* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘PeakSegOptimal’ ...
** package ‘PeakSegOptimal’ 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/Rtmpm2eFCN/R.INSTALL892b546b549a7/PeakSegOptimal/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PeakSegPDPALog.cpp -o PeakSegPDPALog.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33,
from /usr/include/c++/14/bits/allocator.h:46,
from /usr/include/c++/14/list:63,
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++/14/bits/alloc_traits.h:569:17,
inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {int, int, double&, double&, double&, int, double&}; _Tp = PoissonLossPieceLog; _Alloc = std::allocator<PoissonLossPieceLog>]’ at /usr/include/c++/14/bits/stl_list.h:713:33,
inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {int, int, double&, double&, double&, int, double&}; _Tp = PoissonLossPieceLog; _Alloc = std::allocator<PoissonLossPieceLog>]’ at /usr/include/c++/14/bits/stl_list.h:2004:32,
inlined from ‘std::__cxx11::list<_Tp, _Alloc>::reference std::__cxx11::list<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {int, int, double&, double&, double&, int, double&}; _Tp = PoissonLossPieceLog; _Alloc = std::allocator<PoissonLossPieceLog>]’ at /usr/include/c++/14/bits/stl_list.h:1321:19,
inlined from ‘void PiecewisePoissonLossLog::set_to_min_less_of(PiecewisePoissonLossLog*, int)’ at funPieceListLog.cpp:431:6:
/usr/include/c++/14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c interface.cpp -o interface.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o PeakSegOptimal.so PeakSegFPOPLog.o PeakSegPDPALog.o funPieceListLog.o interface.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpm2eFCN/R.INSTALL892b546b549a7/PeakSegOptimal/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpm2eFCN/R.INSTALL892b546b549a7/PeakSegOptimal/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpm2eFCN/R.INSTALL892b546b549a7/PeakSegOptimal/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-PeakSegOptimal/00new/PeakSegOptimal/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘PeakSegOptimal’
finding HTML links ... done
H3K4me3_PGP_immune_chunk24 html
H3K4me3_XJ_immune_chunk1 html
PeakSegFPOP html
PeakSegFPOPchrom html
PeakSegPDPA html
PeakSegPDPAInf html
PeakSegPDPAchrom html
PoissonLoss html
oracleModelComplexity 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 (PeakSegOptimal)