* installing *source* package ‘PeakSegOptimal’ ...
** this is package ‘PeakSegOptimal’ version ‘2024.10.1’
** package ‘PeakSegOptimal’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/PeakSegOptimal/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c PeakSegFPOPLog.cpp -o PeakSegFPOPLog.o
PeakSegFPOPLog.cpp: In function ‘int PeakSegFPOPLog(int*, double*, int, double, double*, int*, double*, int*)’:
PeakSegFPOPLog.cpp:76:37: warning: ‘up_cost_prev’ may be used uninitialized [-Wmaybe-uninitialized]
   76 |           up_cost->set_to_min_env_of(&min_prev_cost, up_cost_prev, true);
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PeakSegFPOPLog.cpp:35:50: note: ‘up_cost_prev’ was declared here
   35 |   PiecewisePoissonLossLog *up_cost, *down_cost, *up_cost_prev, *down_cost_prev;
      |                                                  ^~~~~~~~~~~~
PeakSegFPOPLog.cpp:78:32: warning: ‘down_cost_prev’ may be used uninitialized [-Wmaybe-uninitialized]
   78 |           down_cost_prev->print();
      |           ~~~~~~~~~~~~~~~~~~~~~^~
PeakSegFPOPLog.cpp:35:65: note: ‘down_cost_prev’ was declared here
   35 |   PiecewisePoissonLossLog *up_cost, *down_cost, *up_cost_prev, *down_cost_prev;
      |                                                                 ^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c PeakSegPDPALog.cpp -o PeakSegPDPALog.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c funPieceListLog.cpp -o funPieceListLog.o
funPieceListLog.cpp: In member function ‘void PiecewisePoissonLossLog::set_to_min_less_of(PiecewisePoissonLossLog*, int)’:
funPieceListLog.cpp:292:14: warning: unused variable ‘right_left_equal’ [-Wunused-variable]
  292 |         bool right_left_equal = right_left_diff < NEWTON_EPSILON;
      |              ^~~~~~~~~~~~~~~~
funPieceListLog.cpp: In member function ‘double PiecewisePoissonLossLog::findCost(double)’:
funPieceListLog.cpp:643:11: warning: unused variable ‘verbose’ [-Wunused-variable]
  643 |       int verbose = 0;
      |           ^~~~~~~
funPieceListLog.cpp: In member function ‘void PiecewisePoissonLossLog::Minimize(double*, double*, int*, double*)’:
funPieceListLog.cpp:674:7: warning: unused variable ‘verbose’ [-Wunused-variable]
  674 |   int verbose=false;
      |       ^~~~~~~
funPieceListLog.cpp: In member function ‘int PiecewisePoissonLossLog::check_min_of(PiecewisePoissonLossLog*, PiecewisePoissonLossLog*)’:
funPieceListLog.cpp:698:7: warning: unused variable ‘verbose’ [-Wunused-variable]
  698 |   int verbose = 0;
      |       ^~~~~~~
funPieceListLog.cpp: In member function ‘double PoissonLossPieceLog::get_larger_root(double)’:
funPieceListLog.cpp:123:15: warning: ‘closest_negative_mean’ may be used uninitialized [-Wmaybe-uninitialized]
  123 |        Rprintf("neg_cost=%e neg_mean=%e pos_cost=%e pos_mean=%e\n", closest_negative_cost, closest_negative_mean, closest_positive_cost, closest_positive_mean);
      |        ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
funPieceListLog.cpp:90:45: note: ‘closest_negative_mean’ was declared here
   90 |   double closest_negative_cost = -INFINITY, closest_negative_mean;
      |                                             ^~~~~~~~~~~~~~~~~~~~~
funPieceListLog.cpp:123:15: warning: ‘closest_positive_mean’ may be used uninitialized [-Wmaybe-uninitialized]
  123 |        Rprintf("neg_cost=%e neg_mean=%e pos_cost=%e pos_mean=%e\n", closest_negative_cost, closest_negative_mean, closest_positive_cost, closest_positive_mean);
      |        ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
funPieceListLog.cpp:89:44: note: ‘closest_positive_mean’ was declared here
   89 |   double closest_positive_cost = INFINITY, closest_positive_mean;
      |                                            ^~~~~~~~~~~~~~~~~~~~~
funPieceListLog.cpp: In member function ‘double PoissonLossPieceLog::get_smaller_root(double)’:
funPieceListLog.cpp:201:42: warning: ‘closest_negative_log_mean’ may be used uninitialized [-Wmaybe-uninitialized]
  201 |        return (closest_positive_log_mean + closest_negative_log_mean)/2;
      |               ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
funPieceListLog.cpp:164:45: note: ‘closest_negative_log_mean’ was declared here
  164 |   double closest_negative_cost = -INFINITY, closest_negative_log_mean;
      |                                             ^~~~~~~~~~~~~~~~~~~~~~~~~
funPieceListLog.cpp:201:42: warning: ‘closest_positive_log_mean’ may be used uninitialized [-Wmaybe-uninitialized]
  201 |        return (closest_positive_log_mean + closest_negative_log_mean)/2;
      |               ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
funPieceListLog.cpp:163:44: note: ‘closest_positive_log_mean’ was declared here
  163 |   double closest_positive_cost = INFINITY, closest_positive_log_mean;
      |                                            ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/15/x86_64-redhat-linux/bits/c++allocator.h:33,
                 from /usr/include/c++/15/bits/allocator.h:46,
                 from /usr/include/c++/15/list:65,
                 from funPieceListLog.h:4,
                 from funPieceListLog.cpp:3:
In member function ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = PoissonLossPieceLog; _Args = {int, int, double&, double&, double&, int, double&}; _Tp = std::_List_node<PoissonLossPieceLog>]’,
    inlined from ‘static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = PoissonLossPieceLog; _Args = {int, int, double&, double&, double&, int, double&}; _Tp = std::_List_node<PoissonLossPieceLog>]’ at /usr/include/c++/15/bits/alloc_traits.h:674:17,
    inlined from ‘std::__cxx11::list<_Tp, _Allocator>::_Node_ptr std::__cxx11::list<_Tp, _Allocator>::_M_create_node(_Args&& ...) [with _Args = {int, int, double&, double&, double&, int, double&}; _Tp = PoissonLossPieceLog; _Alloc = std::allocator<PoissonLossPieceLog>]’ at /usr/include/c++/15/bits/stl_list.h:1106:33,
    inlined from ‘void std::__cxx11::list<_Tp, _Allocator>::_M_insert(iterator, _Args&& ...) [with _Args = {int, int, double&, double&, double&, int, double&}; _Tp = PoissonLossPieceLog; _Alloc = std::allocator<PoissonLossPieceLog>]’ at /usr/include/c++/15/bits/stl_list.h:2472:35,
    inlined from ‘std::__cxx11::list<_Tp, _Allocator>::reference std::__cxx11::list<_Tp, _Allocator>::emplace_back(_Args&& ...) [with _Args = {int, int, double&, double&, double&, int, double&}; _Tp = PoissonLossPieceLog; _Alloc = std::allocator<PoissonLossPieceLog>]’ at /usr/include/c++/15/bits/stl_list.h:1819:19,
    inlined from ‘void PiecewisePoissonLossLog::set_to_min_less_of(PiecewisePoissonLossLog*, int)’ at funPieceListLog.cpp:431:6:
/usr/include/c++/15/bits/new_allocator.h:191:11: warning: ‘prev_best_log_mean’ may be used uninitialized [-Wmaybe-uninitialized]
  191 |         { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
funPieceListLog.cpp: In member function ‘void PiecewisePoissonLossLog::set_to_min_less_of(PiecewisePoissonLossLog*, int)’:
funPieceListLog.cpp:265:10: note: ‘prev_best_log_mean’ was declared here
  265 |   double prev_best_log_mean;
      |          ^~~~~~~~~~~~~~~~~~
funPieceListLog.cpp:344:18: warning: ‘next_left_cost’ may be used uninitialized [-Wmaybe-uninitialized]
  344 |           Rprintf("next_left_cost-mu_cost=%e right_cost-mu_cost=%e\n", next_left_cost-mu_cost, right_cost-mu_cost);
      |           ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
funPieceListLog.cpp:276:14: note: ‘next_left_cost’ was declared here
  276 |       double next_left_cost;
      |              ^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c interface.cpp -o interface.o
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o PeakSegOptimal.so PeakSegFPOPLog.o PeakSegPDPALog.o funPieceListLog.o interface.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/PeakSegOptimal/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/PeakSegOptimal/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/PeakSegOptimal/src'
installing to /data/gannet/ripley/R/packages/tests-devel/PeakSegOptimal.Rcheck/00LOCK-PeakSegOptimal/00new/PeakSegOptimal/libs
** R
** data
** 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 (PeakSegOptimal)