##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scde
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘scde’ ...
** this is package ‘scde’ version ‘2.37.0’
** 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-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -Werror=format-security  -c bwpca.cpp -o bwpca.o
bwpca.cpp: In function ‘void set_random_matrix(arma::mat&, arma::mat&)’:
bwpca.cpp:24:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   24 |     for(int j=0;j<target.n_rows;j++) {
      |                 ~^~~~~~~~~~~~~~
bwpca.cpp:31:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   31 |     for(int i=0;i<target.n_cols;i++) {
      |                 ~^~~~~~~~~~~~~~
bwpca.cpp:34:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   34 |         for(int j=0;j<target.n_rows;j++) {
      |                     ~^~~~~~~~~~~~~~
bwpca.cpp: In function ‘void set_random_matrices(arma::mat&, arma::mat&, arma::mat&, arma::mat&)’:
bwpca.cpp:44:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   44 |     for(int j=0;j<target1.n_rows;j++) {
      |                 ~^~~~~~~~~~~~~~~
bwpca.cpp:51:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   51 |     for(int i=0;i<target1.n_cols;i++) {
      |                 ~^~~~~~~~~~~~~~~
bwpca.cpp:54:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   54 |         for(int j=0;j<target1.n_rows;j++) {
      |                     ~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -Werror=format-security  -c jpmatLogBoot.cpp -o jpmatLogBoot.o
jpmatLogBoot.cpp: In function ‘SEXPREC* logBootPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
jpmatLogBoot.cpp:200:36: warning: ‘eT arma::Mat<eT>::max(arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations]
  200 |                 double maxv=nbp.max(maxij);
      |                             ~~~~~~~^~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/current/armadillo:201,
                 from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:32,
                 from jpmatLogBoot.h:4,
                 from jpmatLogBoot.cpp:1:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:545:56: note: declared here
  545 |   [[deprecated("use .index_max() instead")]] inline eT max(uword& index_of_max_val) const;
      |                                                        ^~~
jpmatLogBoot.cpp:200:24: warning: unused variable ‘maxv’ [-Wunused-variable]
  200 |                 double maxv=nbp.max(maxij);
      |                        ^~~~
jpmatLogBoot.cpp: In function ‘SEXPREC* logBootBatchPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
jpmatLogBoot.cpp:443:36: warning: ‘eT arma::Mat<eT>::max(arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations]
  443 |                 double maxv=nbp.max(maxij);
      |                             ~~~~~~~^~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/current/armadillo:692:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:7850:1: note: declared here
 7850 | Mat<eT>::max(uword& index_of_max_val) const
      | ^~~~~~~
jpmatLogBoot.cpp:443:24: warning: unused variable ‘maxv’ [-Wunused-variable]
  443 |                 double maxv=nbp.max(maxij);
      |                        ^~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -Werror=format-security  -c matSlideMult.cpp -o matSlideMult.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -Werror=format-security  -c pagoda.cpp -o pagoda.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o scde.so bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -lpthread -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-scde/00new/scde/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (scde)