at som.cc:34:17:
tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘*code.TNT::Fortran_Matrix<double>::col_’ with nonzero offset 8 [-Wfree-nonheap-object]
161 | delete [] (col_);
| ^~~~~~~~~~~~~~~~
In member function ‘void TNT::Fortran_Matrix<T>::destroy() [with T = double]’,
inlined from ‘TNT::Fortran_Matrix<T>::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16,
inlined from ‘double qerror(TNT::DMatrix&, TNT::DMatrix&, TNT::DMatrix&, TNT::DMatrix&, SomParam&)’ at som.cc:76:38:
tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘<anonymous>.TNT::Fortran_Matrix<double>::col_’ with nonzero offset 8 [-Wfree-nonheap-object]
161 | delete [] (col_);
| ^~~~~~~~~~~~~~~~
In member function ‘void TNT::Fortran_Matrix<T>::destroy() [with T = double]’,
inlined from ‘TNT::Fortran_Matrix<T>::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16,
inlined from ‘void som_top(TNT::DMatrix&, TNT::DMatrix&, TNT::DMatrix&, SomParam&, SomParam&, double*)’ at som.cc:108:1:
tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘cord.TNT::Fortran_Matrix<double>::col_’ with nonzero offset 8 [-Wfree-nonheap-object]
161 | delete [] (col_);
| ^~~~~~~~~~~~~~~~
In member function ‘void TNT::Fortran_Matrix<T>::destroy() [with T = double]’,
inlined from ‘TNT::Fortran_Matrix<T>::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16,
inlined from ‘SEXPREC* som_bat(SEXP, SEXP, SEXP, SEXP)’ at som.cc:225:3:
tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘Vis.TNT::Fortran_Matrix<double>::col_’ with nonzero offset 8 [-Wfree-nonheap-object]
161 | delete [] (col_);
| ^~~~~~~~~~~~~~~~
In member function ‘void TNT::Fortran_Matrix<T>::destroy() [with T = double]’,
inlined from ‘TNT::Fortran_Matrix<T>::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16,
inlined from ‘SEXPREC* som_bat(SEXP, SEXP, SEXP, SEXP)’ at som.cc:225:3:
tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘Code.TNT::Fortran_Matrix<double>::col_’ with nonzero offset 8 [-Wfree-nonheap-object]
161 | delete [] (col_);
| ^~~~~~~~~~~~~~~~
In member function ‘void TNT::Fortran_Matrix<T>::destroy() [with T = double]’,
inlined from ‘TNT::Fortran_Matrix<T>::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16,
inlined from ‘SEXPREC* som_bat(SEXP, SEXP, SEXP, SEXP)’ at som.cc:225:3:
tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘Data.TNT::Fortran_Matrix<double>::col_’ with nonzero offset 8 [-Wfree-nonheap-object]
161 | delete [] (col_);
| ^~~~~~~~~~~~~~~~
In member function ‘void TNT::Fortran_Matrix<T>::destroy() [with T = double]’,
inlined from ‘TNT::Fortran_Matrix<T>::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16,
inlined from ‘SEXPREC* som(SEXP, SEXP, SEXP)’ at som.cc:198:3:
tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘Vis.TNT::Fortran_Matrix<double>::col_’ with nonzero offset 8 [-Wfree-nonheap-object]
161 | delete [] (col_);
| ^~~~~~~~~~~~~~~~
In member function ‘void TNT::Fortran_Matrix<T>::destroy() [with T = double]’,
inlined from ‘TNT::Fortran_Matrix<T>::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16,
inlined from ‘SEXPREC* som(SEXP, SEXP, SEXP)’ at som.cc:198:3:
tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘Cord.TNT::Fortran_Matrix<double>::col_’ with nonzero offset 8 [-Wfree-nonheap-object]
161 | delete [] (col_);
| ^~~~~~~~~~~~~~~~
In member function ‘void TNT::Fortran_Matrix<T>::destroy() [with T = double]’,
inlined from ‘TNT::Fortran_Matrix<T>::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16,
inlined from ‘SEXPREC* som(SEXP, SEXP, SEXP)’ at som.cc:198:3:
tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘Code.TNT::Fortran_Matrix<double>::col_’ with nonzero offset 8 [-Wfree-nonheap-object]
161 | delete [] (col_);
| ^~~~~~~~~~~~~~~~
In member function ‘void TNT::Fortran_Matrix<T>::destroy() [with T = double]’,
inlined from ‘TNT::Fortran_Matrix<T>::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16,
inlined from ‘SEXPREC* som(SEXP, SEXP, SEXP)’ at som.cc:198:3:
tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘Data.TNT::Fortran_Matrix<double>::col_’ with nonzero offset 8 [-Wfree-nonheap-object]
161 | delete [] (col_);
| ^~~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o som.so som.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpoc3SfY/R.INSTALL3de9fc1a60bc70/som/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpoc3SfY/R.INSTALL3de9fc1a60bc70/som/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpoc3SfY/R.INSTALL3de9fc1a60bc70/som/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-som/00new/som/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘som’
finding HTML links ... done
filtering html
normalize html
plot.som html
qerror html
som-internal html
som html
summary html
yeast html
** 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 (som)