##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BASiCS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘BASiCS’ ...
** this is package ‘BASiCS’ version ‘2.23.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c BASiCS.cpp -o BASiCS.o
In file included from updates.h:4,
                 from BASiCS.cpp:1:
utils.h: In function ‘arma::vec DegubInd(arma::vec, int, const arma::vec&, const arma::vec&, const arma::vec&, const double&, const std::string&)’:
utils.h:357:24: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  357 |     if( arma::is_finite(log_aux(i)) & arma::is_finite(y(i)) ) {
      |         ~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/current/armadillo:518,
                 from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:32,
                 from libraries.h:11,
                 from utils.h:4:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
utils.h:357:54: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  357 |     if( arma::is_finite(log_aux(i)) & arma::is_finite(y(i)) ) {
      |                                       ~~~~~~~~~~~~~~~^~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
In file included from /home/biocbuild/bbs-3.23-bioc/R/include/R.h:73,
                 from libraries.h:6:
/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp/exceptions.h: In function ‘void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]’:
/home/biocbuild/bbs-3.23-bioc/R/include/R_ext/Error.h:85:17: warning: infinite recursion detected [-Winfinite-recursion]
   85 | #define warning Rf_warning
      |                 ^~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp/exceptions.h:190:17: note: in expansion of macro ‘warning’
  190 |     inline void warning(const char* fmt, Args&&... args ) {
      |                 ^~~~~~~
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/RcppCommon.h:133,
                 from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:26:
/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp/exceptions.h:191:19: note: recursive call
  191 |         Rf_warning("%s", tfm::format(fmt, std::forward<Args>(args)... ).c_str());
      |         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o BASiCS.so BASiCS.o RcppExports.o -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-BASiCS/00new/BASiCS/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (BASiCS)