* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘ProFAST’ ...
** package ‘ProFAST’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-24) 13.2.0’
make[1]: Entering directory '/tmp/Rtmpdx4Weo/R.INSTALL3c0df938c8e180/ProFAST/src'
g++-13 -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/usr/local/include -D_FORTIFY_SOURCE=3 "-DARMA_64BIT_WORD=1" -fpic -g -O2 -Wall -pedantic -mtune=native -c DR_removebatch.cpp -o DR_removebatch.o
DR_removebatch.cpp: In function ‘void runICM_sp_embed(const arma::field<arma::Mat<double> >&, arma::field<arma::Col<long long int> >&, arma::field<arma::Mat<double> >&, const arma::mat&, const arma::mat&, const arma::cube&, arma::cube&, const arma::field<arma::SpMat<double> >&, const arma::vec&, const arma::vec&, int, double&, arma::field<arma::Mat<double> >&, arma::field<arma::Mat<double> >&, arma::field<arma::Cube<double> >&, arma::field<arma::Cube<double> >&, arma::field<arma::Cube<double> >&, arma::field<arma::Cube<double> >&, arma::field<arma::Cube<double> >&, arma::field<arma::Cube<double> >&, const bool&)’:
DR_removebatch.cpp:432:7: warning: unused variable ‘i’ [-Wunused-variable]
432 | int i, iter, k, n;
| ^
g++-13 -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/usr/local/include -D_FORTIFY_SOURCE=3 "-DARMA_64BIT_WORD=1" -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-13 -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/usr/local/include -D_FORTIFY_SOURCE=3 "-DARMA_64BIT_WORD=1" -fpic -g -O2 -Wall -pedantic -mtune=native -c alignExp.cpp -o alignExp.o
alignExp.cpp: In function ‘Rcpp::List correct_one_gene(const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::vec&, const arma::vec&, const arma::vec&, const arma::vec&, const int&, const double&, const bool&)’:
alignExp.cpp:165:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
165 | if(M != Tm.n_rows){
| ~~^~~~~~~~~~~~
alignExp.cpp:180:7: warning: unused variable ‘n’ [-Wunused-variable]
180 | int n;
| ^
g++-13 -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/usr/local/include -D_FORTIFY_SOURCE=3 "-DARMA_64BIT_WORD=1" -fpic -g -O2 -Wall -pedantic -mtune=native -c alignExps.cpp -o alignExps.o
alignExps.cpp: In function ‘Rcpp::List correct_genes(const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const Rcpp::List&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const int&, const double&, const bool&)’:
alignExps.cpp:255:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
255 | if(M != Tm.n_rows){
| ~~^~~~~~~~~~~~
g++-13 -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/usr/local/include -D_FORTIFY_SOURCE=3 "-DARMA_64BIT_WORD=1" -fpic -g -O2 -Wall -pedantic -mtune=native -c cofast_util.cpp -o cofast_util.o
g++-13 -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/usr/local/include -D_FORTIFY_SOURCE=3 "-DARMA_64BIT_WORD=1" -fpic -g -O2 -Wall -pedantic -mtune=native -c profast.cpp -o profast.o
profast.cpp: In function ‘Rcpp::List profast_g_cpp(const Rcpp::List&, const Rcpp::List&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::cube&, const Rcpp::List&, const int&, const double&, const bool&, const bool&, const bool&)’:
profast.cpp:408:7: warning: variable ‘n’ set but not used [-Wunused-but-set-variable]
408 | int n;
| ^
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o ProFAST.so DR_removebatch.o RcppExports.o alignExp.o alignExps.o cofast_util.o profast.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 '/tmp/Rtmpdx4Weo/R.INSTALL3c0df938c8e180/ProFAST/src'
make[1]: Entering directory '/tmp/Rtmpdx4Weo/R.INSTALL3c0df938c8e180/ProFAST/src'
make[1]: Leaving directory '/tmp/Rtmpdx4Weo/R.INSTALL3c0df938c8e180/ProFAST/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-ProFAST/00new/ProFAST/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘ProFAST’
finding HTML links ... done
AddAdj html
finding level-2 HTML links ... done
AddParSettingFAST html
CosMx_subset html
FAST html
FAST_run html
FAST_single html
FAST_structure html
IntegrateSRTData html
NCFM html
NCFM_fast html
RunHarmonyLouvain html
RuniSCMEB html
SelectHKgenes html
coembed_plot html
coembedding_umap html
diagnostic.cor.eigs html
find.signature.genes html
get.top.signature.dat html
get_r2_mcfadden html
iscmeb_run html
model_set_FAST html
pbmc3k_subset html
pdistance html
top5_signatures html
transferGeneNames html
** 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
* creating tarball
packaged installation of ‘ProFAST’ as ‘ProFAST_1.4_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (ProFAST)