* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘inferCSN’ ...
** package ‘inferCSN’ 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/RtmpdWG848/R.INSTALL3793721e447edd/inferCSN/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 "-Iinclude" -fpic -g -O2 -Wall -pedantic -mtune=native -c BetaVector.cpp -o BetaVector.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 "-Iinclude" -fpic -g -O2 -Wall -pedantic -mtune=native -c CDL012LogisticSwaps.cpp -o CDL012LogisticSwaps.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 "-Iinclude" -fpic -g -O2 -Wall -pedantic -mtune=native -c CDL012SquaredHingeSwaps.cpp -o CDL012SquaredHingeSwaps.o
CDL012SquaredHingeSwaps.cpp: In member function ‘FitResult<T> CDL012SquaredHingeSwaps<T>::_Fit() [with T = arma::Mat<double>]’:
CDL012SquaredHingeSwaps.cpp:120:27: warning: ‘Bmaxindex’ may be used uninitialized [-Wmaybe-uninitialized]
120 | this->B[maxindex] = Bmaxindex;
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
CDL012SquaredHingeSwaps.cpp:37:10: note: ‘Bmaxindex’ was declared here
37 | double Bmaxindex;
| ^~~~~~~~~
CDL012SquaredHingeSwaps.cpp: In member function ‘FitResult<T> CDL012SquaredHingeSwaps<T>::_Fit() [with T = arma::SpMat<double>]’:
CDL012SquaredHingeSwaps.cpp:120:27: warning: ‘Bmaxindex’ may be used uninitialized [-Wmaybe-uninitialized]
120 | this->B[maxindex] = Bmaxindex;
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
CDL012SquaredHingeSwaps.cpp:37:10: note: ‘Bmaxindex’ was declared here
37 | double Bmaxindex;
| ^~~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 "-Iinclude" -fpic -g -O2 -Wall -pedantic -mtune=native -c CDL012Swaps.cpp -o CDL012Swaps.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 "-Iinclude" -fpic -g -O2 -Wall -pedantic -mtune=native -c Grid.cpp -o Grid.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 "-Iinclude" -fpic -g -O2 -Wall -pedantic -mtune=native -c Grid1D.cpp -o Grid1D.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 "-Iinclude" -fpic -g -O2 -Wall -pedantic -mtune=native -c Grid2D.cpp -o Grid2D.o
In file included from /usr/include/c++/14/vector:66,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:61,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
from include/BetaVector.h:3,
from include/FitResult.h:3,
from include/Grid2D.h:3,
from Grid2D.cpp:1:
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘std::vector<std::vector<std::unique_ptr<FitResult<T> > > > Grid2D<T>::Fit() [with T = arma::Mat<double>]’ at Grid2D.cpp:116:21:
/usr/include/c++/14/bits/stl_vector.h:1131:41: warning: ‘index’ may be used uninitialized [-Wmaybe-uninitialized]
1131 | return *(this->_M_impl._M_start + __n);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Grid2D.cpp: In member function ‘std::vector<std::vector<std::unique_ptr<FitResult<T> > > > Grid2D<T>::Fit() [with T = arma::Mat<double>]’:
Grid2D.cpp:87:15: note: ‘index’ was declared here
87 | std::size_t index;
| ^~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘std::vector<std::vector<std::unique_ptr<FitResult<T> > > > Grid2D<T>::Fit() [with T = arma::SpMat<double>]’ at Grid2D.cpp:116:21:
/usr/include/c++/14/bits/stl_vector.h:1131:41: warning: ‘index’ may be used uninitialized [-Wmaybe-uninitialized]
1131 | return *(this->_M_impl._M_start + __n);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Grid2D.cpp: In member function ‘std::vector<std::vector<std::unique_ptr<FitResult<T> > > > Grid2D<T>::Fit() [with T = arma::SpMat<double>]’:
Grid2D.cpp:87:15: note: ‘index’ was declared here
87 | std::size_t index;
| ^~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 "-Iinclude" -fpic -g -O2 -Wall -pedantic -mtune=native -c Interface.cpp -o Interface.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 "-Iinclude" -fpic -g -O2 -Wall -pedantic -mtune=native -c Normalize.cpp -o Normalize.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 "-Iinclude" -fpic -g -O2 -Wall -pedantic -mtune=native -c README.cpp -o README.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 "-Iinclude" -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 "-Iinclude" -fpic -g -O2 -Wall -pedantic -mtune=native -c Test_Interface.cpp -o Test_Interface.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 "-Iinclude" -fpic -g -O2 -Wall -pedantic -mtune=native -c asMatrix.cpp -o asMatrix.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/tbb.h:32,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel/TBB.h:10,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel.h:24,
from asMatrix.cpp:2:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]’:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic<long unsigned int>&’ does not use ‘constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)’ [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&’ does not use ‘constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 "-Iinclude" -fpic -g -O2 -Wall -pedantic -mtune=native -c tableToMatrix.cpp -o tableToMatrix.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 "-Iinclude" -fpic -g -O2 -Wall -pedantic -mtune=native -c utils.cpp -o utils.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o inferCSN.so BetaVector.o CDL012LogisticSwaps.o CDL012SquaredHingeSwaps.o CDL012Swaps.o Grid.o Grid1D.o Grid2D.o Interface.o Normalize.o README.o RcppExports.o Test_Interface.o asMatrix.o tableToMatrix.o utils.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpdWG848/R.INSTALL3793721e447edd/inferCSN/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpdWG848/R.INSTALL3793721e447edd/inferCSN/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpdWG848/R.INSTALL3793721e447edd/inferCSN/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-inferCSN/00new/inferCSN/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘inferCSN’
finding HTML links ... done
as_matrix html
calculate_acc html
calculate_auc html
calculate_gene_rank html
check_sparsity html
coef.srm html
example_ground_truth html
example_matrix html
example_meta_data html
filter_sort_matrix html
fit_sparse_regression html
inferCSN-package html
inferCSN html
log_message html
network_format html
network_sift html
normalization html
parallelize_fun html
plot_contrast_networks html
plot_dynamic_networks html
plot_embedding html
plot_network_heatmap html
plot_scatter html
plot_static_networks html
plot_weight_distribution html
predict.srm html
print.srm html
r_square html
single_network html
sparse_regression html
table_to_matrix html
*** copying figures
** 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 (inferCSN)